SYMBOL INDEX (4078 symbols across 338 files)

FILE: src/juicebox/CommandBroadcaster.java
  class CommandBroadcaster (line 41) | class CommandBroadcaster {
    method broadcast (line 46) | public static void broadcast(String command) {
    method broadcastCommand (line 60) | private static void broadcastCommand(String command, int port) throws ...

FILE: src/juicebox/CommandExecutor.java
  class CommandExecutor (line 37) | class CommandExecutor {
    method CommandExecutor (line 41) | public CommandExecutor(HiC hic) {
    method getArgs (line 45) | private List<String> getArgs(String[] tokens) {
    method execute (line 55) | public String execute(String command) {

FILE: src/juicebox/CommandListener.java
  class CommandListener (line 33) | class CommandListener implements Runnable {
    method CommandListener (line 43) | private CommandListener(int port, HiC hic) throws IOException {
    method start (line 50) | public static synchronized void start(HiC hic) {
    method halt (line 67) | public static synchronized void halt() {
    method run (line 79) | public void run() {
    method processClientRequest (line 109) | private void processClientRequest(CommandExecutor cmdExe) throws IOExc...
    method closeSockets (line 130) | private void closeSockets() {

FILE: src/juicebox/Context.java
  class Context (line 34) | public class Context {
    method Context (line 41) | public Context(Chromosome chromosome) {
    method getBinOrigin (line 45) | public double getBinOrigin() {
    method setBinOrigin (line 49) | public void setBinOrigin(double binOrigin) {
    method getGenomicPositionOrigin (line 53) | public int getGenomicPositionOrigin() {
    method getZoom (line 57) | public HiCZoom getZoom() {
    method setZoom (line 61) | public void setZoom(HiCZoom zoom) {
    method getChrLength (line 65) | public long getChrLength() {
    method getChromosome (line 69) | public Chromosome getChromosome() {

FILE: src/juicebox/DirectoryManager.java
  class DirectoryManager (line 41) | public class DirectoryManager {
    method getUserHome (line 48) | private static File getUserHome() {
    method getUserDirectory (line 60) | public static synchronized File getUserDirectory() {
    method getHiCDirectory (line 73) | public static File getHiCDirectory() {
    method getHiCDirectoryOverride (line 144) | private static File getHiCDirectoryOverride() {
    method canWrite (line 168) | private static boolean canWrite(File directory) {

FILE: src/juicebox/HiC.java
  class HiC (line 56) | public class HiC {
    method HiC (line 88) | public HiC(SuperAdapter superAdapter) {
    method cleanUpNumbersInName (line 101) | private static String cleanUpNumbersInName(String string) {
    method valueOfUnit (line 107) | public static HiC.Unit valueOfUnit(String unit) {
    method getDefaultUnit (line 116) | public Unit getDefaultUnit() {
    method reset (line 120) | public void reset() {
    method clearTracksForReloadState (line 138) | public void clearTracksForReloadState() {
    method clearFeatures (line 154) | private void clearFeatures() {
    method undoZoomAction (line 162) | public void undoZoomAction() {
    method redoZoomAction (line 174) | public void redoZoomAction() {
    method getScaleFactor (line 183) | public double getScaleFactor() {
    method setScaleFactor (line 187) | private void setScaleFactor(double scaleFactor) {
    method loadEigenvectorTrack (line 191) | public void loadEigenvectorTrack() {
    method refreshEigenvectorTrackIfExists (line 204) | public void refreshEigenvectorTrackIfExists() {
    method getResourceTree (line 213) | public ResourceTree getResourceTree() {
    method setResourceTree (line 217) | public void setResourceTree(ResourceTree rTree) {
    method setEncodeAction (line 221) | public void setEncodeAction(LoadEncodeAction eAction) {
    method isLinkedMode (line 225) | public boolean isLinkedMode() {
    method setLinkedMode (line 229) | public void setLinkedMode(boolean linkedMode) {
    method getLoadedTracks (line 233) | public List<HiCTrack> getLoadedTracks() {
    method unsafeLoadHostedTracks (line 237) | public void unsafeLoadHostedTracks(List<ResourceLocator> locators) {
    method unsafeLoadTrack (line 241) | public void unsafeLoadTrack(String path) {
    method loadCoverageTrack (line 245) | public void loadCoverageTrack(String label) {
    method removeTrack (line 253) | public void removeTrack(HiCTrack track) {
    method removeTrack (line 259) | public void removeTrack(ResourceLocator locator) {
    method moveTrack (line 265) | public void moveTrack(HiCTrack track, boolean thisShouldBeMovedUp) {
    method getDataset (line 275) | public Dataset getDataset() {
    method setDataset (line 279) | public void setDataset(Dataset dataset) {
    method getControlDataset (line 283) | public Dataset getControlDataset() {
    method setControlDataset (line 287) | public void setControlDataset(Dataset controlDataset) {
    method setSelectedChromosomes (line 291) | public void setSelectedChromosomes(Chromosome chrX, Chromosome chrY) {
    method getZoom (line 297) | public HiCZoom getZoom() {
    method getZd (line 301) | public MatrixZoomData getZd() throws NullPointerException {
    method getControlZd (line 312) | public MatrixZoomData getControlZd() {
    method getControlMatrix (line 321) | public Matrix getControlMatrix() {
    method getXContext (line 326) | public Context getXContext() {
    method getYContext (line 330) | public Context getYContext() {
    method resetContexts (line 334) | public void resetContexts() {
    method getCursorPoint (line 339) | public Point getCursorPoint() {
    method setCursorPoint (line 343) | public void setCursorPoint(Point point) {
    method getDiagonalCursorPoint (line 347) | public Point getDiagonalCursorPoint() {
    method setDiagonalCursorPoint (line 351) | public void setDiagonalCursorPoint(Point point) {
    method getGWCursorPoint (line 355) | public Point getGWCursorPoint() {
    method setGWCursorPoint (line 359) | public void setGWCursorPoint(Point point) {
    method getCurrentRegionWindowGenomicPositions (line 363) | public long[] getCurrentRegionWindowGenomicPositions() {
    method getXPosition (line 381) | public String getXPosition() {
    method setXPosition (line 385) | public void setXPosition(String txt) {
    method getYPosition (line 389) | public String getYPosition() {
    method setYPosition (line 393) | public void setYPosition(String txt) {
    method getMatrix (line 397) | public Matrix getMatrix() {
    method setSelectedBin (line 418) | public void setSelectedBin(Point point) {
    method getDisplayOption (line 426) | public MatrixType getDisplayOption() {
    method setDisplayOption (line 430) | public void setDisplayOption(MatrixType newDisplay) {
    method isControlLoaded (line 437) | public boolean isControlLoaded() {
    method isWholeGenome (line 441) | public boolean isWholeGenome() {
    method setZoomChanged (line 445) | private void setZoomChanged() {
    method testZoomChanged (line 450) | public synchronized boolean testZoomChanged() {
    method centerFragment (line 458) | public void centerFragment(int fragmentX, int fragmentY) {
    method centerBP (line 478) | public void centerBP(int bpX, int bpY) {
    method center (line 497) | public void center(double binX, double binY) {
    method moveBy (line 513) | public void moveBy(double dxBins, double dyBins) {
    method moveTo (line 525) | private void moveTo(double newBinX, double newBinY) {
    method setDisplayOptionChanged (line 551) | private void setDisplayOptionChanged() {
    method testDisplayOptionChanged (line 556) | public synchronized boolean testDisplayOptionChanged() {
    method setNormalizationTypeChanged (line 564) | private void setNormalizationTypeChanged() {
    method testNormalizationTypeChanged (line 569) | public synchronized boolean testNormalizationTypeChanged() {
    method getObsNormalizationType (line 577) | public NormalizationType getObsNormalizationType() {
    method setObsNormalizationType (line 581) | public void setObsNormalizationType(String label) {
    method getControlNormalizationType (line 589) | public NormalizationType getControlNormalizationType() {
    method setControlNormalizationType (line 593) | public void setControlNormalizationType(String label) {
    method getEigenvector (line 601) | public double[] getEigenvector(final int chrIdx, final int n, boolean ...
    method getExpectedValues (line 616) | public ExpectedValueFunction getExpectedValues() {
    method getExpectedControlValues (line 621) | public ExpectedValueFunction getExpectedControlValues() {
    method getNormalizationVector (line 626) | public NormalizationVector getNormalizationVector(int chrIdx) {
    method getControlNormalizationVector (line 631) | public NormalizationVector getControlNormalizationVector(int chrIdx) {
    method getNormalizedObservedValue (line 637) | public float getNormalizedObservedValue(int binX, int binY) {
    method getNormalizedControlValue (line 648) | public float getNormalizedControlValue(int binX, int binY) {
    method zoomToDrawnBox (line 666) | public void zoomToDrawnBox(final long xBP0, final long yBP0, final dou...
    method setLocation (line 698) | public void setLocation(String chrXName, String chrYName, HiC.Unit uni...
    method unsafeSetLocation (line 710) | public void unsafeSetLocation(String chrXName, String chrYName, String...
    method safeActuallySetZoomAndLocation (line 721) | private boolean safeActuallySetZoomAndLocation(HiCZoom newZoom, long g...
    method safeActuallySetZoomAndLocation (line 728) | private boolean safeActuallySetZoomAndLocation(final String chrXName, ...
    method unsafeActuallySetZoomAndLocation (line 759) | public boolean unsafeActuallySetZoomAndLocation(String chrXName, Strin...
    method computeStandardUnzoomCoordinates (line 869) | private Point computeStandardUnzoomCoordinates(Matrix preZoomMatrix, C...
    method adjustLockButton (line 888) | private void adjustLockButton(boolean savedResolutionLocked) {
    method setChromosomesFromBroadcast (line 894) | private void setChromosomesFromBroadcast(String chrXName, String chrYN...
    method broadcastLocation (line 911) | public void broadcastLocation() {
    method getLocationDescription (line 916) | public String getLocationDescription() {
    method getDefaultLocationDescription (line 928) | public String getDefaultLocationDescription() {
    method restoreLocation (line 941) | public void restoreLocation(String cmd) {
    method loadLoopList (line 949) | public void loadLoopList(String path) {
    method generateTrackFromLocation (line 953) | public void generateTrackFromLocation(int mousePos, boolean isHorizont...
    method safeSave1DTrackToWigFile (line 1021) | private void safeSave1DTrackToWigFile(final Chromosome chromosomeForPo...
    method unsafeSave1DTrackToWigFile (line 1046) | private void unsafeSave1DTrackToWigFile(Chromosome chromosomeForPositi...
    method generateRainbowBed (line 1077) | public void generateRainbowBed() {
    method safeGenerateRainbowBed (line 1090) | private void safeGenerateRainbowBed(final Chromosome chromosome, final...
    method unsafeGenerateRainbowBed (line 1114) | private void unsafeGenerateRainbowBed(Chromosome chromosome, PrintWrit...
    method getRgb (line 1124) | private String getRgb(int i, long size) {
    method isInPearsonsMode (line 1131) | public boolean isInPearsonsMode() {
    method isPearsonEdgeCaseEncountered (line 1135) | public boolean isPearsonEdgeCaseEncountered(HiCZoom zoom) {
    method isResolutionLocked (line 1139) | public boolean isResolutionLocked() {
    method isPearsonsNotAvailableForFile (line 1147) | public boolean isPearsonsNotAvailableForFile(boolean isControl) {
    method isPearsonsNotAvailableAtSpecificZoom (line 1161) | public boolean isPearsonsNotAvailableAtSpecificZoom(boolean isControl,...
    method getColorForRuler (line 1173) | public Color getColorForRuler() {
    method isVSTypeDisplay (line 1185) | public boolean isVSTypeDisplay() {
    method isInControlPearsonsMode (line 1189) | public boolean isInControlPearsonsMode() {
    method getColorScaleKey (line 1193) | public String getColorScaleKey() {
    method getHighlightedFeatures (line 1201) | public List<Feature2D> getHighlightedFeatures() {
    method setHighlightedFeatures (line 1208) | public void setHighlightedFeatures(List<Feature2D> highlightedFeatures) {
    method setShowFeatureHighlight (line 1213) | public void setShowFeatureHighlight(boolean showFeatureHighlight) {
    method getChromosomeHandler (line 1217) | public ChromosomeHandler getChromosomeHandler() {
    method setChromosomeHandler (line 1221) | public void setChromosomeHandler(ChromosomeHandler chromosomeHandler) {
    method getZoomActionTracker (line 1227) | public ZoomActionTracker getZoomActionTracker() {
    method clearAllMatrixZoomDataCache (line 1231) | public void clearAllMatrixZoomDataCache() {
    method clearAllCacheForDataset (line 1238) | private void clearAllCacheForDataset(Dataset ds) {
    method getRTreeHandlerIntersectingFeatures (line 1242) | public List<Pair<GenericLocus, GenericLocus>> getRTreeHandlerIntersect...
    method getNormalizationOptions (line 1250) | public String[] getNormalizationOptions(boolean isControl) {
    method exportDataCenteredAboutRegion (line 1276) | public void exportDataCenteredAboutRegion(int xBinPos, int yBinPos) th...
    method createNewDynamicResolutions (line 1323) | public void createNewDynamicResolutions(int newResolution) {
    type ZoomCallType (line 1331) | public enum ZoomCallType {
    type Unit (line 1335) | public enum Unit {BP, FRAG}

FILE: src/juicebox/HiCGlobals.java
  class HiCGlobals (line 37) | public class HiCGlobals {
    method verifySupportedHiCFileVersion (line 98) | public static void verifySupportedHiCFileVersion(int version) throws R...
    method verifySupportedHiCFileWritingVersion (line 105) | public static void verifySupportedHiCFileWritingVersion(int version) t...
    method font (line 112) | public static Font font(int size, boolean isBold) {
    method getIdealThreadCount (line 118) | public static int getIdealThreadCount() {
    method newFixedThreadPool (line 122) | public static ExecutorService newFixedThreadPool() {
    type menuType (line 126) | public enum menuType {MAP, LOCATION, STATE}

FILE: src/juicebox/IGVUtils.java
  class IGVUtils (line 49) | class IGVUtils {
    method createSocketHelper (line 55) | private static void createSocketHelper() {
    method sendToIGV (line 79) | public static void sendToIGV(final String locus1, final String locus2) {
    class SocketHelper (line 115) | static class SocketHelper {
      method SocketHelper (line 120) | SocketHelper(BufferedReader in, PrintWriter out, Socket socket) {

FILE: src/juicebox/MainWindow.java
  class MainWindow (line 56) | public class MainWindow extends JFrame {
    method MainWindow (line 75) | private MainWindow() {
    method createMainWindow (line 95) | private static MainWindow createMainWindow() {
    method getInstance (line 99) | public static synchronized MainWindow getInstance() {
    method main (line 110) | public static void main(String[] args) {
    method initApplication (line 176) | private static void initApplication() {
    method initComponents (line 193) | private void initComponents() {
    method createCursors (line 220) | private void createCursors() {
    method windowsCreateCursor (line 361) | private BufferedImage windowsCreateCursor(BufferedImage img, int thres...
    method exitActionPerformed (line 413) | public void exitActionPerformed() {
    method executeLongRunningTask (line 447) | public Future<?> executeLongRunningTask(final Runnable runnable, final...
    method executeLongRunningTask (line 451) | public Future<?> executeLongRunningTask(final Runnable runnable, final...
    method showDisabledGlassPane (line 475) | private void showDisabledGlassPane(String caller, String displayMessag...
    method initializeGlassPaneListening (line 483) | private void initializeGlassPaneListening() {
    method hideDisabledGlassPane (line 487) | private void hideDisabledGlassPane(String caller) {//getRootPane().get...
    method updateNamesFromImport (line 495) | public void updateNamesFromImport(String path) {

FILE: src/juicebox/ProcessHelper.java
  class ProcessHelper (line 36) | public class ProcessHelper {
    method ProcessHelper (line 39) | public ProcessHelper() {
    method startNewJavaProcess (line 44) | public Process startNewJavaProcess()
    method createProcess (line 54) | private ProcessBuilder createProcess() {

FILE: src/juicebox/Unused.java
  class Unused (line 31) | class Unused {

FILE: src/juicebox/assembly/AssemblyFileExporter.java
  class AssemblyFileExporter (line 35) | public class AssemblyFileExporter {
    method AssemblyFileExporter (line 43) | public AssemblyFileExporter(AssemblyScaffoldHandler assemblyScaffoldHa...
    method exportAssemblyFile (line 50) | public void exportAssemblyFile() {
    method exportAssembly (line 58) | private void exportAssembly() throws IOException {
    method superscaffoldToString (line 89) | private String superscaffoldToString(List<Integer> scaffoldRow) {
    method buildAssemblyOutputPath (line 101) | private String buildAssemblyOutputPath() {

FILE: src/juicebox/assembly/AssemblyFileImporter.java
  class AssemblyFileImporter (line 39) | public class AssemblyFileImporter {
    method AssemblyFileImporter (line 56) | public AssemblyFileImporter(String assemblyFilePath, boolean modified) {
    method AssemblyFileImporter (line 61) | public AssemblyFileImporter(SuperAdapter superAdapter) {
    method AssemblyFileImporter (line 65) | public AssemblyFileImporter() {
    method importAssembly (line 68) | public void importAssembly() {
    method updateAssemblyScale (line 98) | private int updateAssemblyScale() {
    method parseAssemblyFileNoBundling (line 107) | private void parseAssemblyFileNoBundling() throws IOException {
    method parseAssemblyFile (line 129) | private void parseAssemblyFile() throws IOException {
    method setInitialState (line 243) | private void setInitialState() {
    method setModifiedInitialState (line 260) | private void setModifiedInitialState() {
    method readFile (line 298) | List<String> readFile(String filePath) throws IOException {
    method getAssemblyScaffoldHandler (line 324) | public AssemblyScaffoldHandler getAssemblyScaffoldHandler() {

FILE: src/juicebox/assembly/AssemblyHeatmapHandler.java
  class AssemblyHeatmapHandler (line 39) | public class AssemblyHeatmapHandler {
    method setListOfOSortedAggregateScaffolds (line 46) | public static void setListOfOSortedAggregateScaffolds(List<Scaffold> l...
    method getSuperAdapter (line 51) | public static SuperAdapter getSuperAdapter() {
    method setSuperAdapter (line 55) | public static void setSuperAdapter(SuperAdapter superAdapter) {
    method modifyBlock (line 59) | public static Block modifyBlock(Block block, String key, int binSize, ...
    method getAlteredAsmBin (line 91) | private static int getAlteredAsmBin(int binValue, int binSize) {
    method lookUpOriginalAggregateScaffold (line 109) | private static Scaffold lookUpOriginalAggregateScaffold(long genomicPo...

FILE: src/juicebox/assembly/AssemblyOperationExecutor.java
  class AssemblyOperationExecutor (line 37) | public class AssemblyOperationExecutor {
    method splitContig (line 39) | public static void splitContig(Feature2D originalContig, Feature2D deb...
    method invertSelection (line 45) | public static void invertSelection(SuperAdapter superAdapter, List<Fea...
    method moveSelection (line 53) | public static void moveSelection(SuperAdapter superAdapter, List<Featu...
    method moveAndDisperseSelection (line 61) | public static void moveAndDisperseSelection(SuperAdapter superAdapter,...
    method toggleGroup (line 70) | public static void toggleGroup(SuperAdapter superAdapter, Feature2D up...
    method multiMerge (line 78) | public static void multiMerge(SuperAdapter superAdapter, List<Feature2...
    method multiSplit (line 86) | public static void multiSplit(SuperAdapter superAdapter, List<Feature2...
    method phaseMerge (line 94) | public static void phaseMerge(SuperAdapter superAdapter, List<Integer>...
    method performAssemblyAction (line 102) | private static void performAssemblyAction(final SuperAdapter superAdap...

FILE: src/juicebox/assembly/AssemblyScaffoldHandler.java
  class AssemblyScaffoldHandler (line 39) | public class AssemblyScaffoldHandler {
    method AssemblyScaffoldHandler (line 60) | public AssemblyScaffoldHandler(List<Scaffold> listOfScaffolds, List<Li...
    method AssemblyScaffoldHandler (line 66) | public AssemblyScaffoldHandler(List<Scaffold> listOfScaffolds, List<Li...
    method AssemblyScaffoldHandler (line 73) | public AssemblyScaffoldHandler(AssemblyScaffoldHandler assemblyScaffol...
    method cloneScaffolds (line 83) | private List<Scaffold> cloneScaffolds() {
    method cloneSuperscaffolds (line 91) | private List<List<Integer>> cloneSuperscaffolds() {
    method getListOfScaffolds (line 99) | public List<Scaffold> getListOfScaffolds() {
    method getListOfSuperscaffolds (line 103) | public List<List<Integer>> getListOfSuperscaffolds() {
    method updateAssembly (line 107) | public void updateAssembly(boolean refreshMap) {
    method populateSuperscaffoldFeature2D (line 208) | private Feature2D populateSuperscaffoldFeature2D(long start, long end,...
    method updateSuperscaffolds (line 223) | private void updateSuperscaffolds() {
    method getSignedIndexFromScaffoldFeature2D (line 244) | private int getSignedIndexFromScaffoldFeature2D(Feature2D scaffoldFeat...
    method getUnSignedIndexFromScaffoldFeature2D (line 252) | private int getUnSignedIndexFromScaffoldFeature2D(Feature2D scaffoldFe...
    method getScaffoldFromFeature (line 260) | public Scaffold getScaffoldFromFeature(Feature2D scaffoldFeature2D) {
    method getAggegateScaffoldFromFeature (line 268) | public Scaffold getAggegateScaffoldFromFeature(Feature2D aggregateScaf...
    method editScaffold (line 282) | public void editScaffold(Feature2D targetFeature, Feature2D debrisFeat...
    method editAsm (line 306) | private void editAsm(Scaffold scaffold) {
    method modifyScaffoldId (line 324) | private int modifyScaffoldId(int index, int cutElementId) {
    method editCprops (line 336) | private void editCprops(Scaffold targetScaffold, long startCut, long e...
    method invertSelection (line 404) | public void invertSelection(List<Feature2D> scaffoldFeatures) {
    method moveSelection (line 454) | void moveSelection(List<Feature2D> selectedFeatures, Feature2D upstrea...
    method toggleGroup (line 550) | public void toggleGroup(Feature2D upstreamFeature2D, Feature2D downstr...
    method multiMerge (line 569) | public void multiMerge(Feature2D firstFeature, Feature2D lastFeature) {
    method multiSplit (line 620) | public void multiSplit(List<Feature2D> selectedFeatures) {
    method mergeSuperScaffolds (line 630) | private void mergeSuperScaffolds (int super1, int super2){
    method phaseMerge (line 650) | public void phaseMerge(List<Integer> idListToMerge) {
    method splitSuperscaffold (line 703) | private void splitSuperscaffold(int superscaffoldId, int scaffoldId) {
    method multiSplitSuperscaffolds (line 745) | private void multiSplitSuperscaffolds(int id1, int id2, int super1, in...
    method getSuperscaffoldId (line 791) | private int getSuperscaffoldId(int scaffoldId) {
    method toString (line 806) | @Override
    method getScaffoldFeature2DHandler (line 812) | public Feature2DHandler getScaffoldFeature2DHandler() {
    method getSuperscaffoldFeature2DHandler (line 816) | public Feature2DHandler getSuperscaffoldFeature2DHandler() {
    method getListOfAggregateScaffolds (line 820) | public List<Scaffold> getListOfAggregateScaffolds() {
    method getIntersectingAggregateFeatures (line 824) | public List<Scaffold> getIntersectingAggregateFeatures(long genomicPos...
    method getListOfBundledScaffolds (line 839) | public List<String> getListOfBundledScaffolds() {

FILE: src/juicebox/assembly/AssemblyStateTracker.java
  class AssemblyStateTracker (line 36) | public class AssemblyStateTracker {
    method AssemblyStateTracker (line 44) | public AssemblyStateTracker(AssemblyScaffoldHandler assemblyScaffoldHa...
    method getAssemblyHandler (line 54) | public AssemblyScaffoldHandler getAssemblyHandler() {
    method getNewAssemblyHandler (line 58) | public AssemblyScaffoldHandler getNewAssemblyHandler() {
    method resetState (line 62) | public void resetState() {
    method getInitialAssemblyScaffoldHandler (line 68) | public AssemblyScaffoldHandler getInitialAssemblyScaffoldHandler() {
    method assemblyActionPerformed (line 72) | public void assemblyActionPerformed(AssemblyScaffoldHandler assemblySc...
    method regenerateLayers (line 93) | private void regenerateLayers(boolean refreshMap) {
    method checkUndo (line 101) | public boolean checkUndo() {
    method undo (line 105) | public void undo() {
    method checkRedo (line 115) | public boolean checkRedo() {
    method redo (line 119) | public void redo() {

FILE: src/juicebox/assembly/IGVFeatureCopy.java
  class IGVFeatureCopy (line 38) | public class IGVFeatureCopy implements IGVFeature {
    method IGVFeatureCopy (line 57) | public IGVFeatureCopy(IGVFeature feature) {
    method updateExons (line 76) | public void updateExons(List<Exon> newExons) {
    method updateStrand (line 80) | public void updateStrand(Strand curStrand, boolean inversionState, boo...
    method invertColorFeaturesChk (line 110) | public static void invertColorFeaturesChk() {
    method setStart (line 114) | public void setStart(int newStart) {
    method setEnd (line 118) | public void setEnd(int newEnd) {
    method getStart (line 122) | public int getStart() {
    method getEnd (line 126) | public int getEnd() {
    method getLength (line 130) | public int getLength() {
    method getType (line 134) | public String getType() {
    method getIdentifier (line 138) | public String getIdentifier() {
    method getDescription (line 142) | public String getDescription() {
    method getStrand (line 146) | public Strand getStrand() { return strand; }
    method getAttributes (line 148) | public MultiMap<String, String> getAttributes() {
    method contains (line 152) | public boolean contains(IGVFeature var1) {
    method contains (line 156) | public boolean contains(double var1) {
    method getExons (line 160) | public List<Exon> getExons() {
    method getColor (line 164) | public Color getColor() {
    method getURL (line 168) | public String getURL() {
    method getName (line 172) | public String getName() {
    method getChr (line 176) | public String getChr() {
    method getScore (line 180) | public float getScore() {
    method getValueString (line 184) | public String getValueString(double var1, int mouseX, WindowFunction v...
    method getContig (line 188) | public String getContig() {

FILE: src/juicebox/assembly/OneDimAssemblyTrackLifter.java
  class OneDimAssemblyTrackLifter (line 43) | public class OneDimAssemblyTrackLifter {
    method liftDataArray (line 45) | public static HiCDataPoint[] liftDataArray(HiCDataSource dataSource,
    method liftIGVFeatures (line 152) | public static List<IGVFeatureCopy> liftIGVFeatures(

FILE: src/juicebox/assembly/PsfFileExporter.java
  class PsfFileExporter (line 35) | public class PsfFileExporter {
    method PsfFileExporter (line 41) | public PsfFileExporter(AssemblyScaffoldHandler assemblyScaffoldHandler...
    method exportPsfFile (line 47) | public void exportPsfFile() {
    method exportPsf (line 55) | private void exportPsf() throws IOException {
    method superscaffoldToString (line 79) | private String superscaffoldToString(List<Integer> scaffoldRow) {
    method buildPsfOutputPath (line 97) | private String buildPsfOutputPath() {

FILE: src/juicebox/assembly/PsfFileImporter.java
  class PsfFileImporter (line 39) | public class PsfFileImporter extends AssemblyFileImporter {
    method PsfFileImporter (line 52) | public PsfFileImporter(String psfFilePath, boolean modified) {
    method importAssembly (line 57) | @Override
    method importPsf (line 62) | public void importPsf() {
    method updateAssemblyScale (line 83) | private int updateAssemblyScale() {
    method parsePsfFile (line 92) | private void parsePsfFile() throws IOException {
    method setInitialState (line 127) | private void setInitialState() {
    method setModifiedInitialState (line 144) | private void setModifiedInitialState() {
    method readFile (line 153) | List<String> readFile(String filePath) throws IOException {
    method getAssemblyScaffoldHandler (line 166) | public AssemblyScaffoldHandler getAssemblyScaffoldHandler() {

FILE: src/juicebox/assembly/Scaffold.java
  class Scaffold (line 41) | public class Scaffold extends Feature implements Comparable<Scaffold> {
    method compare (line 45) | public int compare(Scaffold o1, Scaffold o2) {
    method Scaffold (line 75) | public Scaffold(String name, int indexId, long length) {
    method Scaffold (line 83) | public Scaffold(Scaffold scaffold) {
    method getName (line 100) | public String getName() {
    method setName (line 104) | public void setName(String name) {
    method getIndexId (line 108) | public int getIndexId() {
    method setIndexId (line 112) | public void setIndexId(int indexId) {
    method getLength (line 116) | public long getLength() {
    method setLength (line 120) | public void setLength(long length) {
    method getOriginalStart (line 125) | public long getOriginalStart() {
    method setOriginalStart (line 129) | public void setOriginalStart(long originalStart) {
    method getOriginallyInverted (line 133) | public boolean getOriginallyInverted() {
    method setOriginallyInverted (line 137) | public void setOriginallyInverted(boolean originallyInverted) {
    method getCurrentStart (line 142) | public long getCurrentStart() {
    method setCurrentStart (line 146) | public void setCurrentStart(long currentStart) {
    method getInvertedVsInitial (line 151) | public boolean getInvertedVsInitial() {
    method setInvertedVsInitial (line 155) | public void setInvertedVsInitial(boolean invertedVsInitial) {
    method getSignIndexId (line 160) | public int getSignIndexId() {
    method getCurrentFeature2D (line 169) | public Feature2D getCurrentFeature2D() {
    method scale (line 185) | private int scale(long longCoordinate) {
    method isDebris (line 189) | public boolean isDebris() {
    method getOriginalScaffoldName (line 193) | public String getOriginalScaffoldName() {
    method getFragmentNumber (line 201) | public int getFragmentNumber() {
    method getOriginalEnd (line 214) | public long getOriginalEnd() {
    method getCurrentEnd (line 218) | public long getCurrentEnd() {
    method toggleInversion (line 222) | public void toggleInversion() {
    method mergeWith (line 226) | public Scaffold mergeWith(Scaffold scaffold) {
    method getKey (line 244) | @Override
    method deepClone (line 249) | @Override
    method equals (line 254) | @Override
    method toString (line 275) | @Override
    method hashCode (line 280) | @Override
    method compareTo (line 285) | @Override
    method currentContains (line 299) | private boolean currentContains(long x) {
    method originalContains (line 303) | private boolean originalContains(long x) {

FILE: src/juicebox/data/AbstractDatasetReader.java
  class AbstractDatasetReader (line 46) | public abstract class AbstractDatasetReader implements DatasetReader {
    method AbstractDatasetReader (line 50) | AbstractDatasetReader(String path) {
    method getPath (line 54) | public String getPath() {
    method readEigenvector (line 58) | @Override
    method readNormalizationVector (line 109) | @Override

FILE: src/juicebox/data/BinReader.java
  class BinReader (line 32) | public class BinReader {
    method handleBinType (line 33) | public static void handleBinType(LittleEndianInputStream dis, byte typ...
    method handleBothInts (line 74) | private static void handleBothInts(LittleEndianInputStream dis, int bi...
    method handleShortY (line 87) | private static void handleShortY(LittleEndianInputStream dis, int binX...
    method handleShortX (line 101) | private static void handleShortX(LittleEndianInputStream dis, int binX...
    method handleBothShorts (line 115) | private static void handleBothShorts(LittleEndianInputStream dis, int ...

FILE: src/juicebox/data/Block.java
  class Block (line 39) | public class Block {
    method Block (line 45) | public Block(int number, String regionID) {
    method Block (line 51) | public Block(int number, List<ContactRecord> records, String regionID) {
    method getNumber (line 57) | public int getNumber() {
    method getUniqueRegionID (line 61) | public String getUniqueRegionID() {
    method getContactRecords (line 65) | public List<ContactRecord> getContactRecords() {
    method getContactRecords (line 69) | public List<ContactRecord> getContactRecords(double subsampleFraction,...
    method clear (line 85) | public void clear() {

FILE: src/juicebox/data/BlockIndex.java
  class BlockIndex (line 36) | public class BlockIndex {
    method BlockIndex (line 40) | public BlockIndex(int nBlocks) {
    method populateBlocks (line 45) | public void populateBlocks(LittleEndianInputStream dis) throws IOExcep...
    method getBlockNumbers (line 54) | public List<Integer> getBlockNumbers() {
    method getBlockSize (line 58) | public Integer getBlockSize(int num) {
    method getBlock (line 66) | public IndexEntry getBlock(int blockNumber) {

FILE: src/juicebox/data/ChromosomeHandler.java
  class ChromosomeHandler (line 41) | public class ChromosomeHandler {
    method ChromosomeHandler (line 54) | public ChromosomeHandler(List<Chromosome> chromosomes, String genomeID...
    method ChromosomeHandler (line 58) | public ChromosomeHandler(List<Chromosome> chromosomes, String genomeID...
    method isWholeGenomeView (line 87) | public static boolean isWholeGenomeView(Context xContext, Context yCon...
    method cleanUpName (line 92) | public String cleanUpName(String name) {
    method isAllByAll (line 99) | public static boolean isAllByAll(String name) {
    method sort (line 103) | public static void sort(List<Chromosome> indices) {
    method getSetIntersection (line 115) | private static Set<Chromosome> getSetIntersection(Collection<Chromosom...
    method isAllByAll (line 126) | public static boolean isAllByAll(Chromosome chromosome) {
    method generateChromDotSizesBedFile (line 131) | private GenomeWideList<GenericLocus> generateChromDotSizesBedFile() {
    method isGenomeWide (line 145) | private boolean isGenomeWide(Chromosome chromosome) {
    method isGenomeWide (line 149) | private boolean isGenomeWide(String name) {
    method addGenomeWideChromosome (line 153) | public Chromosome addGenomeWideChromosome() {
    method generateAssemblyChromosome (line 158) | public Chromosome generateAssemblyChromosome() {
    method generateCustomChromosomeFromBED (line 174) | public Chromosome generateCustomChromosomeFromBED(File file, int minSi...
    method addCustomChromosome (line 185) | public Chromosome addCustomChromosome(Feature2DList featureList, Strin...
    method getTotalLengthOfAllRegionsInBedFile (line 192) | private int getTotalLengthOfAllRegionsInBedFile(GenomeWideList<Generic...
    method addCustomChromosome (line 205) | private Chromosome addCustomChromosome(GenomeWideList<GenericLocus> re...
    method initializeCleanedChromosomesList (line 215) | private List<Chromosome> initializeCleanedChromosomesList(List<Chromos...
    method initializeInternalVariables (line 225) | private Pair<long[], List<Chromosome[]>> initializeInternalVariables() {
    method getTotalLengthOfAllChromosomes (line 272) | private long getTotalLengthOfAllChromosomes(List<Chromosome> chromosom...
    method getGenomeID (line 281) | public String getGenomeID() {
    method isCustomChromosome (line 285) | public boolean isCustomChromosome(Chromosome chromosome) {
    method isCustomChromosome (line 289) | private boolean isCustomChromosome(int index) {
    method getChromosomeFromName (line 293) | public Chromosome getChromosomeFromName(String name) {
    method doesNotContainChromosome (line 297) | public boolean doesNotContainChromosome(String name) {
    method size (line 301) | public int size() {
    method getChromosomeBoundaries (line 305) | public long[] getChromosomeBoundaries() {
    method getChromosomeArray (line 309) | public Chromosome[] getChromosomeArray() {
    method getChromosomeFromIndex (line 313) | public Chromosome getChromosomeFromIndex(int indx) {
    method getIntersectionWith (line 317) | public ChromosomeHandler getIntersectionWith(ChromosomeHandler handler...
    method getAutosomalChromosomesArray (line 335) | public Chromosome[] getAutosomalChromosomesArray() {
    method getChromosomeArrayWithoutAllByAll (line 339) | public Chromosome[] getChromosomeArrayWithoutAllByAll() {
    method getListOfRegionsInCustomChromosome (line 343) | public GenomeWideList<GenericLocus> getListOfRegionsInCustomChromosome...
    method inferGenomeId (line 347) | public String inferGenomeId() {
    method extractOddOrEvenAutosomes (line 373) | public Chromosome[] extractOddOrEvenAutosomes(boolean extractOdd) {
    class ChromosomeComparator (line 389) | static class ChromosomeComparator implements Comparator<Chromosome> {
      method compare (line 390) | @Override
    method splitAutosomesIntoHalves (line 398) | public Pair<Chromosome[], Chromosome[]> splitAutosomesIntoHalves() {
    method splitAutosomesAndSkipByTwos (line 442) | public Pair<Chromosome[], Chromosome[]> splitAutosomesAndSkipByTwos() {
    method chromosomeListToArray (line 473) | private Chromosome[] chromosomeListToArray(List<Chromosome> chromosome...

FILE: src/juicebox/data/CombinedDatasetReader.java
  class CombinedDatasetReader (line 48) | public class CombinedDatasetReader implements DatasetReader {
    method CombinedDatasetReader (line 54) | public CombinedDatasetReader(List<DatasetReaderV2> readers) {
    method read (line 58) | @Override
    method isActive (line 80) | @Override
    method setActive (line 93) | @Override
    method getVersion (line 98) | @Override
    method getPath (line 104) | @Override
    method getCheckBoxes (line 110) | @Override
    method getNormalizationVector (line 120) | @Override
    method getDepthBase (line 125) | @Override
    method readMatrix (line 135) | @Override
    method readNormalizedBlock (line 161) | @Override
    method getBlockNumbers (line 185) | @Override
    method getBlockSize (line 199) | @Override
    method readEigenvector (line 217) | @Override
    method readNormalizationVector (line 223) | @Override
    method readNormalizationVectorPart (line 228) | @Override
    method readExpectedVectorPart (line 233) | @Override
    method mergeDatasets (line 244) | private Dataset mergeDatasets(List<Dataset> datasetList) {
    method mergeExpectedValues (line 377) | private ExpectedValueFunction mergeExpectedValues(List<ExpectedValueFu...
    method mergeStatistics (line 409) | private String mergeStatistics(List<String> statisticsList) {
    method mergeGraphs (line 459) | private String mergeGraphs(List<String> graphsList) {
    method mergeMatrices (line 526) | private Matrix mergeMatrices(List<Matrix> matrixList) {
    method mergeBlocks (line 616) | private Block mergeBlocks(List<Block> blockList, String blockKey) {

FILE: src/juicebox/data/CombinedExpectedValueFunction.java
  class CombinedExpectedValueFunction (line 40) | public class CombinedExpectedValueFunction implements ExpectedValueFunct...
    method CombinedExpectedValueFunction (line 45) | public CombinedExpectedValueFunction(ExpectedValueFunction densityFunc...
    method addDensityFunction (line 50) | public void addDensityFunction(ExpectedValueFunction densityFunction) {
    method getExpectedValue (line 55) | @Override
    method getExpectedValuesWithNormalization (line 64) | @Override
    method getExpectedValuesNoNormalization (line 83) | @Override
    method getLength (line 98) | @Override
    method getNormalizationType (line 103) | @Override
    method getUnit (line 108) | @Override
    method getBinSize (line 113) | @Override

FILE: src/juicebox/data/ContactRecord.java
  class ContactRecord (line 35) | public class ContactRecord implements Comparable<ContactRecord> {
    method ContactRecord (line 52) | public ContactRecord(int binX, int binY, float counts) {
    method incrementCount (line 58) | public void incrementCount(float score) {
    method getBinX (line 63) | public int getBinX() {
    method getBinY (line 67) | public int getBinY() {
    method getCounts (line 71) | public float getCounts() {
    method compareTo (line 75) | @Override
    method toString (line 84) | public String toString() {
    method hashCode (line 88) | @Override
    method equals (line 93) | @Override
    method getKey (line 105) | public String getKey(NormalizationType normalizationType) {

FILE: src/juicebox/data/CustomMatrixZoomData.java
  class CustomMatrixZoomData (line 48) | public class CustomMatrixZoomData extends MatrixZoomData {
    method CustomMatrixZoomData (line 55) | public CustomMatrixZoomData(Chromosome chr1, Chromosome chr2, Chromoso...
    method expandAvailableZoomDatas (line 64) | public void expandAvailableZoomDatas(String regionKey, MatrixZoomData ...
    method modifyBlock (line 70) | private static Block modifyBlock(Block block, String key, MatrixZoomDa...
    method getNormalizedBlocksOverlapping (line 104) | @Override
    method printFullDescription (line 118) | @Override
    method addNormalizedBlocksToListByGenomeCoordinates (line 125) | private List<Block> addNormalizedBlocksToListByGenomeCoordinates(long ...
    method actuallyLoadGivenBlocks (line 222) | private void actuallyLoadGivenBlocks(final List<Block> blockList, fina...
    method getBoundariesOfCustomChromosomeX (line 317) | public List<Long> getBoundariesOfCustomChromosomeX() {
    method getBoundariesOfCustomChromosomeY (line 321) | public List<Long> getBoundariesOfCustomChromosomeY() {
    method getExpected (line 326) | public double getExpected(int binX, int binY, ExpectedValueFunction df) {
    method getAverageCount (line 355) | @Override
    method getRTreeHandlerIntersectingFeatures (line 361) | public List<Pair<GenericLocus, GenericLocus>> getRTreeHandlerIntersect...

FILE: src/juicebox/data/Dataset.java
  class Dataset (line 53) | public class Dataset {
    method Dataset (line 72) | public Dataset(DatasetReader reader) {
    method getMatrix (line 80) | public Matrix getMatrix(Chromosome chr1, Chromosome chr2) {
    method addDynamicResolution (line 117) | public void addDynamicResolution(int newRes) {
    method getSubcompartments (line 137) | public ResourceLocator getSubcompartments() {
    method getSuperLoops (line 160) | public ResourceLocator getSuperLoops() {
    method getPeaks (line 184) | public ResourceLocator getPeaks() {
    method getBlocks (line 215) | public ResourceLocator getBlocks() {
    method setAttributes (line 246) | public void setAttributes(Map<String, String> map) {
    method getNormalizationTypes (line 256) | public List<NormalizationType> getNormalizationTypes() {
    method setNormalizationTypes (line 260) | public void setNormalizationTypes(List<NormalizationType> normalizatio...
    method addNormalizationType (line 264) | public void addNormalizationType(NormalizationType type) {
    method getNumberZooms (line 268) | public int getNumberZooms(HiC.Unit unit) {
    method getZoom (line 273) | public HiCZoom getZoom(HiC.Unit unit, int index) {
    method getZoomForBPResolution (line 277) | public HiCZoom getZoomForBPResolution(Integer resolution) {
    method getExpectedValues (line 291) | public ExpectedValueFunction getExpectedValues(HiCZoom zoom, Normaliza...
    method getExpectedValuesOrExit (line 297) | public ExpectedValueFunction getExpectedValuesOrExit(HiCZoom zoom, Nor...
    method getExpectedValueFunctionMap (line 306) | public Map<String, ExpectedValueFunction> getExpectedValueFunctionMap() {
    method setExpectedValueFunctionMap (line 310) | public void setExpectedValueFunctionMap(Map<String, ExpectedValueFunct...
    method getChromosomeHandler (line 314) | public ChromosomeHandler getChromosomeHandler() {
    method setChromosomeHandler (line 318) | public void setChromosomeHandler(ChromosomeHandler chromosomeHandler) {
    method getVersion (line 322) | public int getVersion() {
    method getGenomeId (line 326) | public String getGenomeId() {
    method setGenomeId (line 330) | public void setGenomeId(String genomeId) {
    method getRestrictionEnzyme (line 336) | public String getRestrictionEnzyme() {
    method setRestrictionEnzyme (line 340) | void setRestrictionEnzyme(int nSites) {
    method getSoftware (line 344) | private String getSoftware() {
    method getHiCFileScalingFactor (line 349) | public String getHiCFileScalingFactor() {
    method getStatistics (line 354) | public String getStatistics() {
    method convertStats (line 363) | private String convertStats(String oldStats) {
    method getGraphs (line 783) | public String getGraphs() {
    method getBpZooms (line 788) | public List<HiCZoom> getBpZooms() {
    method setBpZooms (line 795) | public void setBpZooms(int[] bpBinSizes) {
    method getFragZooms (line 806) | public List<HiCZoom> getFragZooms() {
    method setFragZooms (line 810) | public void setFragZooms(int[] fragBinSizes) {
    method hasFrags (line 821) | public boolean hasFrags() {
    method getFragmentCounts (line 825) | public Map<String, Integer> getFragmentCounts() {
    method setFragmentCounts (line 829) | public void setFragmentCounts(Map<String, Integer> map) {
    method getNextZoom (line 841) | public HiCZoom getNextZoom(HiCZoom zoom, boolean useIncreasingOrder) {
    method getEigenvector (line 864) | public double[] getEigenvector(Chromosome chr, HiCZoom zoom, int numbe...
    method getNormalizationVector (line 888) | public NormalizationVector getNormalizationVector(int chrIdx, HiCZoom ...
    method getPartNormalizationVector (line 910) | public NormalizationVector getPartNormalizationVector(int chrIdx, HiCZ...
    method addNormalizationVectorDirectlyToRAM (line 927) | public void addNormalizationVectorDirectlyToRAM(NormalizationVector no...
    method findRestrictionEnzyme (line 931) | private String findRestrictionEnzyme(int sites) {
    method setAttributes (line 972) | public void setAttributes(String key, String value) {
    method getCheckBoxes (line 979) | public List<JCheckBox> getCheckBoxes(List<ActionListener> actionListen...
    method getAllPossibleResolutions (line 983) | public List<HiCZoom> getAllPossibleResolutions() {
    method getNormalizationHandler (line 991) | public NormalizationHandler getNormalizationHandler() {
    method getDepthBase (line 995) | public int getDepthBase() {
    method clearCache (line 999) | public void clearCache(boolean onlyClearInter) {
    method clearCache (line 1013) | public void clearCache(boolean onlyClearInter, HiCZoom zoom) {

FILE: src/juicebox/data/DatasetReader.java
  type DatasetReader (line 42) | public interface DatasetReader {
    method isActive (line 44) | boolean isActive();
    method setActive (line 46) | void setActive(boolean status);
    method getVersion (line 48) | int getVersion();
    method read (line 50) | Dataset read() throws IOException;
    method readMatrix (line 52) | Matrix readMatrix(String key) throws IOException;
    method readNormalizedBlock (line 54) | Block readNormalizedBlock(int blockNumber, MatrixZoomData zd, Normaliz...
    method getBlockNumbers (line 62) | List<Integer> getBlockNumbers(MatrixZoomData matrixZoomData);
    method getBlockSize (line 64) | Integer getBlockSize(MatrixZoomData matrixZoomData, int blockNum);
    method readEigenvector (line 66) | double[] readEigenvector(String chrName, HiCZoom zoom, int number, Str...
    method readNormalizationVector (line 68) | NormalizationVector readNormalizationVector(NormalizationType type, in...
    method readNormalizationVectorPart (line 70) | NormalizationVector readNormalizationVectorPart(NormalizationType type...
    method readExpectedVectorPart (line 72) | ListOfDoubleArrays readExpectedVectorPart(long position, long nVals) t...
    method getPath (line 74) | String getPath();
    method getCheckBoxes (line 76) | List<JCheckBox> getCheckBoxes(List<ActionListener> actionListeners);
    method getNormalizationVector (line 78) | NormalizationVector getNormalizationVector(int chr1Idx, HiCZoom zoom, ...
    method getDepthBase (line 80) | int getDepthBase();

FILE: src/juicebox/data/DatasetReaderFactory.java
  class DatasetReaderFactory (line 47) | public class DatasetReaderFactory {
    method getReader (line 49) | public static DatasetReader getReader(List<String> fileList) throws IO...
    method getReaderForFile (line 67) | private static DatasetReaderV2 getReaderForFile(String file) throws IO...
    method getMagicString (line 83) | static String getMagicString(String path) throws IOException {

FILE: src/juicebox/data/DatasetReaderV2.java
  class DatasetReaderV2 (line 58) | public class DatasetReaderV2 extends AbstractDatasetReader {
    method DatasetReaderV2 (line 80) | public DatasetReaderV2(String path) throws IOException {
    method read (line 85) | @Override
    method getValidStream (line 239) | private SeekableStream getValidStream() throws IOException {
    method getCheckBoxes (line 247) | @Override
    method getNormalizationVector (line 265) | @Override
    method getDepthBase (line 270) | @Override
    method readMatrixZoomData (line 275) | private Pair<MatrixZoomData, Long> readMatrixZoomData(Chromosome chr1,...
    method checkGraphs (line 332) | private String checkGraphs(String graphs) {
    method readGraphs (line 374) | private String readGraphs(String graphFileName) throws IOException {
    method isActive (line 393) | @Override
    method setActive (line 398) | @Override
    method getVersion (line 403) | @Override
    method getNviHeaderPosition (line 408) | public long getNviHeaderPosition() {
    method readFooter (line 412) | private void readFooter(long position) throws IOException {
    method readVectorOfFloats (line 649) | private long readVectorOfFloats(LittleEndianInputStream dis, long nVal...
    method readVectorOfDoubles (line 657) | private long readVectorOfDoubles(LittleEndianInputStream dis, long nVa...
    method readSites (line 665) | private int[] readSites(long position, int nSites) throws IOException {
    method readMatrix (line 676) | @Override
    method getFragCount (line 726) | int getFragCount(Chromosome chromosome) {
    method retrieveFragmentSitesFromCache (line 736) | private synchronized int[] retrieveFragmentSitesFromCache(Chromosome c...
    method getBlockNumbers (line 750) | @Override
    method getBlockSize (line 756) | @Override
    method getNormVectorIndex (line 768) | public Map<String, LargeIndexEntry> getNormVectorIndex() {
    method getNormFilePosition (line 772) | public long getNormFilePosition() {
    class FragIndexEntry (line 776) | static class FragIndexEntry {
      method FragIndexEntry (line 780) | FragIndexEntry(long position, int nSites) {
    method readNormalizationVector (line 787) | @Override
    method readNormalizationVectorPart (line 830) | @Override
    method readExpectedVectorPart (line 872) | @Override
    method seekAndFullyReadCompressedBytes (line 890) | private byte[] seekAndFullyReadCompressedBytes(IndexEntry idx) throws ...
    method seekAndFullyReadLargeCompressedBytes (line 899) | private List<byte[]> seekAndFullyReadLargeCompressedBytes(LargeIndexEn...
    method readNormalizedBlock (line 916) | @Override
    method readBlock (line 961) | private Block readBlock(int blockNumber, MatrixZoomData zd) throws IOE...
    method decompress (line 1031) | private byte[] decompress(byte[] compressedBytes) {

FILE: src/juicebox/data/DynamicBlock.java
  class DynamicBlock (line 32) | public class DynamicBlock extends Block {
    method DynamicBlock (line 35) | public DynamicBlock(int number, ContactRecord record, String regionID) {
    method getContactRecords (line 40) | @Override
    method addContactRecord (line 45) | public void addContactRecord(ContactRecord cr) {

FILE: src/juicebox/data/DynamicBlockIndex.java
  class DynamicBlockIndex (line 36) | public class DynamicBlockIndex extends BlockIndex {
    method DynamicBlockIndex (line 44) | public DynamicBlockIndex(SeekableStream stream, int numBlocks, int max...
    method getBlockNumbers (line 53) | @Override
    method getBlock (line 59) | @Override
    method searchForBlockIndexEntry (line 96) | private IndexEntry searchForBlockIndexEntry(int blockNumber, long boun...

FILE: src/juicebox/data/DynamicMatrixZoomData.java
  class DynamicMatrixZoomData (line 32) | public class DynamicMatrixZoomData extends MatrixZoomData {
    method DynamicMatrixZoomData (line 42) | public DynamicMatrixZoomData(HiCZoom zoom, MatrixZoomData higherResZD) {
    method getNormalizedBlocksOverlapping (line 48) | @Override
    method createBlocksForLowerRes (line 61) | private List<Block> createBlocksForLowerRes(List<Block> highResBlocks,...
    method printFullDescription (line 114) | @Override

FILE: src/juicebox/data/ExpectedValueFunction.java
  type ExpectedValueFunction (line 36) | public interface ExpectedValueFunction {
    method getExpectedValue (line 38) | double getExpectedValue(int chrIdx, long distance);
    method getLength (line 40) | long getLength();
    method getNormalizationType (line 42) | NormalizationType getNormalizationType();
    method getUnit (line 44) | HiC.Unit getUnit();
    method getBinSize (line 46) | int getBinSize();
    method getExpectedValuesNoNormalization (line 48) | ListOfDoubleArrays getExpectedValuesNoNormalization();
    method getExpectedValuesWithNormalization (line 50) | ListOfDoubleArrays getExpectedValuesWithNormalization(int chrIdx);

FILE: src/juicebox/data/ExpectedValueFunctionImpl.java
  class ExpectedValueFunctionImpl (line 42) | public class ExpectedValueFunctionImpl implements ExpectedValueFunction {
    method ExpectedValueFunctionImpl (line 62) | public ExpectedValueFunctionImpl(NormalizationType type, HiC.Unit unit...
    method ExpectedValueFunctionImpl (line 73) | public ExpectedValueFunctionImpl(NormalizationType type, HiC.Unit unit...
    method getKey (line 85) | public static String getKey(HiCZoom zoom, NormalizationType normType) {
    method getNormFactors (line 90) | public Map<Integer, Double> getNormFactors() {
    method getExpectedValuesNoNormalization (line 100) | @Override
    method getExpectedValue (line 122) | @Override
    method getExpectedValuesWithNormalization (line 170) | @Override
    method getLength (line 197) | @Override
    method getNormalizationType (line 202) | @Override
    method getUnit (line 207) | @Override
    method getBinSize (line 212) | @Override

FILE: src/juicebox/data/GeneLocation.java
  class GeneLocation (line 28) | public class GeneLocation {
    method GeneLocation (line 33) | public GeneLocation(Chromosome chromosome, int centerPosition) {
    method getCenterPosition (line 38) | public int getCenterPosition() {
    method getChromosome (line 42) | public Chromosome getChromosome() {

FILE: src/juicebox/data/HiCFileLoader.java
  class HiCFileLoader (line 52) | public class HiCFileLoader {
    method loadMenuItemActionPerformed (line 59) | public static File loadMenuItemActionPerformed(SuperAdapter superAdapt...
    method loadFromRecentActionPerformed (line 83) | public static void loadFromRecentActionPerformed(SuperAdapter superAda...
    method loadFromURLActionPerformed (line 92) | public static void loadFromURLActionPerformed(SuperAdapter superAdapte...
    method loadFromListActionPerformed (line 115) | public static void loadFromListActionPerformed(SuperAdapter superAdapt...
    method initProperties (line 129) | private static void initProperties() {
    method loadPropertiesViaURL (line 163) | private static void loadPropertiesViaURL(String url) throws IOException {
    method changeJuiceboxPropertiesFile (line 171) | public static void changeJuiceboxPropertiesFile(String newURL) {
    method setPropertiesFileURL (line 195) | private static void setPropertiesFileURL(String propertiesFileURL) {

FILE: src/juicebox/data/HiCFileTools.java
  class HiCFileTools (line 43) | public class HiCFileTools {
    method extractDatasetForCLT (line 45) | public static Dataset extractDatasetForCLT(List<String> files, boolean...
    method extractDatasetReaderForCLT (line 81) | public static DatasetReader extractDatasetReaderForCLT(List<String> fi...
    method loadChromosomes (line 120) | public static ChromosomeHandler loadChromosomes(String idOrFile) {
    method filterResolutions (line 189) | public static List<Integer> filterResolutions(List<HiCZoom> availableZ...
    method closestValue (line 204) | private static int closestValue(int val, TreeSet<Integer> valSet) {
    method getChromosomeSetIntersection (line 227) | public static ChromosomeHandler getChromosomeSetIntersection(Chromosom...
    method getZoomSetIntersection (line 231) | public static Set<HiCZoom> getZoomSetIntersection(Collection<HiCZoom> ...
    method stringToChromosomes (line 248) | public static ChromosomeHandler stringToChromosomes(List<String> chrom...
    method equivalentChromosome (line 276) | public static boolean equivalentChromosome(String token, Chromosome ch...
    method openWriter (line 282) | public static PrintWriter openWriter(File file) {
    method extractLocalBoundedRegion (line 294) | public static RealMatrix extractLocalBoundedRegion(MatrixZoomData zd, ...
    method extractLocalBoundedRegion (line 299) | public static RealMatrix extractLocalBoundedRegion(MatrixZoomData zd, ...
    method extractLocalBoundedRegion (line 310) | public static RealMatrix extractLocalBoundedRegion(MatrixZoomData zd, ...
    method getAllRegionBlocks (line 356) | public static List<Block> getAllRegionBlocks(MatrixZoomData zd, long b...
    method extractChromosomeExpectedVector (line 385) | public static ListOfDoubleArrays extractChromosomeExpectedVector(Datas...
    method triggerNormError (line 397) | public static void triggerNormError(NormalizationType normalizationTyp...
    method createValidDirectory (line 409) | public static File createValidDirectory(String directoryPath) {
    method getTruncatedText (line 420) | public static String getTruncatedText(String text, int maxLengthEntryN...
    method isDropboxURL (line 430) | public static boolean isDropboxURL(String url) {
    method cleanUpDropboxURL (line 434) | public static String cleanUpDropboxURL(String url) {
    method getMatrixZoomData (line 439) | public static MatrixZoomData getMatrixZoomData(Dataset ds, Chromosome ...
    method getMatrixZoomData (line 445) | public static MatrixZoomData getMatrixZoomData(Dataset ds, Chromosome ...

FILE: src/juicebox/data/Matrix.java
  class Matrix (line 44) | public class Matrix {
    method compare (line 55) | @Override
    method Matrix (line 68) | public Matrix(int chr1, int chr2, List<MatrixZoomData> zoomDataList) {
    method createCustomChromosomeMatrix (line 74) | public static Matrix createCustomChromosomeMatrix(Chromosome chr1, Chr...
    method initZoomDataMap (line 146) | private void initZoomDataMap(List<MatrixZoomData> zoomDataList) {
    method generateKey (line 171) | public static String generateKey(int chr1, int chr2) {
    method createAssemblyChromosomeMatrix (line 176) | public static Matrix createAssemblyChromosomeMatrix(ChromosomeHandler ...
    method createDynamicResolutionMZD (line 245) | public void createDynamicResolutionMZD(Pair<Integer, Integer> resPair,...
    method getIndicesFromSubChromosomes (line 257) | private static List<Chromosome> getIndicesFromSubChromosomes(final Chr...
    method updateCustomZoomDataRegions (line 280) | private static void updateCustomZoomDataRegions(Chromosome chr1, Chrom...
    method generateKey (line 290) | public static String generateKey(Chromosome chr1, Chromosome chr2) {
    method getKey (line 296) | public String getKey() {
    method getFirstZoomData (line 300) | public MatrixZoomData getFirstZoomData() {
    method getFirstZoomData (line 308) | public MatrixZoomData getFirstZoomData(HiC.Unit unit) {
    method getFirstPearsonZoomData (line 316) | public MatrixZoomData getFirstPearsonZoomData(HiC.Unit unit) {
    method getZoomData (line 325) | public MatrixZoomData getZoomData(HiCZoom zoom) {
    method getZoomData (line 360) | public MatrixZoomData getZoomData(int index) {
    method getNumBPResolutions (line 372) | public int getNumBPResolutions() {
    method getNumFragResolutions (line 376) | public int getNumFragResolutions() {
    method isNotIntra (line 380) | public boolean isNotIntra() {
    method getChr1Idx (line 384) | public int getChr1Idx() {
    method getChr2Idx (line 388) | public int getChr2Idx() {
    method setBpBinSizes (line 392) | public void setBpBinSizes(ArrayList<Integer> bpBinSizes) {
    method setFragBinSizes (line 396) | public void setFragBinSizes(ArrayList<Integer> fragBinSizes) {

FILE: src/juicebox/data/MatrixZoomData.java
  class MatrixZoomData (line 76) | public class MatrixZoomData {
    method MatrixZoomData (line 111) | public MatrixZoomData(Chromosome chr1, Chromosome chr2, HiCZoom zoom, ...
    method getChr1 (line 160) | public Chromosome getChr1() {
    method getChr2 (line 164) | public Chromosome getChr2() {
    method getXGridAxis (line 168) | public HiCGridAxis getXGridAxis() {
    method getYGridAxis (line 172) | public HiCGridAxis getYGridAxis() {
    method getBinSize (line 176) | public int getBinSize() {
    method getChr1Idx (line 180) | public int getChr1Idx() {
    method getChr2Idx (line 184) | public int getChr2Idx() {
    method getZoom (line 188) | public HiCZoom getZoom() {
    method getBlockColumnCount (line 192) | public int getBlockColumnCount() {
    method getBlockBinCount (line 196) | public int getBlockBinCount() { return blockBinCount; }
    method getKey (line 198) | public String getKey() {
    method getKey (line 203) | private String getKey(int chr1, int chr2) {
    method getBlockKey (line 207) | public String getBlockKey(int blockNumber, NormalizationType no) {
    method getNormLessBlockKey (line 211) | public String getNormLessBlockKey(Block block) {
    method getBlockKey (line 215) | private String getBlockKey(int blockNumber, NormalizationType no, int ...
    method getColorScaleKey (line 219) | public String getColorScaleKey(MatrixType displayOption, Normalization...
    method getTileKey (line 223) | public String getTileKey(int tileRow, int tileColumn, MatrixType displ...
    method getNormalizedBlocksOverlapping (line 238) | public List<Block> getNormalizedBlocksOverlapping(long binX1, long bin...
    method getBlockNumberVersion9FromPADAndDepth (line 289) | public int getBlockNumberVersion9FromPADAndDepth(int positionAlongDiag...
    method populateBlocksToLoadV9 (line 293) | private void populateBlocksToLoadV9(int positionAlongDiagonal, int dep...
    method addNormalizedBlocksToListV9 (line 305) | private List<Block> addNormalizedBlocksToListV9(final List<Block> bloc...
    method populateBlocksToLoad (line 335) | private void populateBlocksToLoad(int r, int c, NormalizationType no, ...
    method addNormalizedBlocksToList (line 356) | private List<Block> addNormalizedBlocksToList(final List<Block> blockL...
    method addNormalizedBlocksToList (line 386) | private List<Block> addNormalizedBlocksToList(final List<Block> blockL...
    method addNormalizedBlocksToListAssembly (line 410) | private List<Block> addNormalizedBlocksToListAssembly(final List<Block...
    method actuallyLoadGivenBlocks (line 527) | private void actuallyLoadGivenBlocks(final List<Block> blockList, Set<...
    method actuallyLoadGivenBlocks (line 583) | private void actuallyLoadGivenBlocks(final List<Block> blockList, Set<...
    method getObservedValue (line 646) | public float getObservedValue(int binX, int binY, NormalizationType no...
    method computeEigenvector (line 708) | public double[] computeEigenvector(ExpectedValueFunction df, int which) {
    method getSubsetOfMatrix (line 739) | private RealMatrix getSubsetOfMatrix(int[] newPosToOrig, int subsetN, ...
    method getMapNewPosToOriginal (line 754) | private int[] getMapNewPosToOriginal(int dim, BitSet bitSet) {
    method getNormSquared (line 765) | public BasicMatrix getNormSquared(NormalizationType normalizationType) {
    method computeNormSquared (line 779) | private BasicMatrix computeNormSquared(NormalizationType normalization...
    method getPearsons (line 800) | public BasicMatrix getPearsons(ExpectedValueFunction df) {
    method getPearsonValue (line 825) | public float getPearsonValue(int binX, int binY, NormalizationType typ...
    method computePearsons (line 841) | private BasicMatrix computePearsons(ExpectedValueFunction df) {
    method populateOEMatrixAndBitset (line 868) | private void populateOEMatrixAndBitset(double[][] oeMatrix, BitSet bit...
    method getDescription (line 893) | public String getDescription() {
    method printFullDescription (line 897) | public void printFullDescription() {
    method getBlockNumbers (line 909) | public List<Integer> getBlockNumbers() {
    method getBlockNumbersForRegionFromGenomePosition (line 920) | List<Integer> getBlockNumbersForRegionFromGenomePosition(long[] region...
    method getBlockNumbersForRegionFromBinPosition (line 930) | private List<Integer> getBlockNumbersForRegionFromBinPosition(long[] r...
    method dump (line 963) | public void dump(PrintWriter printWriter, LittleEndianOutputStream les...
    method dump1DTrackFromCrossHairAsWig (line 1137) | public void dump1DTrackFromCrossHairAsWig(PrintWriter printWriter, lon...
    method getAverageCount (line 1203) | public double getAverageCount() {
    method getSumCount (line 1207) | public double getSumCount() {
    method setAverageCount (line 1216) | public void setAverageCount(double averageCount) {
    method setSumCount (line 1220) | public void setSumCount(double sumCount) {
    method clearCache (line 1224) | public void clearCache(boolean onlyClearInter) {
    method getNewContactRecordIterator (line 1235) | private Iterator<ContactRecord> getNewContactRecordIterator() {
    method getIteratorContainer (line 1240) | public IteratorContainer getIteratorContainer() {
    method getFromFileIteratorContainer (line 1247) | public IteratorContainer getFromFileIteratorContainer() {
    method mergeAndWriteBlocks (line 1252) | public Pair<List<IndexEntry>,ExpectedValueCalculation> mergeAndWriteBl...
    method mergeAndWriteBlocks (line 1283) | public Pair<List<IndexEntry>,ExpectedValueCalculation> mergeAndWriteBl...
    method writeBlockChunk (line 1411) | private void writeBlockChunk(int startBlock, int endBlock, List<Intege...
    method writeBlock (line 1439) | protected void writeBlock(Block block, LittleEndianOutputStream los, D...
    method compress (line 1617) | protected byte[] compress(byte[] data, Deflater compressor) {
    method computeExpected (line 1647) | public ExpectedValueCalculation computeExpected(boolean calculateExpec...
    method calculateExpectedBlockChunk (line 1750) | private void calculateExpectedBlockChunk(int startBlock, int endBlock,...
    method calcExpectedBlock (line 1766) | protected void calcExpectedBlock(Block block, ExpectedValueCalculation...

FILE: src/juicebox/data/NormFactorMapReader.java
  class NormFactorMapReader (line 33) | public class NormFactorMapReader {
    method NormFactorMapReader (line 37) | public NormFactorMapReader(int nFactors, int version, LittleEndianInpu...
    method getNormFactors (line 52) | public Map<Integer, Double> getNormFactors() {
    method getOffset (line 56) | public int getOffset() {

FILE: src/juicebox/data/NormalizationVector.java
  class NormalizationVector (line 42) | public class NormalizationVector {
    method NormalizationVector (line 51) | public NormalizationVector(NormalizationType type, int chrIdx, HiC.Uni...
    method NormalizationVector (line 59) | public NormalizationVector(NormalizationType type, int chrIdx, HiC.Uni...
    method getKey (line 64) | public static String getKey(NormalizationType type, int chrIdx, String...
    method getChrIdx (line 68) | public int getChrIdx() {
    method getResolution (line 72) | public int getResolution() {
    method getKey (line 76) | public String getKey() {
    method getData (line 80) | public ListOfDoubleArrays getData() {
    method doesItNeedToBeScaledTo (line 84) | public boolean doesItNeedToBeScaledTo() {
    method mmbaScaleToVector (line 88) | public NormalizationVector mmbaScaleToVector(Dataset ds) {
    method mmbaScaleToVector (line 95) | public NormalizationVector mmbaScaleToVector(IteratorContainer ic) {

FILE: src/juicebox/data/ZoomAction.java
  class ZoomAction (line 33) | public class ZoomAction {
    method ZoomAction (line 42) | public ZoomAction(String chromosomeX, String chromosomeY, HiCZoom hiCZ...
    method equals (line 55) | public boolean equals(ZoomAction other) {
    method getChromosomeX (line 59) | public String getChromosomeX() {
    method getChromosomeY (line 63) | public String getChromosomeY() {
    method getHiCZoom (line 67) | public HiCZoom getHiCZoom() {
    method getGenomeX (line 71) | public long getGenomeX() {
    method getGenomeY (line 75) | public long getGenomeY() {
    method getScaleFactor (line 79) | public double getScaleFactor() {
    method setScaleFactor (line 83) | public void setScaleFactor(double newScaleFactor) {
    method getResetZoom (line 87) | public boolean getResetZoom() {
    method getZoomCallType (line 91) | public HiC.ZoomCallType getZoomCallType() {
    method getResolutionLocked (line 95) | public int getResolutionLocked() {

FILE: src/juicebox/data/ZoomActionTracker.java
  class ZoomActionTracker (line 32) | public class ZoomActionTracker {
    method undoZoom (line 38) | public void undoZoom() {
    method redoZoom (line 45) | public void redoZoom() {
    method validateUndoZoom (line 52) | public boolean validateUndoZoom() {
    method validateRedoZoom (line 56) | public boolean validateRedoZoom() {
    method addZoomState (line 60) | public void addZoomState(ZoomAction newZoomAction) {
    method clear (line 69) | public void clear() {
    method equals (line 75) | public boolean equals(ZoomActionTracker other) {
    method getCurrentZoomAction (line 87) | public ZoomAction getCurrentZoomAction() {
    method setCurrentZoomAction (line 91) | private void setCurrentZoomAction(ZoomAction zoomAction) {
    method getUndoZoomActions (line 95) | private Stack<ZoomAction> getUndoZoomActions() {
    method getRedoZoomActions (line 99) | private Stack<ZoomAction> getRedoZoomActions() {

FILE: src/juicebox/data/anchor/BEDTools.java
  class BEDTools (line 32) | class BEDTools {
    method merge (line 42) | public static List<GenericLocus> merge(List<GenericLocus> anchors) {
    method mergeTakeSmaller (line 62) | public static List<GenericLocus> mergeTakeSmaller(List<GenericLocus> a...
    method intersect (line 92) | public static List<GenericLocus> intersect(List<GenericLocus> topAncho...
    method intersection (line 155) | private static GenericLocus intersection(GenericLocus anchor1, Generic...
    method preservativeIntersect (line 195) | public static List<GenericLocus> preservativeIntersect(List<GenericLoc...
    method preservativeIntersection (line 258) | private static GenericLocus preservativeIntersection(GenericLocus anch...

FILE: src/juicebox/data/anchor/GenericLocus.java
  class GenericLocus (line 34) | public class GenericLocus extends Feature implements Comparable<GenericL...
    method GenericLocus (line 50) | public GenericLocus(String chr, long x1, long x2) {
    method GenericLocus (line 62) | public GenericLocus(String chr, int x1, int x2, String name) {
    method GenericLocus (line 76) | public GenericLocus(String chrIndex, long x1, long x2, List<Feature2D>...
    method getKey (line 82) | @Override
    method deepClone (line 87) | @Override
    method cloneToMotifAnchor (line 94) | public Feature cloneToMotifAnchor() {
    method getChr (line 103) | public String getChr() {
    method getX1 (line 110) | public long getX1() {
    method getX2 (line 117) | public long getX2() {
    method getWidth (line 124) | public int getWidth() {
    method widenMargins (line 133) | public void widenMargins(int width) {
    method contains (line 142) | public boolean contains(long x) {
    method isStrictlyToTheLeftOf (line 150) | public boolean isStrictlyToTheLeftOf(GenericLocus anchor) {
    method isStrictlyToTheRightOf (line 158) | public boolean isStrictlyToTheRightOf(GenericLocus anchor) {
    method hasOverlapWith (line 166) | public boolean hasOverlapWith(GenericLocus anchor) {
    method mergeWith (line 171) | public void mergeWith(GenericLocus anchor) {
    method mergeWithTakeSmaller (line 182) | public void mergeWithTakeSmaller(GenericLocus anchor) {
    method toString (line 201) | @Override
    method equals (line 207) | @Override
    method hashCode (line 219) | @Override
    method compareTo (line 224) | @Override
    method addFeatureReferencesFrom (line 235) | public void addFeatureReferencesFrom(GenericLocus anchor) {
    method updateOriginalFeatures (line 240) | public void updateOriginalFeatures(String prefix) {
    method getOriginalFeatures1 (line 253) | public List<Feature2D> getOriginalFeatures1() {
    method getOriginalFeatures2 (line 257) | public List<Feature2D> getOriginalFeatures2() {
    method isDirectionalAnchor (line 261) | public boolean isDirectionalAnchor(boolean direction) {
    method getName (line 269) | public String getName() {

FILE: src/juicebox/data/anchor/GenericLocusParser.java
  class GenericLocusParser (line 42) | public class GenericLocusParser {
    method loadFromBEDFile (line 48) | public static GenomeWideList<GenericLocus> loadFromBEDFile(ChromosomeH...
    method parseBEDFile (line 75) | private static List<GenericLocus> parseBEDFile(BufferedReader buffered...

FILE: src/juicebox/data/anchor/GenericLocusTools.java
  class GenericLocusTools (line 41) | public class GenericLocusTools {
    method extractAnchorsFromIntrachromosomalFeatures (line 47) | public static GenomeWideList<GenericLocus> extractAnchorsFromIntrachro...
    method extractAllAnchorsFromAllFeatures (line 70) | public static GenomeWideList<GenericLocus> extractAllAnchorsFromAllFea...
    method getMinSizeForExpansionFromGUI (line 90) | public static int getMinSizeForExpansionFromGUI() {
    method mergeAnchors (line 108) | private static void mergeAnchors(GenomeWideList<GenericLocus> anchorLi...
    method mergeAnchorsTakeSmaller (line 117) | private static void mergeAnchorsTakeSmaller(GenomeWideList<GenericLocu...
    method updateOriginalFeatures (line 129) | public static void updateOriginalFeatures(GenomeWideList<GenericLocus>...
    method intersectLists (line 143) | public static void intersectLists(final GenomeWideList<GenericLocus> f...
    method preservativeIntersectLists (line 157) | public static void preservativeIntersectLists(final GenomeWideList<Gen...
    method expandSmallAnchors (line 174) | private static void expandSmallAnchors(GenomeWideList<GenericLocus> an...
    method expandSmallAnchors (line 191) | private static void expandSmallAnchors(List<GenericLocus> anchors, int...
    method extractDirectionalAnchors (line 201) | public static GenomeWideList<GenericLocus> extractDirectionalAnchors(G...
    method mergeAndExpandSmallAnchors (line 218) | public static void mergeAndExpandSmallAnchors(GenomeWideList<GenericLo...
    method callMergeAnchors (line 224) | public static void callMergeAnchors(GenomeWideList<GenericLocus> locus...

FILE: src/juicebox/data/anchor/MotifAnchor.java
  class MotifAnchor (line 39) | public class MotifAnchor extends GenericLocus {
    method MotifAnchor (line 60) | public MotifAnchor(String chr, long x1, long x2) {
    method MotifAnchor (line 64) | public MotifAnchor(String chr, int x1, int x2, String name) {
    method MotifAnchor (line 77) | public MotifAnchor(String chrIndex, long x1, long x2, List<Feature2D> ...
    method getKey (line 81) | @Override
    method deepClone (line 86) | @Override
    method cloneToMotifAnchor (line 97) | @Override
    method toString (line 102) | @Override
    method equals (line 107) | @Override
    method hashCode (line 119) | @Override
    method compareTo (line 124) | @Override
    method setFIMOAttributes (line 140) | public void setFIMOAttributes(double score, double pValue, double qVal...
    method getScore (line 150) | public double getScore() {
    method hasFIMOAttributes (line 154) | public boolean hasFIMOAttributes() {
    method addFIMOAttributesFrom (line 158) | public void addFIMOAttributesFrom(MotifAnchor anchor) {
    method addFeatureReferencesFrom (line 162) | public void addFeatureReferencesFrom(MotifAnchor anchor) {
    method updateOriginalFeatures (line 167) | public void updateOriginalFeatures(boolean uniqueStatus, int specificS...
    method getSequence (line 213) | public String getSequence() {
    method getStrand (line 220) | public boolean getStrand() {

FILE: src/juicebox/data/anchor/MotifAnchorParser.java
  class MotifAnchorParser (line 52) | public class MotifAnchorParser {
    method loadMotifsFromGenomeID (line 54) | public static GenomeWideList<MotifAnchor> loadMotifsFromGenomeID(Strin...
    method loadMotifsFromLocalFile (line 58) | public static GenomeWideList<MotifAnchor> loadMotifsFromLocalFile(Stri...
    method loadMotifsFromURL (line 62) | public static GenomeWideList<MotifAnchor> loadMotifsFromURL(String pat...
    method loadGlobalMotifs (line 66) | private static GenomeWideList<MotifAnchor> loadGlobalMotifs(String pat...
    method extractProperMotifFilePath (line 112) | private static String extractProperMotifFilePath(String genomeID, Stri...
    method parseMotifFile (line 128) | private static GenomeWideList<MotifAnchor> parseMotifFile(String path,...
    method parseGlobalMotifFile (line 155) | private static List<MotifAnchor> parseGlobalMotifFile(BufferedReader b...
    method loadFromBEDFile (line 239) | public static GenomeWideList<MotifAnchor> loadFromBEDFile(ChromosomeHa...
    method parseBEDFile (line 266) | private static List<MotifAnchor> parseBEDFile(BufferedReader bufferedR...
    method downloadFromUrl (line 312) | public static String downloadFromUrl(URL url, String localFilename) th...
    method uncompressFromGzip (line 346) | public static String uncompressFromGzip(String compressedFile, String ...
    type MotifLocation (line 393) | public enum MotifLocation {VIA_ID, URL, LOCAL}

FILE: src/juicebox/data/anchor/MotifAnchorTools.java
  class MotifAnchorTools (line 39) | public class MotifAnchorTools extends GenericLocusTools {
    method updateOriginalFeatures (line 44) | public static void updateOriginalFeatures(GenomeWideList<MotifAnchor> ...
    method expandSmallAnchors (line 59) | private static void expandSmallAnchors(GenomeWideList<MotifAnchor> anc...
    method expandSmallAnchors (line 76) | private static void expandSmallAnchors(List<MotifAnchor> anchors, int ...
    method extractUniqueMotifs (line 90) | public static GenomeWideList<MotifAnchor> extractUniqueMotifs(GenomeWi...
    method extractBestMotifs (line 130) | public static GenomeWideList<MotifAnchor> extractBestMotifs(GenomeWide...
    method searchForFeature (line 156) | public static MotifAnchor searchForFeature(final String chrID, final S...
    method searchForFeature (line 171) | public static MotifAnchor searchForFeature(final String chrID, final i...
    method searchForFeatureWithin (line 186) | public static MotifAnchor searchForFeatureWithin(final String chrID, f...
    method searchForFeaturesWithin (line 201) | public static List<MotifAnchor> searchForFeaturesWithin(final String c...
    method retainProteinsInLocus (line 217) | public static void retainProteinsInLocus(final GenomeWideList<GenericL...
    method retainProteinsInLocus (line 231) | private static List<GenericLocus> retainProteinsInLocus(List<GenericLo...
    method retainBestMotifsInLocus (line 314) | public static void retainBestMotifsInLocus(final GenomeWideList<MotifA...
    method retainBestMotifsInLocus (line 327) | private static List<MotifAnchor> retainBestMotifsInLocus(List<MotifAnc...
    method calculateConvergenceHistogram (line 411) | public static int[] calculateConvergenceHistogram(Feature2DList featur...

FILE: src/juicebox/data/basics/Chromosome.java
  class Chromosome (line 28) | public class Chromosome {
    method Chromosome (line 33) | public Chromosome(int index, String name, long length) {
    method getIndex (line 39) | public int getIndex() {
    method setIndex (line 43) | public void setIndex(int ii) {
    method getLength (line 47) | public long getLength() {
    method getName (line 51) | public String getName() {
    method toString (line 55) | public String toString() {
    method equals (line 59) | public boolean equals(Object obj) {
    method hashCode (line 63) | public int hashCode() {
    method toIGVChromosome (line 67) | public org.broad.igv.feature.Chromosome toIGVChromosome() {

FILE: src/juicebox/data/basics/ListOfDoubleArrays.java
  class ListOfDoubleArrays (line 34) | public class ListOfDoubleArrays {
    method ListOfDoubleArrays (line 40) | public ListOfDoubleArrays(long length) {
    method ListOfDoubleArrays (line 54) | public ListOfDoubleArrays(long totSize, double defaultValue) {
    method clear (line 61) | public void clear() {
    method get (line 65) | public double get(long index) {
    method set (line 78) | public void set(long index, double value) {
    method getLength (line 88) | public long getLength() {
    method deepClone (line 92) | public ListOfDoubleArrays deepClone() {
    method divideBy (line 100) | public void divideBy(long index, double value) {
    method multiplyBy (line 110) | public void multiplyBy(long index, double value) {
    method addTo (line 120) | public void addTo(long index, double value) {
    method addValuesFrom (line 137) | public void addValuesFrom(ListOfDoubleArrays other) {
    method getFirstValue (line 149) | public double getFirstValue() {
    method getLastValue (line 153) | public double getLastValue() {
    method getValues (line 158) | public List<double[]> getValues() {
    method multiplyEverythingBy (line 162) | public void multiplyEverythingBy(double val) {
    method convertToFloats (line 170) | public ListOfFloatArrays convertToFloats() {

FILE: src/juicebox/data/basics/ListOfFloatArrays.java
  class ListOfFloatArrays (line 34) | public class ListOfFloatArrays {
    method ListOfFloatArrays (line 40) | public ListOfFloatArrays(long length) {
    method ListOfFloatArrays (line 54) | public ListOfFloatArrays(long totSize, float defaultValue) {
    method clear (line 61) | public void clear() {
    method get (line 65) | public float get(long index) {
    method set (line 78) | public void set(long index, float value) {
    method getLength (line 88) | public long getLength() {
    method getMaxRow (line 92) | public long getMaxRow() {
    method deepClone (line 106) | public ListOfFloatArrays deepClone() {
    method divideBy (line 114) | public void divideBy(long index, float value) {
    method multiplyBy (line 124) | public void multiplyBy(long index, float value) {
    method addTo (line 134) | public void addTo(long index, float value) {
    method addValuesFrom (line 151) | public void addValuesFrom(ListOfFloatArrays other) {
    method getFirstValue (line 165) | public float getFirstValue() {
    method getLastValue (line 169) | public float getLastValue() {
    method getValues (line 174) | public List<float[]> getValues() {
    method multiplyEverythingBy (line 178) | public void multiplyEverythingBy(double val) {
    method convertToDoubles (line 186) | public ListOfDoubleArrays convertToDoubles() {

FILE: src/juicebox/data/basics/ListOfIntArrays.java
  class ListOfIntArrays (line 34) | public class ListOfIntArrays {
    method ListOfIntArrays (line 40) | public ListOfIntArrays(long length) {
    method ListOfIntArrays (line 54) | public ListOfIntArrays(long totSize, int defaultValue) {
    method clear (line 61) | public void clear() {
    method get (line 65) | public int get(long index) {
    method set (line 76) | public void set(long index, int value) {
    method getLength (line 89) | public long getLength() {
    method deepClone (line 93) | public ListOfIntArrays deepClone() {
    method divideBy (line 101) | public void divideBy(long index, int value) {
    method addValuesFrom (line 113) | public void addValuesFrom(ListOfIntArrays other) {
    method addTo (line 125) | public void addTo(long index, int value) {
    method getValues (line 135) | public List<int[]> getValues() {

FILE: src/juicebox/data/censoring/CustomMZDRegionHandler.java
  class CustomMZDRegionHandler (line 36) | public class CustomMZDRegionHandler {
    method getAllRegionsFromSubChromosomes (line 42) | private static Pair<List<GenericLocus>, List<GenericLocus>> getAllRegi...
    method initialize (line 80) | public void initialize(Chromosome chr1, Chromosome chr2, HiCZoom zoom,...
    method getBoundariesOfCustomChromosomeX (line 93) | public List<Long> getBoundariesOfCustomChromosomeX() {
    method getBoundariesOfCustomChromosomeY (line 97) | public List<Long> getBoundariesOfCustomChromosomeY() {
    method populateRegions (line 101) | private void populateRegions(Chromosome chr, ChromosomeHandler handler...
    method getIntersectingFeatures (line 114) | public List<Pair<GenericLocus, GenericLocus>> getIntersectingFeatures(...
    method getIntersectingFeatures (line 131) | public List<Pair<GenericLocus, GenericLocus>> getIntersectingFeatures(...

FILE: src/juicebox/data/censoring/OneDimSearchUtils.java
  class OneDimSearchUtils (line 29) | class OneDimSearchUtils {
    method indexedBinaryNearestSearch (line 45) | public static <T> int indexedBinaryNearestSearch(List<? extends Compar...

FILE: src/juicebox/data/censoring/OneDimTrackCensoring.java
  class OneDimTrackCensoring (line 39) | public class OneDimTrackCensoring {
    method getFilteredData (line 42) | public static HiCDataPoint[] getFilteredData(HiCDataSource dataSource,...
    method translateDataPointArray (line 76) | private static HiCDataPoint[] translateDataPointArray(int binSize, HiC...
    method mergeDataPoints (line 115) | private static HiCDataPoint[] mergeDataPoints(List<HiCDataPoint[]> dat...

FILE: src/juicebox/data/censoring/RegionPair.java
  class RegionPair (line 34) | public class RegionPair {
    method RegionPair (line 43) | private RegionPair(int xI, Pair<GenericLocus, GenericLocus> xLocalRegion,
    method generateRegionPair (line 53) | public static RegionPair generateRegionPair(Pair<GenericLocus, Generic...
    method getDescription (line 67) | public String getDescription() {
    method getOriginalGenomeRegion (line 71) | public long[] getOriginalGenomeRegion() {
    method equals (line 77) | @Override
    method hashCode (line 93) | @Override

FILE: src/juicebox/data/feature/Feature.java
  class Feature (line 30) | public abstract class Feature {
    method getKey (line 31) | public abstract String getKey();
    method deepClone (line 33) | public abstract Feature deepClone();

FILE: src/juicebox/data/feature/FeatureFilter.java
  type FeatureFilter (line 32) | public interface FeatureFilter<T> {
    method filter (line 33) | List<T> filter(String chr, List<T> featureList);

FILE: src/juicebox/data/feature/FeatureFunction.java
  type FeatureFunction (line 32) | public interface FeatureFunction<T> {
    method process (line 33) | void process(String chr, List<T> featureList);

FILE: src/juicebox/data/feature/GenomeWideList.java
  class GenomeWideList (line 38) | public class GenomeWideList<T extends Feature> {
    method GenomeWideList (line 52) | public GenomeWideList() {
    method GenomeWideList (line 58) | public GenomeWideList(ChromosomeHandler handler) {
    method GenomeWideList (line 68) | public GenomeWideList(ChromosomeHandler handler, List<T> features) {
    method GenomeWideList (line 82) | public GenomeWideList(final GenomeWideList<T> gwList) {
    method containsKey (line 97) | public boolean containsKey(String key) {
    method setFeatures (line 105) | public synchronized void setFeatures(String key, List<T> features) {
    method getFeatures (line 113) | public List<T> getFeatures(String key) {
    method size (line 120) | public synchronized int size() {
    method addAll (line 131) | @SuppressWarnings("unchecked")
    method filterLists (line 143) | public synchronized void filterLists(FeatureFilter<T> filter) {
    method processLists (line 156) | public synchronized void processLists(FeatureFunction<T> function) {
    method deepClone (line 165) | public GenomeWideList<T> deepClone() {
    method cloneFeatureList (line 177) | @SuppressWarnings("unchecked")
    method keySet (line 189) | public Set<String> keySet() {
    method addFeature (line 199) | public synchronized void addFeature(String key, T feature) {
    method simpleExport (line 209) | public void simpleExport(final File file) {

FILE: src/juicebox/data/iterator/BigContactRecordList.java
  class BigContactRecordList (line 31) | public class BigContactRecordList {
    method populateListOfListsFromSingleIterator (line 37) | public static BigContactRecordList populateListOfListsFromSingleIterat...
    method addAllSubLists (line 56) | public void addAllSubLists(BigContactRecordList other) {
    method addSubList (line 63) | private void addSubList(List<ContactRecord> cList) {
    method getTotalSize (line 68) | public long getTotalSize() {
    method getNumLists (line 72) | public int getNumLists() {
    method getSubList (line 76) | public List<ContactRecord> getSubList(int index) {
    method clear (line 80) | public void clear() {
    method sort (line 89) | public void sort() {
    method collapse (line 93) | public void collapse() {
    method getIndexOfMin (line 116) | private int getIndexOfMin(int[] counts) {

FILE: src/juicebox/data/iterator/ContactRecordIterator.java
  class ContactRecordIterator (line 39) | public /**
    method ContactRecordIterator (line 54) | ContactRecordIterator(DatasetReader reader, MatrixZoomData zd, LRUCach...
    method hasNext (line 68) | @Override
    method next (line 104) | @Override
    method remove (line 112) | @Override

FILE: src/juicebox/data/iterator/CoupledIteratorAndOffset.java
  class CoupledIteratorAndOffset (line 31) | public class CoupledIteratorAndOffset implements Iterator<ContactRecord> {
    method CoupledIteratorAndOffset (line 36) | public CoupledIteratorAndOffset(Iterator<ContactRecord> iterator, int ...
    method hasNext (line 42) | @Override
    method next (line 47) | @Override

FILE: src/juicebox/data/iterator/GWIteratorContainer.java
  class GWIteratorContainer (line 40) | public class GWIteratorContainer extends IteratorContainer {
    method GWIteratorContainer (line 47) | public GWIteratorContainer(Dataset dataset, ChromosomeHandler handler,
    method calculateMatrixSize (line 57) | private static long calculateMatrixSize(ChromosomeHandler handler, HiC...
    method getNewContactRecordIterator (line 65) | @Override
    method getAllFromFileContactRecordIterators (line 70) | public List<Iterator<ContactRecord>> getAllFromFileContactRecordIterat...
    method sparseMultiply (line 74) | @Override
    method clear (line 99) | @Override

FILE: src/juicebox/data/iterator/GenomeWideIterator.java
  class GenomeWideIterator (line 35) | public class GenomeWideIterator implements Iterator<ContactRecord> {
    method GenomeWideIterator (line 47) | public GenomeWideIterator(Dataset dataset, ChromosomeHandler handler,
    method hasNext (line 56) | @Override
    method getAllFromFileIterators (line 67) | public static List<Iterator<ContactRecord>> getAllFromFileIterators(Da...
    method getNextIterator (line 96) | private boolean getNextIterator() {
    method next (line 123) | @Override

FILE: src/juicebox/data/iterator/IteratorContainer.java
  class IteratorContainer (line 33) | public abstract class IteratorContainer {
    method IteratorContainer (line 39) | public IteratorContainer(long matrixSize) {
    method getNewContactRecordIterator (line 43) | abstract public Iterator<ContactRecord> getNewContactRecordIterator();
    method setNumberOfContactRecords (line 45) | protected void setNumberOfContactRecords(long numberOfContactRecords) {
    method getNumberOfContactRecords (line 49) | public long getNumberOfContactRecords() {
    method getMatrixSize (line 62) | public long getMatrixSize() {
    method getIsThereEnoughMemoryForNormCalculation (line 66) | public boolean getIsThereEnoughMemoryForNormCalculation() {
    method sparseMultiply (line 73) | public abstract ListOfFloatArrays sparseMultiply(ListOfFloatArrays vec...
    method clear (line 75) | public abstract void clear();
    method getArrayOfFloatVectors (line 77) | protected static ListOfFloatArrays[] getArrayOfFloatVectors(int size, ...
    method getArrayOfDoubleVectors (line 85) | protected static ListOfDoubleArrays[] getArrayOfDoubleVectors(int size...

FILE: src/juicebox/data/iterator/ListIteratorContainer.java
  class ListIteratorContainer (line 36) | public class ListIteratorContainer extends IteratorContainer {
    method ListIteratorContainer (line 40) | public ListIteratorContainer(List<ContactRecord> readList, long matrix...
    method getNewContactRecordIterator (line 46) | @Override
    method getIsThereEnoughMemoryForNormCalculation (line 51) | @Override
    method sparseMultiplyByListContacts (line 58) | public static ListOfFloatArrays sparseMultiplyByListContacts(List<Cont...
    method matrixVectorMult (line 81) | public static void matrixVectorMult(ListOfFloatArrays vector, ListOfDo...
    method sparseMultiply (line 93) | @Override
    method clear (line 98) | @Override

FILE: src/juicebox/data/iterator/ListOfListGenerator.java
  class ListOfListGenerator (line 37) | public class ListOfListGenerator {
    method createFromZD (line 39) | public static IteratorContainer createFromZD(DatasetReader reader, Mat...
    method createForWholeGenome (line 45) | public static IteratorContainer createForWholeGenome(Dataset dataset, ...
    method tryToCreateIteratorInRAM (line 51) | private static IteratorContainer tryToCreateIteratorInRAM(IteratorCont...
    method populateListOfLists (line 80) | private static BigContactRecordList populateListOfLists(IteratorContai...
    method checkMemory (line 105) | private static boolean checkMemory(IteratorContainer ic) {

FILE: src/juicebox/data/iterator/ListOfListIterator.java
  class ListOfListIterator (line 31) | public class ListOfListIterator implements Iterator<ContactRecord> {
    method ListOfListIterator (line 37) | public ListOfListIterator(BigContactRecordList allContactRecords) {
    method hasNext (line 42) | @Override
    method getNextIterator (line 52) | private boolean getNextIterator() {
    method next (line 63) | @Override

FILE: src/juicebox/data/iterator/ListOfListIteratorContainer.java
  class ListOfListIteratorContainer (line 36) | public class ListOfListIteratorContainer extends IteratorContainer {
    method ListOfListIteratorContainer (line 40) | public ListOfListIteratorContainer(BigContactRecordList allContactReco...
    method getNewContactRecordIterator (line 47) | @Override
    method getIsThereEnoughMemoryForNormCalculation (line 52) | @Override
    method sparseMultiply (line 59) | @Override
    method clear (line 75) | @Override
    method sparseMultiplyAcrossLists (line 80) | private ListOfFloatArrays sparseMultiplyAcrossLists(ListOfFloatArrays ...

FILE: src/juicebox/data/iterator/ParallelizedListOperations.java
  class ParallelizedListOperations (line 27) | public class ParallelizedListOperations {
    method createCutoffs (line 29) | public static int[] createCutoffs(int n, int listSize) {

FILE: src/juicebox/data/iterator/ZDIteratorContainer.java
  class ZDIteratorContainer (line 37) | public class ZDIteratorContainer extends IteratorContainer {
    method ZDIteratorContainer (line 43) | public ZDIteratorContainer(DatasetReader reader, MatrixZoomData zd, LR...
    method getNewContactRecordIterator (line 50) | @Override
    method matrixVectorMultiplyOnIterator (line 55) | public static ListOfFloatArrays matrixVectorMultiplyOnIterator(Iterato...
    method sparseMultiply (line 65) | @Override
    method clear (line 70) | @Override

FILE: src/juicebox/data/v9depth/ConstantDepth.java
  class ConstantDepth (line 27) | public class ConstantDepth extends V9Depth {
    method ConstantDepth (line 29) | public ConstantDepth(int base, int blockBinCount) {
    method logBase (line 34) | @Override

FILE: src/juicebox/data/v9depth/LogDepth.java
  class LogDepth (line 27) | public class LogDepth extends V9Depth {
    method LogDepth (line 29) | public LogDepth(int base, int blockBinCount) {
    method logBase (line 34) | @Override

FILE: src/juicebox/data/v9depth/V9Depth.java
  class V9Depth (line 27) | public abstract class V9Depth {
    method V9Depth (line 31) | V9Depth(int blockBinCount) {
    method setDepthMethod (line 35) | public static V9Depth setDepthMethod(int depthBase, int blockBinCount) {
    method getDepth (line 46) | public int getDepth(int val1, int val2) {
    method logBase (line 50) | protected abstract int logBase(double value);

FILE: src/juicebox/encode/EncodeFileBrowser.java
  class EncodeFileBrowser (line 57) | public class EncodeFileBrowser extends JDialog {
    method EncodeFileBrowser (line 68) | private EncodeFileBrowser(Frame owner, EncodeTableModel model) {
    method getInstance (line 76) | public synchronized static EncodeFileBrowser getInstance(String genome...
    method getEncodeGenomeId (line 94) | private static String getEncodeGenomeId(String genomeId) {
    method getEncodeFileRecords (line 100) | private static Pair<String[], List<EncodeFileRecord>> getEncodeFileRec...
    method init (line 155) | private void init(final EncodeTableModel model) {
    method updateFilter (line 192) | private void updateFilter() {
    method loadButtonActionPerformed (line 211) | private void loadButtonActionPerformed(ActionEvent e) {
    method cancelButtonActionPerformed (line 216) | private void cancelButtonActionPerformed(ActionEvent e) {
    method isCanceled (line 221) | public boolean isCanceled() {
    method getSelectedRecords (line 229) | public List<EncodeFileRecord> getSelectedRecords() {
    method checkEncodeTracks (line 246) | public void checkEncodeTracks(String track) {
    method remove (line 259) | public void remove(ResourceLocator locator) {
    method initComponents (line 277) | private void initComponents() {
    class RegexFilter (line 377) | private class RegexFilter extends RowFilter<EncodeTableModel, Object> {
      method RegexFilter (line 381) | RegexFilter(String text) {
      method include (line 414) | @Override

FILE: src/juicebox/encode/EncodeFileRecord.java
  class EncodeFileRecord (line 37) | public class EncodeFileRecord {
    method EncodeFileRecord (line 44) | public EncodeFileRecord(String path, Map<String, String> attributes) {
    method getPath (line 49) | public String getPath() {
    method getFileType (line 53) | public String getFileType() {
    method getAttributeValue (line 63) | public String getAttributeValue(String name) {
    method getAttributeNames (line 69) | public Collection<String> getAttributeNames() {
    method containsText (line 73) | public boolean containsText(String filter) {
    method isSelected (line 80) | boolean isSelected() {
    method setSelected (line 84) | public void setSelected(boolean selected) {
    method getTrackName (line 93) | public String getTrackName() {
    method hasMetaData (line 116) | public boolean hasMetaData() {

FILE: src/juicebox/encode/EncodeTableModel.java
  class EncodeTableModel (line 60) | class EncodeTableModel extends AbstractTableModel {
    method EncodeTableModel (line 67) | public EncodeTableModel(String[] headings, List<EncodeFileRecord> reco...
    method getSorter (line 94) | public TableRowSorter<EncodeTableModel> getSorter() {
    method getColumnClass (line 98) | @Override
    method getColumnName (line 103) | @Override
    method getRowCount (line 108) | @Override
    method getColumnCount (line 113) | @Override
    method getValueAt (line 118) | @Override
    method isCellEditable (line 135) | @Override
    method setValueAt (line 140) | @Override
    method getRecords (line 148) | public List<EncodeFileRecord> getRecords() {

FILE: src/juicebox/encode/UCSCEncodeUtils.java
  class UCSCEncodeUtils (line 41) | class UCSCEncodeUtils {
    method main (line 55) | public static void main(String[] args) throws IOException {
    method parseTableFile (line 84) | private static List<EncodeFileRecord> parseTableFile(String url) throw...
    method updateEncodeTableFile (line 114) | private static void updateEncodeTableFile(String inputFile, String out...
    method outputRecords (line 151) | private static void outputRecords(String outputFile, List<EncodeFileRe...
    method parseFilesDotTxt (line 178) | private static void parseFilesDotTxt(String url, List<EncodeFileRecord...

FILE: src/juicebox/gui/BoundsPopupMenuListener.java
  class BoundsPopupMenuListener (line 43) | class BoundsPopupMenuListener<E> implements PopupMenuListener {
    method BoundsPopupMenuListener (line 54) | public BoundsPopupMenuListener() {
    method BoundsPopupMenuListener (line 66) | public BoundsPopupMenuListener(boolean popupWider, boolean popupAbove) {
    method BoundsPopupMenuListener (line 77) | public BoundsPopupMenuListener(int maximumWidth) {
    method BoundsPopupMenuListener (line 91) | private BoundsPopupMenuListener(
    method getMaximumWidth (line 104) | public int getMaximumWidth() {
    method setMaximumWidth (line 115) | private void setMaximumWidth(int maximumWidth) {
    method isPopupAbove (line 124) | public boolean isPopupAbove() {
    method setPopupAbove (line 134) | private void setPopupAbove(boolean popupAbove) {
    method isPopupWider (line 143) | public boolean isPopupWider() {
    method setPopupWider (line 154) | private void setPopupWider(boolean popupWider) {
    method isScrollBarRequired (line 163) | public boolean isScrollBarRequired() {
    method setScrollBarRequired (line 176) | private void setScrollBarRequired(boolean scrollBarRequired) {
    method popupMenuWillBecomeVisible (line 183) | @Override
    method customizePopup (line 201) | private void customizePopup(BasicComboPopup popup) {
    method popupWider (line 231) | private void popupWider(BasicComboPopup popup) {
    method checkHorizontalScrollBar (line 263) | private void checkHorizontalScrollBar(BasicComboPopup popup) {
    method getScrollPane (line 302) | private JScrollPane getScrollPane(BasicComboPopup popup) {
    method getScrollBarWidth (line 314) | private int getScrollBarWidth(BasicComboPopup popup, JScrollPane scrol...
    method horizontalScrollBarWillBeVisible (line 331) | private boolean horizontalScrollBarWillBeVisible(BasicComboPopup popup...
    method popupMenuCanceled (line 340) | @Override
    method popupMenuWillBecomeInvisible (line 344) | @Override

FILE: src/juicebox/gui/MainMenuBar.java
  class MainMenuBar (line 49) | public class MainMenuBar extends JMenuBar {
    method MainMenuBar (line 85) | public MainMenuBar(SuperAdapter superAdapter) {
    method exitAssemblyMode (line 89) | public static void exitAssemblyMode() {
    method unsavedEditsExist (line 98) | public boolean unsavedEditsExist() {
    method addRecentMapMenuEntry (line 103) | public void addRecentMapMenuEntry(String title, boolean status) {
    method addRecentStateMenuEntry (line 108) | private void addRecentStateMenuEntry(String title, boolean status) {
    method createMenuBar (line 112) | private void createMenuBar(final SuperAdapter superAdapter) {
    method getRecentLocationMenu (line 865) | public RecentMenu getRecentLocationMenu() {
    method setEnableForAllElements (line 869) | public void setEnableForAllElements(boolean status) {
    method setEnableAssemblyMenuOptions (line 880) | public void setEnableAssemblyMenuOptions(boolean status) {
    method enableAssemblyEditsOnImport (line 890) | public void enableAssemblyEditsOnImport(SuperAdapter superAdapter) {
    method updatePrevStateNameFromImport (line 895) | public void updatePrevStateNameFromImport(String path) {
    method updateMainMapHasBeenLoaded (line 899) | public void updateMainMapHasBeenLoaded(boolean status) {
    method updateControlMapHasBeenLoaded (line 906) | public void updateControlMapHasBeenLoaded(boolean status) {
    method setAnnotationPanelMenuItemSelected (line 910) | public void setAnnotationPanelMenuItemSelected(boolean status) {

FILE: src/juicebox/gui/MainViewPanel.java
  class MainViewPanel (line 55) | public class MainViewPanel {
    method setIgnoreUpdateThumbnail (line 109) | public void setIgnoreUpdateThumbnail(boolean flag) {
    method getChrBox2 (line 113) | public JComboBox<Chromosome> getChrBox2() {
    method getChrBox1 (line 117) | public JComboBox<Chromosome> getChrBox1() {
    method getMenuBar (line 121) | public MainMenuBar getMenuBar() {
    method initializeMainView (line 125) | public void initializeMainView(final SuperAdapter superAdapter, Contai...
    method initialSetToFalse (line 465) | private void initialSetToFalse() {
    method resetAllColors (line 473) | public void resetAllColors() {
    method getHiCPanel (line 499) | public JPanel getHiCPanel() {
    method updateToolTipText (line 503) | public void updateToolTipText(String s) {
    method isResolutionLocked (line 509) | public boolean isResolutionLocked() {
    method getHeatmapPanel (line 513) | public HeatmapPanel getHeatmapPanel() {
    method updateZoom (line 517) | public void updateZoom(HiCZoom newZoom) {
    method updateAndResetZoom (line 521) | public void updateAndResetZoom(HiCZoom newZoom) {
    method unsafeSetSelectedChromosomes (line 530) | public void unsafeSetSelectedChromosomes(SuperAdapter superAdapter, Ch...
    method unsafeRefreshChromosomes (line 536) | public void unsafeRefreshChromosomes(SuperAdapter superAdapter) {
    method setSelectedChromosomesNoRefresh (line 564) | public void setSelectedChromosomesNoRefresh(Chromosome xChrom, Chromos...
    method setChromosomes (line 579) | void setChromosomes(ChromosomeHandler handler) {
    method isInterChromosomal (line 585) | private boolean isInterChromosomal() {
    method isWholeGenome (line 595) | private boolean isWholeGenome() {
    method ifControlIsLoaded (line 601) | private boolean ifControlIsLoaded() {
    method isWholeGenome (line 605) | private boolean isWholeGenome(HiC hic) {
    method setNormalizationDisplayState (line 611) | public void setNormalizationDisplayState(HiC hic) {
    method repaintTrackPanels (line 631) | public void repaintTrackPanels() {
    method repaintGridRulerPanels (line 636) | public void repaintGridRulerPanels() {
    method getTrackPanelPrintouts (line 641) | public String getTrackPanelPrintouts(int x, int y) {
    method updateThumbnail (line 655) | public void updateThumbnail(HiC hic) {
    method invertAssemblyMatCheck (line 686) | public static void invertAssemblyMatCheck() {
    method chrBox1ActionPerformed (line 690) | private void chrBox1ActionPerformed(ActionEvent e) {
    method chrBox2ActionPerformed (line 698) | private void chrBox2ActionPerformed(ActionEvent e) {
    method setResolutionSliderVisible (line 706) | public boolean setResolutionSliderVisible(boolean state, SuperAdapter ...
    method updateTrackPanel (line 722) | public void updateTrackPanel(boolean hasTracks) {
    method setShowChromosomeFig (line 749) | public void setShowChromosomeFig(boolean showFigure) {
    method getShowGridLines (line 785) | public boolean getShowGridLines() {
    method setShowGridLines (line 789) | public void setShowGridLines(boolean status) {
    method getToolTip (line 795) | public String getToolTip() {
    method setDisplayBox (line 799) | public void setDisplayBox(int indx) {
    method setNormalizationEnabledForReload (line 803) | public void setNormalizationEnabledForReload() {
    method setPositionChrLeft (line 809) | public void setPositionChrLeft(String newPositionDate) {
    method setPositionChrTop (line 813) | public void setPositionChrTop(String newPositionDate) {
    method setEnableForAllElements (line 817) | public void setEnableForAllElements(SuperAdapter superAdapter, boolean...
    method getColorRangeValues (line 833) | public String getColorRangeValues() {
    method getColorRangeScaleFactor (line 837) | public double getColorRangeScaleFactor() {
    method updateRatioColorSlider (line 841) | public void updateRatioColorSlider(HiC hic, double maxColor, double up...
    method updateColorSlider (line 845) | public void updateColorSlider(HiC hic, double lowColor, double upColor...
    method setEnabledForNormalization (line 849) | public void setEnabledForNormalization(boolean isControl, String[] nor...
    method getDisplayOptionComboBox (line 870) | public JComboBox<MatrixType> getDisplayOptionComboBox() {
    method resetResolutionSlider (line 874) | public void resetResolutionSlider(HiC.Unit unit) {
    method setSelectedDisplayOption (line 879) | public void setSelectedDisplayOption(boolean isControl, boolean isCont...
    method getMouseHoverTextPanel (line 905) | public JEditorPane getMouseHoverTextPanel() {
    method getResolutionSlider (line 909) | public ResolutionControl getResolutionSlider() {
    method getColorRangePanel (line 913) | public JColorRangePanel getColorRangePanel() {
    method isTooltipAllowedToUpdate (line 917) | public boolean isTooltipAllowedToUpdate() {
    method toggleToolTipUpdates (line 921) | public void toggleToolTipUpdates(boolean tooltipAllowedToUpdated) {
    method getObservedNormalizationComboBox (line 925) | public JComboBox<String> getObservedNormalizationComboBox() {
    method getControlNormalizationComboBox (line 929) | public JComboBox<String> getControlNormalizationComboBox() {
    method getRulerPanelY (line 933) | public HiCRulerPanel getRulerPanelY() {
    method getRulerPanelX (line 937) | public HiCRulerPanel getRulerPanelX() {
    method getChromosomeFigPanelY (line 941) | public HiCChromosomeFigPanel getChromosomeFigPanelY() {
    method getChromosomeFigPanelX (line 945) | public HiCChromosomeFigPanel getChromosomeFigPanelX() {
    method setAnnotationsPanelToggleButtonSelected (line 949) | public void setAnnotationsPanelToggleButtonSelected(boolean status) {
    method updateMiniAnnotationsLayerPanel (line 954) | public void updateMiniAnnotationsLayerPanel(SuperAdapter superAdapter) {
    method unsavedEditsExist (line 960) | public boolean unsavedEditsExist() {
    method addRecentMapMenuEntry (line 964) | public void addRecentMapMenuEntry(String title, boolean status) {
    method updatePrevStateNameFromImport (line 968) | public void updatePrevStateNameFromImport(String path) {

FILE: src/juicebox/gui/PseudoCountEditor.java
  class PseudoCountEditor (line 35) | public class PseudoCountEditor extends JDialog {
    method PseudoCountEditor (line 39) | public PseudoCountEditor(final SuperAdapter superAdapter) {

FILE: src/juicebox/gui/SuperAdapter.java
  class SuperAdapter (line 68) | public class SuperAdapter {
    method getDatasetTitle (line 86) | public static String getDatasetTitle() {
    method setDatasetTitle (line 90) | public static void setDatasetTitle(String newDatasetTitle) {
    method showMessageDialog (line 94) | public static void showMessageDialog(String message) {
    method showConfirmDialog (line 98) | public static int showConfirmDialog(String message) {
    method setAdapters (line 105) | public void setAdapters(MainWindow mainWindow, HiC hic, MainViewPanel ...
    method unsavedEditsExist (line 111) | public boolean unsavedEditsExist() {
    method addRecentMapMenuEntry (line 115) | public void addRecentMapMenuEntry(String title, boolean status) {
    method showDataSetMetrics (line 121) | public void showDataSetMetrics(boolean isControl) {
    method exportDataLauncher (line 138) | public void exportDataLauncher() {
    method setEnableForAllElements (line 147) | public void setEnableForAllElements(boolean status) {
    method resetControlMap (line 154) | public void resetControlMap() {
    method toggleAdvancedViews (line 162) | public void toggleAdvancedViews() {
    method launchSlideShow (line 167) | public void launchSlideShow() {
    method launchImportState (line 171) | public void launchImportState(File fileForExport) {
    method launchLoadStateFromXML (line 175) | public void launchLoadStateFromXML(String mapPath) {
    method launchPearsonColorScaleEditor (line 179) | public void launchPearsonColorScaleEditor() {
    method launchSetPseudoCountEditor (line 183) | public void launchSetPseudoCountEditor() {
    method restoreLocation (line 187) | public void restoreLocation(String loc) {
    method getEncodeAction (line 191) | public LoadEncodeAction getEncodeAction() {
    method getTrackLoadAction (line 199) | public LoadAction getTrackLoadAction() {
    method updatePrevStateNameFromImport (line 203) | public void updatePrevStateNameFromImport(String path) {
    method loadFromListActionPerformed (line 207) | public void loadFromListActionPerformed(boolean control) {
    method launchExportPDF (line 214) | public void launchExportPDF() {
    method launchExportSVG (line 218) | public void launchExportSVG() {
    method loadFromRecentActionPerformed (line 222) | public void loadFromRecentActionPerformed(String url, String title, bo...
    method clearCustomAnnotationDialog (line 229) | public int clearCustomAnnotationDialog() {
    method deleteCustomAnnotationDialog (line 237) | public int deleteCustomAnnotationDialog(String layerName) {
    method repaint (line 245) | public void repaint() {
    method safeLoadFromURLActionPerformed (line 251) | public void safeLoadFromURLActionPerformed(final Runnable refresh1DLay...
    method getLocationDescription (line 274) | public String getLocationDescription() {
    method getDescription (line 278) | public String getDescription(String item) {
    method addNewStateToXML (line 283) | public void addNewStateToXML(String stateDescription) {
    method setNormalizationDisplayState (line 287) | public void setNormalizationDisplayState() {
    method centerMap (line 291) | public void centerMap(int xBP, int yBP) {
    method moveMapBy (line 295) | public void moveMapBy(int dxBP, int dyBP) {
    method shouldVisibleWindowBeRendered (line 299) | public boolean shouldVisibleWindowBeRendered() {
    method getHiCScaleFactor (line 303) | public double getHiCScaleFactor() {
    method getHiCOrigin (line 307) | public Point2D.Double getHiCOrigin() {
    method getHiCScale (line 311) | public Point2D.Double getHiCScale(int width, int height) {
    method getHeatMapPanelDimensions (line 321) | public Point getHeatMapPanelDimensions() {
    method initializeMainView (line 325) | public void initializeMainView(Container contentPane, Dimension screen...
    method unsafeSetInitialZoom (line 329) | private void unsafeSetInitialZoom() {
    method refresh (line 373) | public void refresh() {
    method unsafeClearAllMatrixZoomCache (line 379) | public void unsafeClearAllMatrixZoomCache() {
    method refreshMainOnly (line 384) | private void refreshMainOnly() {
    method genomesAreCompatible (line 389) | private static boolean genomesAreCompatible(Dataset dataset1, Dataset ...
    method unsafeLoad (line 405) | private boolean unsafeLoad(final List<String> files, final boolean con...
    method safeLoad (line 505) | public void safeLoad(final List<String> files, final boolean control, ...
    method unsafeLoadWithTitleFix (line 516) | public void unsafeLoadWithTitleFix(List<String> files, boolean control...
    method getNewHiCKeyDispatcher (line 544) | public KeyEventDispatcher getNewHiCKeyDispatcher() {
    method launchLoadFileDialog (line 548) | public LoadDialog launchLoadFileDialog(Properties properties) {
    method safeRefreshButtonActionPerformed (line 552) | void safeRefreshButtonActionPerformed() {
    method safeDisplayOptionComboBoxActionPerformed (line 562) | public boolean safeDisplayOptionComboBoxActionPerformed() {
    method safeNormalizationComboBoxActionPerformed (line 573) | void safeNormalizationComboBoxActionPerformed(final ActionEvent e, fin...
    method unsafeDisplayOptionComboBoxActionPerformed (line 582) | public boolean unsafeDisplayOptionComboBoxActionPerformed() {
    method getHiC (line 637) | public HiC getHiC() {
    method getMainWindow (line 646) | public MainWindow getMainWindow() {
    method getLayersPanel (line 650) | public LayersPanel getLayersPanel() {
    method getMainMenuBar (line 654) | public MainMenuBar getMainMenuBar() {
    method revalidate (line 658) | public void revalidate() {
    method updateMainViewPanelToolTipText (line 663) | public void updateMainViewPanelToolTipText(String text) {
    method setPositionChrTop (line 667) | public void setPositionChrTop(String positionChrTop) {
    method setPositionChrLeft (line 671) | public void setPositionChrLeft(String positionChrLeft) {
    method getToolTip (line 675) | public String getToolTip() {
    method repaintTrackPanels (line 679) | public void repaintTrackPanels() {
    method repaintGridRulerPanels (line 683) | public void repaintGridRulerPanels() {
    method isResolutionLocked (line 688) | public boolean isResolutionLocked() {
    method updateThumbnail (line 692) | public void updateThumbnail() {
    method updateZoom (line 696) | public void updateZoom(HiCZoom newZoom) {
    method updateAndResetZoom (line 700) | public void updateAndResetZoom(HiCZoom newZoom) {
    method launchFileLoadingError (line 704) | public void launchFileLoadingError(String urlString) {
    method updateTitle (line 709) | private void updateTitle(boolean control, String title) {
    method updateTitle (line 717) | private void updateTitle() {
    method launchGenericMessageDialog (line 735) | public void launchGenericMessageDialog(String message, String error, i...
    method getHeatmapPanel (line 739) | public HeatmapPanel getHeatmapPanel() {
    method updateTrackPanel (line 743) | public void updateTrackPanel() {
    method unsafeNormalizationComboBoxActionPerformed (line 747) | private void unsafeNormalizationComboBoxActionPerformed(boolean isForC...
    method getMainViewPanel (line 758) | public MainViewPanel getMainViewPanel() {
    method isTooltipAllowedToUpdated (line 762) | public boolean isTooltipAllowedToUpdated() {
    method toggleToolTipUpdates (line 766) | public void toggleToolTipUpdates(boolean b) {
    method executeLongRunningTask (line 770) | public void executeLongRunningTask(Runnable runnable, String s) {
    method updateRatioColorSlider (line 774) | public void updateRatioColorSlider(int max, double val) {
    method updateColorSlider (line 778) | public void updateColorSlider(double low, double high) {
    method unsafeSetSelectedChromosomes (line 782) | public void unsafeSetSelectedChromosomes(Chromosome xC, Chromosome yC) {
    method setSelectedChromosomesNoRefresh (line 786) | public void setSelectedChromosomesNoRefresh(Chromosome chrX, Chromosom...
    method unsafeUpdateHiCChromosomes (line 791) | public void unsafeUpdateHiCChromosomes(Chromosome chrX, Chromosome chr...
    method setShowChromosomeFig (line 802) | public void setShowChromosomeFig(boolean status) {
    method getShowGridLines (line 806) | public boolean getShowGridLines() {
    method setShowGridLines (line 810) | public void setShowGridLines(boolean status) {
    method getActiveLayerHandler (line 814) | public AnnotationLayerHandler getActiveLayerHandler() {
    method setActiveLayerHandler (line 818) | public void setActiveLayerHandler(AnnotationLayerHandler activeLayer) {
    method getAllLayers (line 826) | public List<AnnotationLayerHandler> getAllLayers() {
    method getAssemblyLayerHandlers (line 831) | public List<AnnotationLayerHandler> getAssemblyLayerHandlers() {
    method getAssemblyLayerHandler (line 844) | private AnnotationLayerHandler getAssemblyLayerHandler(AnnotationLayer...
    method getMainLayer (line 853) | public AnnotationLayerHandler getMainLayer() {
    method getGroupLayer (line 857) | public AnnotationLayerHandler getGroupLayer() {
    method getEditLayer (line 861) | public AnnotationLayerHandler getEditLayer() {
    method exitActionPerformed (line 865) | public void exitActionPerformed() {
    method createNewLayer (line 876) | public AnnotationLayerHandler createNewLayer(File temp) {
    method updateLayerDeleteStatus (line 890) | public void updateLayerDeleteStatus() {
    method removeLayer (line 897) | public int removeLayer(AnnotationLayerHandler handler) {
    method resetAnnotationLayers (line 912) | private void resetAnnotationLayers() {
    method moveDownIndex (line 921) | public int moveDownIndex(AnnotationLayerHandler handler) {
    method moveUpIndex (line 931) | public int moveUpIndex(AnnotationLayerHandler handler) {
    method setPearsonColorScale (line 941) | public void setPearsonColorScale(PearsonColorScale pearsonColorScale) {
    method getTrackPanelPrintouts (line 945) | public String getTrackPanelPrintouts(int x, int y) {
    method setLayersPanelVisible (line 949) | public void setLayersPanelVisible(boolean status) {
    method intializeLayersPanel (line 958) | public void intializeLayersPanel() {
    method setLayersPanelGUIControllersSelected (line 962) | public void setLayersPanelGUIControllersSelected(boolean status) {
    method togglePanelVisible (line 966) | public void togglePanelVisible() {
    method getAssemblyStateTracker (line 970) | public AssemblyStateTracker getAssemblyStateTracker() {
    method setAssemblyStateTracker (line 974) | public void setAssemblyStateTracker(AssemblyStateTracker assemblyState...
    method createCustomChromosomesFromBED (line 978) | public void createCustomChromosomesFromBED() {
    method createAssemblyChromosome (line 1001) | public void createAssemblyChromosome() {
    method createCustomChromosomeMap (line 1006) | public void createCustomChromosomeMap(Feature2DList featureList, Strin...
    method updateChrHandlerAndMVP (line 1011) | private void updateChrHandlerAndMVP(Chromosome custom) {
    method updateMiniAnnotationsLayerPanel (line 1017) | public void updateMiniAnnotationsLayerPanel() {
    method updateMainLayersPanel (line 1024) | public void updateMainLayersPanel() {
    method updatePreviousTempSelectedGroups (line 1031) | public void updatePreviousTempSelectedGroups(Feature2D tempSelectedGro...
    method safeClearAllMZDCache (line 1035) | public void safeClearAllMZDCache() {
    method exitAssemblyMode (line 1045) | public boolean exitAssemblyMode() {
    method safeLaunchImportNormalizations (line 1070) | public void safeLaunchImportNormalizations(boolean isControl) {
    method createGenomewideChromosomeFromChromDotSizes (line 1097) | public void createGenomewideChromosomeFromChromDotSizes() {
    method getNewResolutionGUI (line 1102) | public static int getNewResolutionGUI() {
    method safeLaunchCreateNewResolution (line 1117) | public void safeLaunchCreateNewResolution() {
    method clearEditsAndUpdateLayers (line 1127) | public void clearEditsAndUpdateLayers() {

FILE: src/juicebox/mapcolorui/BoundingBoxRenderer.java
  class BoundingBoxRenderer (line 35) | public class BoundingBoxRenderer {
    method BoundingBoxRenderer (line 40) | public BoundingBoxRenderer(HeatmapPanel heatmapPanel) {
    method drawAllByAllGrid (line 44) | public void drawAllByAllGrid(Graphics2D g, MatrixZoomData zd, boolean ...
    method getGridLineWidthLimit (line 90) | private int getGridLineWidthLimit(MatrixZoomData zd, long maxPosition,...
    method getGridLineHeightLimit (line 98) | private int getGridLineHeightLimit(MatrixZoomData zd, long maxPosition...
    method setChromosomeBoundaries (line 106) | public void setChromosomeBoundaries(long[] chromosomeBoundaries) {
    method drawRegularGrid (line 110) | public void drawRegularGrid(Graphics2D g, MatrixZoomData zd, boolean s...

FILE: src/juicebox/mapcolorui/ColorRangeDialog.java
  class ColorRangeDialog (line 43) | class ColorRangeDialog extends JDialog {
    method ColorRangeDialog (line 56) | public ColorRangeDialog(SuperAdapter superAdapter, JColorRangePanel co...
    method initComponents (line 73) | private void initComponents(final SuperAdapter superAdapter, final JCo...
    method setDimension (line 204) | private void setDimension(JTextField field) {
    method okButtonActionPerformed (line 210) | private void okButtonActionPerformed(ActionEvent e, SuperAdapter super...

FILE: src/juicebox/mapcolorui/ColorScaleHandler.java
  class ColorScaleHandler (line 42) | public class ColorScaleHandler {
    method getPearsonColorScale (line 48) | public PearsonColorScale getPearsonColorScale() {
    method reset (line 52) | public void reset() {
    method getDenseMatrixColor (line 57) | public Color getDenseMatrixColor(String key, float score, PearsonColor...
    method setNewDisplayRange (line 71) | public void setNewDisplayRange(MatrixType displayOption, double min, d...
    method getColorScale (line 98) | public ColorScale getColorScale(String key, MatrixType displayOption, ...
    method getColorScale (line 106) | public ColorScale getColorScale(String key, MatrixType displayOption, ...
    method updateColorSliderFromColorScale (line 139) | public void updateColorSliderFromColorScale(SuperAdapter superAdapter,...
    method computePercentile (line 158) | public float computePercentile(List<Block> blocks, double p) {
    method computePercentile (line 173) | public float computePercentile(BasicMatrix bm, double p) {
    method computePercentile (line 184) | public float computePercentile(BasicMatrix bm1, BasicMatrix bm2, doubl...

FILE: src/juicebox/mapcolorui/CursorRenderer.java
  class CursorRenderer (line 29) | public class CursorRenderer {
    method CursorRenderer (line 32) | public CursorRenderer(HeatmapPanel heatmapPanel) {
    method drawCursors (line 36) | public void drawCursors(Graphics2D g, Point cursorPoint, Point diagona...

FILE: src/juicebox/mapcolorui/Feature2DHandler.java
  class Feature2DHandler (line 47) | public class Feature2DHandler {
    method Feature2DHandler (line 59) | public Feature2DHandler() {
    method Feature2DHandler (line 64) | public Feature2DHandler(Feature2DList inputList) {
    method getRectangleFromFeature (line 69) | public Rectangle getRectangleFromFeature(HiCGridAxis xAxis, HiCGridAxi...
    method convertFeaturesToFeaturePairs (line 92) | public List<Feature2DGuiContainer> convertFeaturesToFeaturePairs(Annot...
    method clearLists (line 108) | protected void clearLists() {
    method getLayerVisibility (line 114) | public boolean getLayerVisibility() {
    method setLayerVisibility (line 118) | public void setLayerVisibility(boolean showLoops) {
    method remakeRTree (line 123) | protected void remakeRTree() {
    method setLoopList (line 143) | public resultContainer setLoopList(String path, ChromosomeHandler chro...
    method createNewMergedLoopLists (line 165) | public void createNewMergedLoopLists(List<Feature2DList> lists) {
    method setLoopList (line 176) | public void setLoopList(Feature2DList feature2DList) {
    method addToLoopList (line 181) | private void addToLoopList(Feature2DList feature2DList, boolean remake...
    method getAllVisibleLoops (line 188) | public Feature2DList getAllVisibleLoops() {
    method getNearbyFeatures (line 196) | public List<Feature2D> getNearbyFeatures(MatrixZoomData zd, int chrIdx...
    method getIntersectingFeatures (line 239) | public List<Feature2D> getIntersectingFeatures(int chrIdx1, int chrIdx...
    method getContainedFeatures (line 267) | public List<Feature2D> getContainedFeatures(int chrIdx1, int chrIdx2, ...
    method getGenomicPointFromXYCoordinate (line 292) | private net.sf.jsi.Point getGenomicPointFromXYCoordinate(double x, dou...
    method setSparsePlottingEnabled (line 299) | public void setSparsePlottingEnabled(boolean status) {
    method getIsSparsePlottingEnabled (line 303) | public boolean getIsSparsePlottingEnabled() {
    method getIsTransparent (line 307) | public boolean getIsTransparent() {
    method setIsTransparent (line 311) | public void setIsTransparent(boolean status) {
    method getIsEnlarged (line 315) | public boolean getIsEnlarged() {
    method setIsEnlarged (line 319) | public void setIsEnlarged(boolean status) {
    method setColorOfAllAnnotations (line 323) | public void setColorOfAllAnnotations(Color color) {
    method getFeatureList (line 328) | public Feature2DList getFeatureList() {
    method getContainedFeatures (line 332) | public List<Feature2D> getContainedFeatures(Chromosome chrom, int rect...
    class resultContainer (line 341) | public class resultContainer {
      method resultContainer (line 346) | resultContainer(int n, Color color, ArrayList<String> attributes) {

FILE: src/juicebox/mapcolorui/FeatureRenderer.java
  class FeatureRenderer (line 39) | public class FeatureRenderer {
    method render (line 43) | public static void render(Graphics2D g2, AnnotationLayerHandler annota...
    method plotSimple (line 128) | private static void plotSimple(Graphics2D g2, int x, int y, int w, int...
    method plotInUpperRight (line 137) | private static void plotInUpperRight(Graphics2D g2, int x, int y, int ...
    method plotInLowerLeft (line 146) | private static void plotInLowerLeft(Graphics2D g2, int x, int y, int w...
    method getNextState (line 155) | public static PlottingOption getNextState(PlottingOption state) {
    type PlottingOption (line 166) | public enum PlottingOption {ONLY_LOWER_LEFT, ONLY_UPPER_RIGHT, EVERYTH...
    type LineStyle (line 168) | public enum LineStyle {DASHED, SOLID}

FILE: src/juicebox/mapcolorui/GeneralTileManager.java
  class GeneralTileManager (line 37) | public class GeneralTileManager {
    method GeneralTileManager (line 42) | public GeneralTileManager(ColorScaleHandler colorScaleHandler) {
    method renderHiCTiles (line 46) | public boolean renderHiCTiles(HeatmapRenderer renderer, double binOrig...
    method bypassTileAndDirectlyDrawOnGraphics (line 160) | private void bypassTileAndDirectlyDrawOnGraphics(HeatmapRenderer rende...
    method clearTileCache (line 208) | public void clearTileCache() {
    class ImageTile (line 212) | static class ImageTile {
      method ImageTile (line 217) | ImageTile(Image image, int bLeft, int py0) {

FILE: src/juicebox/mapcolorui/HeatmapClickListener.java
  class HeatmapClickListener (line 48) | class HeatmapClickListener extends MouseAdapter implements ActionListener {
    method HeatmapClickListener (line 56) | HeatmapClickListener(HeatmapPanel heatmapPanel) {
    method actionPerformed (line 61) | @Override
    method mouseClicked (line 67) | @Override
    method unsafeMouseClickSubActionA (line 73) | private void unsafeMouseClickSubActionA(final MouseEvent eF) {
    method unsafeMouseClickSubActionB (line 107) | private void unsafeMouseClickSubActionB(double centerBinX, double cent...
    method safeMouseClicked (line 124) | private void safeMouseClicked(final MouseEvent eF) {
    method singleClick (line 150) | private void singleClick(final MouseEvent lastMouseEvent) {
    method removeAndRepaint (line 203) | private void removeAndRepaint() {
    method doubleClick (line 208) | private void doubleClick(MouseEvent lastMouseEvent) {

FILE: src/juicebox/mapcolorui/HeatmapMouseHandler.java
  class HeatmapMouseHandler (line 62) | public class HeatmapMouseHandler extends MouseAdapter {
    method HeatmapMouseHandler (line 102) | public HeatmapMouseHandler(HiC hic, SuperAdapter superAdapter, Heatmap...
    method getHighlightedFeature (line 113) | public List<Feature2D> getHighlightedFeature() {
    method eraseHighlightedFeatures (line 117) | public void eraseHighlightedFeatures() {
    method clearSelectedFeatures (line 122) | public void clearSelectedFeatures() {
    method getIsActivelyEditingAssembly (line 128) | public boolean getIsActivelyEditingAssembly() {
    method clearFeaturePairs (line 132) | public void clearFeaturePairs() {
    method getShouldShowHighlight (line 140) | public boolean getShouldShowHighlight() {
    method setActivelyEditingAssembly (line 144) | public void setActivelyEditingAssembly(boolean bool) {
    method getPopupMenu (line 148) | private JidePopupMenu getPopupMenu(final int xMousePos, final int yMou...
    method getDebrisFeature (line 448) | public Feature2D getDebrisFeature() {
    method getTempSelectedGroup (line 452) | public Feature2D getTempSelectedGroup() {
    method setTempSelectedGroup (line 456) | public void setTempSelectedGroup(Feature2D feature2D) {
    method getSelectedFeatures (line 460) | public List<Feature2D> getSelectedFeatures() {
    method addHighlightedFeatures (line 464) | private void addHighlightedFeatures(List<Feature2D> feature2DList) {
    method updateSelectedFeatures (line 474) | private void updateSelectedFeatures(boolean status) {
    method resetCurrentPromptedAssemblyAction (line 480) | public void resetCurrentPromptedAssemblyAction() {
    method getFloatString (line 484) | private String getFloatString(float value) {
    method getExpectedValue (line 496) | private double getExpectedValue(int c1, int c2, int binX, int binY, Ma...
    method executeSplitMenuAction (line 510) | private void executeSplitMenuAction() {
    method setFeatureOptionMenuEnabled (line 543) | public void setFeatureOptionMenuEnabled(boolean bool) {
    method getCurrentPromptedAssemblyAction (line 547) | public PromptedAssemblyAction getCurrentPromptedAssemblyAction() {
    method getPromptedAssemblyActionOnClick (line 551) | public PromptedAssemblyAction getPromptedAssemblyActionOnClick() {
    method setPromptedAssemblyActionOnClick (line 555) | public void setPromptedAssemblyActionOnClick(PromptedAssemblyAction pr...
    method mouseEntered (line 561) | @Override
    method reset (line 566) | public void reset() {
    method setProperCursor (line 570) | private void setProperCursor() {
    method addHighlightedFeature (line 578) | private void addHighlightedFeature(Feature2D feature2D) {
    method renderMouseAnnotations (line 588) | public void renderMouseAnnotations(Graphics2D g2) {
    method addAllFeatures (line 598) | public void addAllFeatures(AnnotationLayerHandler handler, List<Featur...
    method mouseExited (line 612) | @Override
    method mousePressed (line 620) | @Override
    method mouseReleased (line 737) | @Override
    method translationInProgressMouseReleased (line 971) | private void translationInProgressMouseReleased(List<Feature2D> newSel...
    method generateDebrisFeature (line 985) | Feature2D generateDebrisFeature(final MouseEvent eF, int debrisFeature...
    method restoreDefaultVariables (line 1000) | private void restoreDefaultVariables() {
    method unsafeDragging (line 1014) | private void unsafeDragging() {
    method mouseDragged (line 1042) | @Override
    method mouseMoved (line 1152) | @Override
    method mouseWheelMoved (line 1455) | @Override
    method calculateSelectionPoint (line 1495) | private Point calculateSelectionPoint(int unscaledX, int unscaledY) {
    method setDebrisFeauture (line 1514) | private void setDebrisFeauture(Feature2D debrisFeature) {
    method getMouseHoverSuperscaffold (line 1518) | private Feature2DGuiContainer getMouseHoverSuperscaffold(int x, int y) {
    method toolTipText (line 1534) | private String toolTipText(int x, int y) {
    method appendWithSpan (line 1800) | private void appendWithSpan(StringBuilder txt, List<Feature2D> selecte...
    method appendSectionWithSpan (line 1813) | private void appendSectionWithSpan(StringBuilder txt, String content) {
    method getChromFromBoundaries (line 1819) | private Chromosome getChromFromBoundaries(long[] chromosomeBoundaries,...
    method addJumpToDiagonalMenuItems (line 1830) | private void addJumpToDiagonalMenuItems(JidePopupMenu menu, int xMouse...
    method getAssemblyPopupMenu (line 1919) | private JidePopupMenu getAssemblyPopupMenu(final int xMousePos, final ...
    method moveSelectionToEndAndDisperse (line 2022) | void moveSelectionToEndAndDisperse() {
    method getCurrentUpstreamFeature (line 2030) | public Feature2DGuiContainer getCurrentUpstreamFeature() {
    method getCurrentDownstreamFeature (line 2034) | public Feature2DGuiContainer getCurrentDownstreamFeature() {
    type PromptedAssemblyAction (line 2038) | public enum PromptedAssemblyAction {REGROUP, PASTE, INVERT, CUT, ADJUS...
    type DragMode (line 2040) | private enum DragMode {ZOOM, ANNOTATE, RESIZE, PAN, SELECT, NONE}
    type AdjustAnnotation (line 2042) | private enum AdjustAnnotation {LEFT, RIGHT, NONE}

FILE: src/juicebox/mapcolorui/HeatmapPanel.java
  class HeatmapPanel (line 53) | public class HeatmapPanel extends JComponent {
    method HeatmapPanel (line 67) | public HeatmapPanel(SuperAdapter superAdapter) {
    method getChromosomeBoundaries (line 80) | public long[] getChromosomeBoundaries() {
    method setChromosomeBoundaries (line 84) | public void setChromosomeBoundaries(long[] chromosomeBoundaries) {
    method getMinimumDimension (line 89) | public int getMinimumDimension() {
    method paintComponent (line 93) | @Override
    method getThumbnailImage (line 212) | public Image getThumbnailImage(MatrixZoomData zd0, MatrixZoomData ctrl...
    method getShowGridLines (line 252) | public boolean getShowGridLines() {
    method setShowGridLines (line 256) | public void setShowGridLines(boolean showGridLines) {
    method getHiC (line 260) | public HiC getHiC() {
    method getMainWindow (line 264) | public MainWindow getMainWindow() {
    method getSuperAdapter (line 268) | public SuperAdapter getSuperAdapter() {
    method unsafeSetSelectedChromosomes (line 272) | public void unsafeSetSelectedChromosomes(Chromosome xChrom, Chromosome...
    method updateThumbnail (line 276) | public void updateThumbnail() {
    method clearTileCache (line 280) | public void clearTileCache() {
    method launchColorSelectionMenu (line 284) | public void launchColorSelectionMenu(Pair<Rectangle, Feature2D> select...
    method enableAssemblyEditing (line 295) | public void enableAssemblyEditing() {
    method disableAssemblyEditing (line 301) | public void disableAssemblyEditing() {
    method removeHighlightedFeature (line 309) | public void removeHighlightedFeature() {
    method removeSelection (line 316) | public void removeSelection() {
    method moveSelectionToEnd (line 339) | public void moveSelectionToEnd() {
    method reset (line 348) | public void reset() {
    method setNewDisplayRange (line 353) | public void setNewDisplayRange(MatrixType displayOption, double min, d...
    method getCurrentPromptedAssemblyAction (line 359) | public HeatmapMouseHandler.PromptedAssemblyAction getCurrentPromptedAs...
    method getPromptedAssemblyActionOnClick (line 363) | public HeatmapMouseHandler.PromptedAssemblyAction getPromptedAssemblyA...
    method setPromptedAssemblyActionOnClick (line 367) | public void setPromptedAssemblyActionOnClick(HeatmapMouseHandler.Promp...
    method getSelectedFeatures (line 371) | public List<Feature2D> getSelectedFeatures() {
    method getCurrentUpstreamFeature (line 375) | public Feature2DGuiContainer getCurrentUpstreamFeature() {
    method getCurrentDownstreamFeature (line 379) | public Feature2DGuiContainer getCurrentDownstreamFeature() {

FILE: src/juicebox/mapcolorui/HeatmapRenderer.java
  class HeatmapRenderer (line 46) | public class HeatmapRenderer {
    method HeatmapRenderer (line 53) | public HeatmapRenderer(Graphics2D g, ColorScaleHandler colorScaleHandl...
    method getColorScaleCacheKey (line 58) | public static String getColorScaleCacheKey(MatrixZoomData zd, MatrixTy...
    method render (line 62) | @SuppressWarnings("SuspiciousNameCombination")
    method renderLogRatioWithExpMap (line 362) | private void renderLogRatioWithExpMap(List<Block> blocks, List<Block> ...
    method convertBlockListToMap (line 422) | private Map<String, Block> convertBlockListToMap(List<Block> ctrlBlock...
    method renderLogRatioWithAvgMap (line 430) | private void renderLogRatioWithAvgMap(List<Block> blocks, List<Block> ...
    method renderDiffMap (line 457) | private void renderDiffMap(List<Block> blocks, List<Block> ctrlBlocks,
    method renderRatioWithExpMap (line 488) | private void renderRatioWithExpMap(List<Block> blocks, List<Block> ctr...
    method renderRatioWithAvgMap (line 515) | private void renderRatioWithAvgMap(List<Block> blocks, List<Block> ctr...
    method renderOERatioMinus (line 543) | private void renderOERatioMinus(List<Block> blocks, List<Block> ctrlBl...
    method linkRecords (line 611) | private Map<String, ContactRecord> linkRecords(MatrixZoomData zd, Norm...
    method renderOERatioMap (line 622) | private void renderOERatioMap(List<Block> blocks, List<Block> ctrlBlocks,
    method renderNewBaseEMap (line 689) | private void renderNewBaseEMap(int chr1, List<Block> blocks, ExpectedV...
    method renderExpectedMap (line 729) | private void renderExpectedMap(MatrixZoomData zd, ExpectedValueFunctio...
    method renderLogObsMinusExpVSMap (line 756) | private void renderLogObsMinusExpVSMap(int chr1, List<Block> blocks, L...
    method renderLogObsOverExpVSMap (line 803) | private void renderLogObsOverExpVSMap(int chr1, List<Block> blocks, Li...
    method renderSimpleLogVSMap (line 844) | private void renderSimpleLogVSMap(List<Block> blocks, List<Block> ctrl...
    method renderSimpleVSMap (line 887) | private void renderSimpleVSMap(List<Block> blocks, List<Block> ctrlBlo...
    method renderLogObservedBaseExpectedMap (line 929) | private void renderLogObservedBaseExpectedMap(int chromosome, List<Blo...
    method renderObservedOverExpectedVSMap (line 970) | private void renderObservedOverExpectedVSMap(int chromosome, List<Bloc...
    method getExpectedValue (line 1018) | private float getExpectedValue(ExpectedValueFunction df, int chromosom...
    method getExpectedValue (line 1022) | private float getExpectedValue(ExpectedValueFunction df, int chromosom...
    method renderObservedOverExpectedMap (line 1027) | private void renderObservedOverExpectedMap(int chromosome, List<Block>...
    method renderSimpleMap (line 1069) | private void renderSimpleMap(List<Block> blocks, ColorScale cs,
    method renderSimpleLogMap (line 1082) | private void renderSimpleLogMap(List<Block> blocks, ColorScale cs,
    method renderPearsonVS (line 1095) | private void renderPearsonVS(MatrixZoomData zd, MatrixZoomData controlZD,
    method renderPearson (line 1110) | private void renderPearson(MatrixZoomData zd, ExpectedValueFunction df,
    method renderNorm2VS (line 1120) | private void renderNorm2VS(MatrixZoomData zd, MatrixZoomData controlZD,
    method renderNorm2 (line 1135) | private void renderNorm2(MatrixZoomData zd, boolean isWholeGenome,
    method getTheBlocks (line 1145) | private List<Block> getTheBlocks(MatrixZoomData zd, int x, int y, int ...
    method renderDenseMatrix (line 1168) | private void renderDenseMatrix(BasicMatrix bm1, BasicMatrix bm2, int o...
    method updateColorSliderFromColorScale (line 1195) | public void updateColorSliderFromColorScale(SuperAdapter superAdapter,...
    method interPainting (line 1199) | private void interPainting(int originX, int originY, int width, int he...
    method simplePainting (line 1203) | private void simplePainting(ColorScale cs, int width, int height, bool...
    method logPainting (line 1211) | private boolean logPainting(ColorScale cs, float num, float den, float...
    method ratioPainting (line 1218) | private void ratioPainting(int originX, int originY, int width, int he...
    method intraPainting2 (line 1225) | private void intraPainting2(int originX, int originY, int width, int h...
    method intraPainting (line 1230) | private void intraPainting(int originX, int originY, int width, int he...
    method belowDiagonalPainting (line 1235) | @SuppressWarnings("SuspiciousNameCombination")
    method aboveDiagonalPainting (line 1245) | private void aboveDiagonalPainting(int originX, int originY, int width...
    method actualDiagonalPainting (line 1249) | private void actualDiagonalPainting(int originX, int originY, int widt...
    method directDensePainting (line 1257) | private void directDensePainting(int originX, int originY, int binX, i...
    method setColor (line 1263) | protected void setColor(Color color) {
    method directPixelPainting (line 1267) | protected void directPixelPainting(int px, int py) {
    method translate (line 1271) | public void translate(int x, int y) {
    method scale (line 1275) | public void scale(double sx, double sy) {
    method drawImage (line 1279) | public void drawImage(Image image, int xDest0, int yDest0, int xDest1,...
    method drawRect (line 1283) | public void drawRect(int x, int y, int width, int height) {

FILE: src/juicebox/mapcolorui/HiCMapTileManager.java
  class HiCMapTileManager (line 40) | public class HiCMapTileManager {
    method HiCMapTileManager (line 45) | public HiCMapTileManager(ColorScaleHandler colorScaleHandler) {
    method clearTileCache (line 49) | public void clearTileCache() {
    method getImageTile (line 53) | public GeneralTileManager.ImageTile getImageTile(MatrixZoomData zd, Ma...
    method renderDataWithCPU (line 85) | private BufferedImage renderDataWithCPU(JComponent parent, int bx0, in...
    method updateColorSliderFromColorScale (line 106) | public void updateColorSliderFromColorScale(SuperAdapter superAdapter,...

FILE: src/juicebox/mapcolorui/JColorRangePanel.java
  class JColorRangePanel (line 50) | public class JColorRangePanel extends JPanel {
    method JColorRangePanel (line 59) | public JColorRangePanel(final SuperAdapter superAdapter, final Heatmap...
    method setColorRangeSliderVisible (line 227) | public boolean setColorRangeSliderVisible(boolean state, SuperAdapter ...
    method updateColorSlider (line 241) | public void updateColorSlider(HiC hic, double lower, double upper, dou...
    method updateRatioColorSlider (line 293) | public void updateRatioColorSlider(HiC hic, double max, double val) {
    method getColorRangeValues (line 343) | public String getColorRangeValues() {
    method getColorRangeScaleFactor (line 354) | public double getColorRangeScaleFactor() {
    method colorRangeSliderUpdateToolTip (line 358) | private void colorRangeSliderUpdateToolTip(MatrixType displayOption) {
    method setElementsVisible (line 394) | public void setElementsVisible(boolean val, SuperAdapter superAdapter) {
    method handleNewFileLoading (line 401) | public void handleNewFileLoading(MatrixType option) {

FILE: src/juicebox/mapcolorui/OEColorScale.java
  class OEColorScale (line 38) | class OEColorScale implements ColorScale {
    method OEColorScale (line 44) | public OEColorScale(MatrixType type) {
    method resetThreshold (line 50) | private void resetThreshold() {
    method getColor (line 59) | public Color getColor(float score) {
    method getColor (line 109) | public Color getColor(String symbol) {
    method getNoDataColor (line 113) | public Color getNoDataColor() {
    method asString (line 117) | public String asString() {
    method isDefault (line 121) | public boolean isDefault() {
    method getMax (line 125) | public double getMax() {
    method getThreshold (line 133) | public float getThreshold() {
    method setThreshold (line 141) | public void setThreshold(double max) {

FILE: src/juicebox/mapcolorui/PearsonColorScale.java
  class PearsonColorScale (line 36) | public class PearsonColorScale {
    method PearsonColorScale (line 43) | public PearsonColorScale() {
    method getPosMax (line 46) | public float getPosMax(String key) {
    method getPosMin (line 50) | public float getPosMin(String key) {
    method getNegMax (line 54) | public float getNegMax(String key) {
    method getNegMin (line 58) | public float getNegMin(String key) {
    method setMinMax (line 62) | public void setMinMax(String key, float min, float max) {
    method setMinMax (line 66) | public void setMinMax(String key, float negMin, float negMax, float po...
    method getColor (line 74) | public Color getColor(String key, float score) {
    method getColor (line 99) | public Color getColor(String symbol) {
    method getNoDataColor (line 104) | public Color getNoDataColor() {
    method asString (line 108) | public String asString() {
    method isDefault (line 112) | public boolean isDefault() {
    method doesNotContainKey (line 116) | public boolean doesNotContainKey(String key) {
    method resetValues (line 120) | public void resetValues(String key) {

FILE: src/juicebox/mapcolorui/PearsonColorScaleEditor.java
  class PearsonColorScaleEditor (line 39) | public class PearsonColorScaleEditor extends JDialog {
    method PearsonColorScaleEditor (line 43) | public PearsonColorScaleEditor(final SuperAdapter superAdapter, final ...

FILE: src/juicebox/mapcolorui/RangeSlider.java
  class RangeSlider (line 40) | class RangeSlider extends JSlider {
    method RangeSlider (line 49) | public RangeSlider() {
    method initSlider (line 56) | private void initSlider() {
    method updateUI (line 64) | @Override
    method getLowerValue (line 74) | public int getLowerValue() {
    method setLowerValue (line 78) | public void setLowerValue(int value) {
    method setValue (line 86) | @Override
    method getUpperValue (line 106) | public int getUpperValue() {
    method setUpperValue (line 113) | public void setUpperValue(int value) {
    method setDisplayToOE (line 122) | public void setDisplayToOE(boolean colorIsOE) {
    method setDisplayToBlank (line 126) | public void setDisplayToBlank(boolean colorIsBlank) {

FILE: src/juicebox/mapcolorui/RangeSliderUI.java
  class RangeSliderUI (line 42) | class RangeSliderUI extends BasicSliderUI {
    method RangeSliderUI (line 83) | public RangeSliderUI(RangeSlider b) {
    method installUI (line 90) | @Override
    method createTrackListener (line 99) | @Override
    method createChangeListener (line 107) | @Override
    method calculateThumbSize (line 115) | @Override
    method calculateThumbLocation (line 127) | @Override
    method getThumbSize (line 177) | @Override
    method paint (line 186) | @Override
    method paintTrack (line 214) | @Override
    method drawSubTrackRectangles (line 281) | private void drawSubTrackRectangles(Graphics2D g, LinearGradientPaint ...
    method paintThumb (line 298) | @Override
    method paintLowerThumb (line 306) | private void paintLowerThumb(Graphics g) {
    method paintUpperThumb (line 314) | private void paintUpperThumb(Graphics g) {
    method setUpperThumbLocation (line 329) | private void setUpperThumbLocation(int x, int y) {
    method scrollByBlock (line 343) | public void scrollByBlock(int direction) {
    method scrollByUnit (line 365) | public void scrollByUnit(int direction) {
    method setDisplayToOE (line 379) | public void setDisplayToOE(boolean isOE) {
    method setDisplayToBlank (line 383) | public void setDisplayToBlank(boolean isBlank) {
    class ChangeHandler (line 394) | private class ChangeHandler implements ChangeListener {
      method stateChanged (line 395) | public void stateChanged(ChangeEvent arg0) {
    class RangeTrackListener (line 406) | class RangeTrackListener extends TrackListener {
      method mousePressed (line 408) | @Override
      method mouseReleased (line 470) | @Override
      method mouseDragged (line 481) | @Override
      method shouldScroll (line 501) | @Override
      method moveLowerThumb (line 510) | private void moveLowerThumb() {
      method moveUpperThumb (line 579) | private void moveUpperThumb() {

FILE: src/juicebox/mapcolorui/ResolutionControl.java
  class ResolutionControl (line 51) | public class ResolutionControl extends JPanel {
    method ResolutionControl (line 84) | public ResolutionControl(final SuperAdapter superAdapter) {
    method getUnitLabel (line 275) | private String getUnitLabel() {
    method setEnabled (line 279) | public void setEnabled(boolean enabled) {
    method reset (line 287) | public void reset() {
    method sizeToLabel (line 334) | private String sizeToLabel(int binSize) {
    method removeTrailingZeros (line 358) | private String removeTrailingZeros(String label) {
    method setZoom (line 362) | public void setZoom(HiCZoom newZoom) {
    method toggleLockButton (line 376) | private void toggleLockButton() {
    method updateLockButton (line 381) | private void updateLockButton() {
    method isResolutionLocked (line 385) | public boolean isResolutionLocked() {
    method setResolutionLocked (line 389) | public void setResolutionLocked(boolean resolutionLocked) {

FILE: src/juicebox/mapcolorui/ThumbnailPanel.java
  class ThumbnailPanel (line 41) | public class ThumbnailPanel extends JComponent {
    method ThumbnailPanel (line 50) | public ThumbnailPanel(final SuperAdapter superAdapter) {
    method setImage (line 102) | public void setImage(Image image) {
    method getName (line 106) | public String getName() {
    method setName (line 110) | public void setName(String nm) {
    method paintComponent (line 114) | @Override
    method renderVisibleWindow (line 127) | private void renderVisibleWindow(Graphics2D g) {
    class SquareDonut (line 170) | private static class SquareDonut implements Shape {
      method SquareDonut (line 173) | SquareDonut(Rectangle outerRectangle, Rectangle innerRectangle) {
      method getBounds (line 178) | public Rectangle getBounds() {
      method getBounds2D (line 182) | public Rectangle2D getBounds2D() {
      method contains (line 186) | public boolean contains(double v, double v1) {
      method contains (line 190) | public boolean contains(Point2D point2D) {
      method intersects (line 194) | public boolean intersects(double v, double v1, double v2, double v3) {
      method intersects (line 198) | public boolean intersects(Rectangle2D rectangle2D) {
      method contains (line 202) | public boolean contains(double v, double v1, double v2, double v3) {
      method contains (line 206) | public boolean contains(Rectangle2D rectangle2D) {
      method getPathIterator (line 210) | public PathIterator getPathIterator(AffineTransform affineTransform) {
      method getPathIterator (line 214) | public PathIterator getPathIterator(AffineTransform affineTransform,...

FILE: src/juicebox/matrix/BasicMatrix.java
  type BasicMatrix (line 32) | public interface BasicMatrix {
    method getEntry (line 34) | float getEntry(int row, int col);
    method getRowDimension (line 36) | int getRowDimension();
    method getColumnDimension (line 38) | int getColumnDimension();
    method getLowerValue (line 40) | float getLowerValue();
    method getUpperValue (line 42) | float getUpperValue();
    method setEntry (line 44) | void setEntry(int i, int j, float corr);

FILE: src/juicebox/matrix/DiskResidentBlockMatrix.java
  class DiskResidentBlockMatrix (line 59) | public class DiskResidentBlockMatrix implements BasicMatrix {
    method DiskResidentBlockMatrix (line 76) | public DiskResidentBlockMatrix(String path) throws IOException {
    method getChr1 (line 81) | public String getChr1() {
    method getEntry (line 85) | @Override
    method loadBlockData (line 112) | private synchronized float[][] loadBlockData(int blockRowIdx, int bloc...
    method getRowDimension (line 169) | @Override
    method getColumnDimension (line 174) | @Override
    method getLowerValue (line 180) | public float getLowerValue() {
    method getUpperValue (line 184) | public float getUpperValue() {
    method setEntry (line 188) | @Override
    method init (line 193) | private void init() throws IOException {

FILE: src/juicebox/matrix/InMemoryMatrix.java
  class InMemoryMatrix (line 40) | public class InMemoryMatrix implements BasicMatrix {
    method InMemoryMatrix (line 49) | public InMemoryMatrix(int dim) {
    method InMemoryMatrix (line 54) | public InMemoryMatrix(int dim, float[] data) {
    method fill (line 59) | public void fill(float value) {
    method getEntry (line 68) | @Override
    method setEntry (line 75) | public void setEntry(int row, int col, float value) {
    method getRowDimension (line 86) | @Override
    method getColumnDimension (line 91) | @Override
    method getLowerValue (line 96) | @Override
    method getUpperValue (line 105) | @Override
    method computeBounds (line 113) | private void computeBounds() {

FILE: src/juicebox/matrix/RealMatrixWrapper.java
  class RealMatrixWrapper (line 37) | public class RealMatrixWrapper implements BasicMatrix {
    method RealMatrixWrapper (line 43) | public RealMatrixWrapper(RealMatrix matrix) {
    method getEntry (line 48) | @Override
    method getRowDimension (line 53) | @Override
    method getColumnDimension (line 58) | @Override
    method getLowerValue (line 63) | @Override
    method getUpperValue (line 68) | @Override
    method setEntry (line 73) | @Override
    method computePercentiles (line 78) | private void computePercentiles() {
    method getMatrix (line 101) | public RealMatrix getMatrix() {

FILE: src/juicebox/matrix/SparseSymmetricMatrix.java
  class SparseSymmetricMatrix (line 43) | public class SparseSymmetricMatrix implements BasicMatrix {
    method SparseSymmetricMatrix (line 53) | public SparseSymmetricMatrix(int numValsEstimate) {
    method populateMatrix (line 60) | public void populateMatrix(List<ContactRecord> list, int[] offset) {
    method multiply (line 71) | public double[] multiply(double[] vector) {
    method getEntry (line 111) | @Override
    method notImplementedDontCall (line 120) | private void notImplementedDontCall() {
    method getRowDimension (line 125) | @Override
    method getColumnDimension (line 131) | @Override
    method getLowerValue (line 137) | @Override
    method getUpperValue (line 143) | @Override
    method setEntry (line 149) | @Override

FILE: src/juicebox/matrix/SparseVector.java
  class SparseVector (line 33) | class SparseVector {
    method SparseVector (line 38) | public SparseVector(int length) {
    method set (line 43) | public void set(Integer i, Double v) {
    method getLength (line 50) | public int getLength() {
    method get (line 54) | public Double get(Integer idx) {
    method getIndeces (line 58) | public Collection<Integer> getIndeces() {
    method getMean (line 67) | public Double getMean() {

FILE: src/juicebox/matrix/SymmetricMatrix.java
  class SymmetricMatrix (line 41) | public class SymmetricMatrix implements BasicMatrix {
    method SymmetricMatrix (line 49) | public SymmetricMatrix(int dim) {
    method nullColumn (line 57) | public void nullColumn(int i) {
    method getNullColumns (line 61) | public Set<Integer> getNullColumns() {
    method fill (line 65) | public void fill(float value) {
    method setEntry (line 69) | public void setEntry(int i, int j, float value) {
    method getIdx (line 74) | private int getIdx(int i, int j) {
    method getColumnMean (line 82) | public float getColumnMean(int j) {
    method getRowMean (line 95) | public float getRowMean(int i) {
    method getEntry (line 109) | @Override
    method getRowDimension (line 115) | @Override
    method getColumnDimension (line 120) | @Override
    method getLowerValue (line 125) | @Override
    method getUpperValue (line 133) | @Override
    method computePercentiles (line 141) | private void computePercentiles() {

FILE: src/juicebox/state/ImportStateFileDialog.java
  class ImportStateFileDialog (line 46) | public class ImportStateFileDialog extends JFileChooser {
    method ImportStateFileDialog (line 51) | public ImportStateFileDialog(File currentStates, MainWindow mainWindow) {
    method copyFile (line 56) | private static void copyFile(File sourceFile, File destFile) throws IO...
    method loadFile (line 78) | private void loadFile(File currentFile, MainWindow mainWindow) {
    class SimpleErrorHandler (line 114) | private static class SimpleErrorHandler implements ErrorHandler {
      method warning (line 115) | public void warning(SAXParseException e) {
      method error (line 119) | public void error(SAXParseException e) {
      method fatalError (line 123) | public void fatalError(SAXParseException e) {

FILE: src/juicebox/state/LoadStateFromXMLFile.java
  class LoadStateFromXMLFile (line 42) | public class LoadStateFromXMLFile {
    method reloadSelectedState (line 44) | public static void reloadSelectedState(SuperAdapter superAdapter, Stri...
    method loadSavedStatePreliminaryStep (line 54) | private static void loadSavedStatePreliminaryStep(String[] infoForRelo...
    method safeLoadStateFromXML (line 99) | private static void safeLoadStateFromXML(final SuperAdapter superAdapt...
    method unsafeLoadStateFromXML (line 115) | private static void unsafeLoadStateFromXML(SuperAdapter superAdapter, ...

FILE: src/juicebox/state/SaveFileDialog.java
  class SaveFileDialog (line 43) | public class SaveFileDialog extends JFileChooser {
    method SaveFileDialog (line 46) | public SaveFileDialog(File fileToSave) {
    method copyFile (line 71) | private static void copyFile(File sourceFile, File destFile) throws IO...

FILE: src/juicebox/state/Slideshow.java
  class Slideshow (line 50) | public class Slideshow extends JDialog {
    method Slideshow (line 64) | public Slideshow(MainWindow mainWindow, final SuperAdapter superAdapte...
    method currentSlideNumber (line 180) | public int currentSlideNumber() {
    method currentSlideName (line 184) | public String currentSlideName(int count) {

FILE: src/juicebox/state/State.java
  class State (line 30) | class State {

FILE: src/juicebox/state/XMLFileHandling.java
  class XMLFileHandling (line 46) | public class XMLFileHandling {
    method addNewStateToXML (line 47) | public static void addNewStateToXML(String stateID, SuperAdapter super...

FILE: src/juicebox/state/XMLFileParser.java
  class XMLFileParser (line 40) | class XMLFileParser {
    method parseXML (line 42) | public static String[] parseXML(String mapSelection) {
    class SimpleErrorHandler (line 89) | private static class SimpleErrorHandler implements ErrorHandler {
      method warning (line 90) | public void warning(SAXParseException e) {
      method error (line 94) | public void error(SAXParseException e) {
      method fatalError (line 98) | public void fatalError(SAXParseException e) {

FILE: src/juicebox/state/XMLFileWriter.java
  class XMLFileWriter (line 46) | public class XMLFileWriter {
    method overwriteXMLFile (line 51) | public static void overwriteXMLFile() {
    method initXML (line 68) | private static Element initXML() throws ParserConfigurationException {
    method convert (line 78) | private static void convert(String s, Element root) {
    method writeXML (line 118) | private static void writeXML() throws TransformerException {

FILE: src/juicebox/tools/HiCTools.java
  class HiCTools (line 42) | public class HiCTools {
    method main (line 44) | public static void main(String[] argv) throws CmdLineParser.UnknownOpt...

FILE: src/juicebox/tools/chrom/sizes/ChromosomeSizes.java
  class ChromosomeSizes (line 30) | public class ChromosomeSizes {

FILE: src/juicebox/tools/clt/AggregateProcessing.java
  class AggregateProcessing (line 31) | class AggregateProcessing {
    method main (line 32) | public static void main(String[] argv) throws Exception {

FILE: src/juicebox/tools/clt/CLTFactory.java
  class CLTFactory (line 42) | public class CLTFactory {
    method generalUsage (line 66) | public static void generalUsage() {
    method getCLTCommand (line 78) | public static JuiceboxCLT getCLTCommand(String cmd) {

FILE: src/juicebox/tools/clt/CommandLineParser.java
  class CommandLineParser (line 36) | public class CommandLineParser extends CmdLineParser {
    method CommandLineParser (line 98) | public CommandLineParser() {
    method optionToBoolean (line 105) | protected boolean optionToBoolean(Option option) {
    method getHelpOption (line 110) | public boolean getHelpOption() { return optionToBoolean(helpOption);}
    method getDiagonalsOption (line 112) | public boolean getDiagonalsOption() {
    method useCacheMemory (line 116) | public boolean useCacheMemory() {
    method getVerboseOption (line 120) | public boolean getVerboseOption() {
    method getNoNormOption (line 124) | public boolean getNoNormOption() { return optionToBoolean(noNormOption...
    method getAllPearsonsOption (line 126) | public boolean getAllPearsonsOption() {
    method getNoFragNormOption (line 130) | public boolean getNoFragNormOption() {
    method getVersionOption (line 134) | public boolean getVersionOption() {
    method getRandomizePositionsOption (line 138) | public boolean getRandomizePositionsOption() {
    method getThrowIntraFragOption (line 142) | public boolean getThrowIntraFragOption() {
    method getDontPutAllContactsIntoRAM (line 146) | public boolean getDontPutAllContactsIntoRAM() {
    method shouldCheckRAMUsage (line 150) | public boolean shouldCheckRAMUsage() {
    method getFromHICOption (line 154) | public boolean getFromHICOption() { return optionToBoolean(fromHIC); }
    method optionToString (line 159) | protected String optionToString(Option option) {
    method getFragmentOption (line 164) | public String getFragmentOption() {
    method getStatsOption (line 168) | public String getStatsOption() {
    method getGraphOption (line 172) | public String getGraphOption() {
    method getGenomeOption (line 176) | public String getGenomeOption() { return optionToString(genomeIDOption...
    method getTmpdirOption (line 178) | public String getTmpdirOption() {
    method getExpectedVectorOption (line 182) | public String getExpectedVectorOption() {
    method getMndIndexOption (line 186) | public String getMndIndexOption() {
    method getLigationOption (line 190) | public String getLigationOption() {
    method getShellOption (line 194) | public String getShellOption() {
    method getAlignmentOption (line 198) | public Alignment getAlignmentOption() {
    method optionToInt (line 222) | protected int optionToInt(Option option) {
    method getBlockCapacityOption (line 227) | public int getBlockCapacityOption() {
    method getCountThresholdOption (line 231) | public int getCountThresholdOption() {
    method getMapqThresholdOption (line 235) | public int getMapqThresholdOption() {
    method getGenomeWideOption (line 239) | public int getGenomeWideOption() {
    method optionToLong (line 243) | protected long optionToLong(Option option) {
    method getRandomPositionSeedOption (line 248) | public long getRandomPositionSeedOption() {
    type Alignment (line 252) | public enum Alignment {INNER, OUTER, LL, RR, TANDEM}
    method getNumThreads (line 254) | public int getNumThreads() {
    method getNumMatrixOperationThreads (line 258) | public int getNumMatrixOperationThreads() {
    method getV9DepthBase (line 262) | public int getV9DepthBase() {
    method optionToDouble (line 269) | protected double optionToDouble(Option option) {
    method getScalingOption (line 274) | public double getScalingOption() {
    method getSubsampleOption (line 280) | public double getSubsampleOption() { return optionToDouble(subsampleOp...
    method optionToStringSet (line 285) | protected Set<String> optionToStringSet(Option option) {
    method optionToStringList (line 290) | protected List<String> optionToStringList(Option option) {
    method getChromosomeSetOption (line 295) | public Set<String> getChromosomeSetOption() {
    method getResolutionOption (line 299) | public List<String> getResolutionOption() {
    method getRandomizePositionMaps (line 303) | public Set<String> getRandomizePositionMaps() {return optionToStringSe...
    method optionToIntList (line 308) | protected List<Integer> optionToIntList(Option option) {
    method getMultipleMapQOptions (line 321) | public List<Integer> getMultipleMapQOptions() {return optionToIntList(...
    method getAllNormalizationTypesOption (line 323) | public List<NormalizationType> getAllNormalizationTypesOption() {
    method retrieveNormalization (line 338) | protected NormalizationType retrieveNormalization(String norm, Normali...

FILE: src/juicebox/tools/clt/CommandLineParserForJuicer.java
  class CommandLineParserForJuicer (line 36) | public class CommandLineParserForJuicer extends CommandLineParser {
    method CommandLineParserForJuicer (line 74) | public CommandLineParserForJuicer() {
    method isJuicerCommand (line 77) | public static boolean isJuicerCommand(String cmd) {
    method getLegacyOutputOption (line 84) | public boolean getLegacyOutputOption() {
    method getIncludeInterChromosomal (line 88) | public boolean getIncludeInterChromosomal() {
    method getAPASaveAllData (line 93) | public boolean getAPASaveAllData() {
    method getAPADontIncludePlots (line 97) | public boolean getAPADontIncludePlots() {
    method getNormalizationTypeOption (line 104) | public NormalizationType getNormalizationTypeOption(NormalizationHandl...
    method getBothNormalizationTypeOption (line 108) | public NormalizationType[] getBothNormalizationTypeOption(Normalizatio...
    method getAPAWindowSizeOption (line 132) | public int getAPAWindowSizeOption() {
    method getMatrixSizeOption (line 136) | public int getMatrixSizeOption() {
    method getExpandSize (line 140) | public int getExpandSize() { return optionToInt(expandSize);}
    method getNumPeaks (line 142) | public int getNumPeaks() { return optionToInt(numPeaks);}
    method getAPAMinVal (line 148) | public double getAPAMinVal() {
    method getAPAMaxVal (line 152) | public double getAPAMaxVal() {
    method getChromosomeListOption (line 160) | List<String> getChromosomeListOption() {
    method getMultipleResolutionOptions (line 165) | public List<String> getMultipleResolutionOptions() {
    method getAPACornerRegionDimensionOptions (line 169) | public List<String> getAPACornerRegionDimensionOptions() {
    method getFDROptions (line 173) | public List<String> getFDROptions() {
    method getPeakOptions (line 177) | public List<String> getPeakOptions() {
    method getWindowOptions (line 181) | public List<String> getWindowOptions() {
    method getClusterRadiusOptions (line 185) | public List<String> getClusterRadiusOptions() {
    method getThresholdOptions (line 189) | public List<String> getThresholdOptions() {
    method getCPUVersionOfHiCCUPSOptions (line 193) | public boolean getCPUVersionOfHiCCUPSOptions() {
    method restrictSearchRegionsOptions (line 198) | public boolean restrictSearchRegionsOptions() {

FILE: src/juicebox/tools/clt/JuiceboxCLT.java
  class JuiceboxCLT (line 37) | public abstract class JuiceboxCLT {
    method JuiceboxCLT (line 46) | protected JuiceboxCLT(String usage) {
    method splitToList (line 50) | public static String[] splitToList(String nextLine) {
    method readArguments (line 54) | public abstract void readArguments(String[] args, CommandLineParser pa...
    method run (line 56) | public abstract void run();
    method setUsage (line 58) | private void setUsage(String newUsage) {
    method printUsageAndExit (line 62) | public void printUsageAndExit() {
    method printUsageAndExit (line 67) | public void printUsageAndExit(int exitcode) {
    method setDatasetAndNorm (line 72) | protected void setDatasetAndNorm(String files, String normType, boolea...
    method getAppropriateNumberOfThreads (line 84) | public static int getAppropriateNumberOfThreads(int numThreads, int de...
    method updateNumberOfCPUThreads (line 94) | protected void updateNumberOfCPUThreads(CommandLineParser parser, int ...
    method updateSecondaryNumberOfCPUThreads (line 100) | protected void updateSecondaryNumberOfCPUThreads(CommandLineParser par...

FILE: src/juicebox/tools/clt/JuicerCLT.java
  class JuicerCLT (line 41) | public abstract class JuicerCLT extends JuiceboxCLT {
    method JuicerCLT (line 46) | protected JuicerCLT(String usage) {
    method determineHowManyChromosomesWillActuallyRun (line 50) | protected int determineHowManyChromosomesWillActuallyRun(Dataset ds, C...
    method readArguments (line 61) | @Override
    method readJuicerArguments (line 68) | protected abstract void readJuicerArguments(String[] args, CommandLine...
    method assessIfChromosomesHaveBeenSpecified (line 70) | private void assessIfChromosomesHaveBeenSpecified(CommandLineParserFor...

FILE: src/juicebox/tools/clt/UnitTests.java
  class UnitTests (line 48) | class UnitTests {
    method pearsonsAndEigenvector (line 50) | public static void pearsonsAndEigenvector() {
    method toDenseMatrix (line 78) | private static float[][] toDenseMatrix(BasicMatrix bm1) {
    method testingMergerOfHiCCUPSPostprocessing (line 88) | private static void testingMergerOfHiCCUPSPostprocessing() {
    method testingHiCCUPSPostprocessing (line 129) | public static void testingHiCCUPSPostprocessing() {

FILE: src/juicebox/tools/clt/juicer/ABCompartmentsDiff.java
  class ABCompartmentsDiff (line 47) | public class ABCompartmentsDiff extends JuicerCLT {
    method ABCompartmentsDiff (line 54) | public ABCompartmentsDiff() {
    method readJuicerArguments (line 59) | @Override
    method run (line 96) | @Override

FILE: src/juicebox/tools/clt/juicer/APA.java
  class APA (line 116) | public class APA extends JuicerCLT {
    method APA (line 137) | public APA() {
    method getBasicUsage (line 144) | public static String getBasicUsage() {
    method initializeDirectly (line 148) | public void initializeDirectly(String inputHiCFileName, String inputPe...
    method readJuicerArguments (line 161) | @Override
    method run (line 216) | @Override
    method runWithReturn (line 222) | public APARegionStatistics runWithReturn() {

FILE: src/juicebox/tools/clt/juicer/Arrowhead.java
  class Arrowhead (line 106) | public class Arrowhead extends JuicerCLT {
    method Arrowhead (line 117) | public Arrowhead() {
    method getBasicUsage (line 123) | public static String getBasicUsage() {
    method readJuicerArguments (line 127) | @Override
    method run (line 175) | @Override

FILE: src/juicebox/tools/clt/juicer/CompareLists.java
  class CompareLists (line 41) | public class CompareLists extends JuicerCLT {
    method CompareLists (line 55) | public CompareLists() {
    method readJuicerArguments (line 63) | @Override
    method run (line 92) | @Override
    method generateHistogramMetrics (line 117) | private void generateHistogramMetrics(Feature2DList list) {
    method compareTwoLists (line 123) | private void compareTwoLists(Feature2DList listA, Feature2DList listB,...

FILE: src/juicebox/tools/clt/juicer/HiCCUPS.java
  class HiCCUPS (line 158) | public class HiCCUPS extends JuicerCLT {
    method HiCCUPS (line 205) | public HiCCUPS() {
    method getBasicUsage (line 213) | public static String getBasicUsage() {
    method readJuicerArguments (line 217) | @Override
    method initializeDirectly (line 265) | public void initializeDirectly(Dataset dataset, String outputDirectory...
    method run (line 301) | @Override
    method runHiccupsProcessing (line 367) | private Feature2DList runHiccupsProcessing(Dataset ds, final HiCCUPSCo...
    method runCoreCodeForHiCCUPS (line 475) | private void runCoreCodeForHiCCUPS(HiCCUPSConfiguration conf, AtomicIn...
    method buildGPUController (line 556) | private GPUController buildGPUController(HiCCUPSConfiguration conf) {
    method determineValidConfigurations (line 573) | private void determineValidConfigurations(CommandLineParserForJuicer j...
    method determineValidMatrixSize (line 601) | private void determineValidMatrixSize(CommandLineParserForJuicer juice...
    method determineValidMatrixSize (line 605) | private void determineValidMatrixSize(int specifiedMatrixSize) {
    method setHiCCUPSFDROEThresholds (line 615) | private void setHiCCUPSFDROEThresholds(double[] thresholds) {

FILE: src/juicebox/tools/clt/juicer/HiCCUPS2.java
  class HiCCUPS2 (line 72) | public class HiCCUPS2 extends JuicerCLT {
    method HiCCUPS2 (line 121) | public HiCCUPS2() {
    method getBasicUsage (line 128) | public static String getBasicUsage() {
    method readJuicerArguments (line 132) | @Override
    method initializeDirectly (line 181) | public void initializeDirectly(Dataset dataset, String outputDirectory...
    method run (line 220) | @Override
    method runHiccups2Processing (line 287) | private Feature2DList runHiccups2Processing(Dataset ds, final HiCCUPSC...
    method runCoreCodeForHiCCUPS2 (line 458) | private void runCoreCodeForHiCCUPS2(HiCCUPSConfiguration conf, AtomicI...
    method buildGPUController (line 545) | private GPUController2 buildGPUController(HiCCUPSConfiguration conf) {
    method determineValidConfigurations (line 562) | private void determineValidConfigurations(CommandLineParserForJuicer j...
    method determineValidMatrixSize (line 595) | private void determineValidMatrixSize(CommandLineParserForJuicer juice...
    method determineValidMatrixSize (line 599) | private void determineValidMatrixSize(int specifiedMatrixSize) {
    method setHiCCUPSFDROEThresholds (line 609) | private void setHiCCUPSFDROEThresholds(double[] thresholds) {

FILE: src/juicebox/tools/clt/juicer/HiCCUPSDiff.java
  class HiCCUPSDiff (line 63) | public class HiCCUPSDiff extends JuicerCLT {
    method HiCCUPSDiff (line 75) | public HiCCUPSDiff() {
    method getBasicUsage (line 83) | public static String getBasicUsage() {
    method readJuicerArguments (line 87) | @Override
    method run (line 194) | @Override

FILE: src/juicebox/tools/clt/juicer/HiCCUPSRegionHandler.java
  class HiCCUPSRegionHandler (line 42) | public class HiCCUPSRegionHandler {
    method HiCCUPSRegionHandler (line 49) | public HiCCUPSRegionHandler(Dataset ds, ChromosomeHandler chromosomeHa...
    method calculateRegionBounds (line 120) | private int[] calculateRegionBounds(int index, int regionWidth, int ch...
    method getSize (line 133) | public int getSize() {
    method getRegionFromIndex (line 137) | public synchronized HiCCUPSRegionContainer getRegionFromIndex(int inde...
    method getZoomData (line 141) | public MatrixZoomData getZoomData(HiCCUPSRegionContainer regionContain...
    method getNormalizationVector (line 145) | public double[] getNormalizationVector(HiCCUPSRegionContainer regionCo...
    method getExpectedVector (line 149) | public double[] getExpectedVector(HiCCUPSRegionContainer regionContain...

FILE: src/juicebox/tools/clt/juicer/HiCCUPSscores.java
  class HiCCUPSscores (line 62) | public class HiCCUPSscores extends JuicerCLT {
    method HiCCUPSscores (line 111) | public HiCCUPSscores() {
    method getBasicUsage (line 118) | public static String getBasicUsage() {
    method readJuicerArguments (line 122) | @Override
    method initializeDirectly (line 170) | public void initializeDirectly(Dataset dataset, String outputDirectory...
    method run (line 209) | @Override
    method runHiccupsScoresProcessing (line 267) | private void runHiccupsScoresProcessing(Dataset ds, final HiCCUPSConfi...
    method runCoreCodeForHiCCUPS2 (line 333) | private void runCoreCodeForHiCCUPS2(HiCCUPSConfiguration conf, AtomicI...
    method buildGPUController (line 401) | private GPUController2 buildGPUController(HiCCUPSConfiguration conf) {
    method determineValidConfigurations (line 418) | private void determineValidConfigurations(CommandLineParserForJuicer j...
    method determineValidMatrixSize (line 451) | private void determineValidMatrixSize(CommandLineParserForJuicer juice...
    method determineValidMatrixSize (line 455) | private void determineValidMatrixSize(int specifiedMatrixSize) {
    method setHiCCUPSFDROEThresholds (line 465) | private void setHiCCUPSFDROEThresholds(double[] thresholds) {

FILE: src/juicebox/tools/clt/juicer/Localizer.java
  class Localizer (line 65) | public class Localizer extends JuicerCLT {
    method Localizer (line 92) | public Localizer() {
    method getBasicUsage (line 99) | public static String getBasicUsage() {
    method initializeDirectly (line 103) | public void initializeDirectly(String inputHiCFileName, String inputPe...
    method readJuicerArguments (line 117) | @Override
    method run (line 172) | @Override

FILE: src/juicebox/tools/clt/juicer/LoopDomains.java
  class LoopDomains (line 43) | public class LoopDomains extends JuicerCLT {
    method LoopDomains (line 73) | public LoopDomains() {
    method readJuicerArguments (line 80) | @Override
    method run (line 110) | @Override

FILE: src/juicebox/tools/clt/juicer/MotifFinder.java
  class MotifFinder (line 44) | public class MotifFinder extends JuicerCLT {
    method MotifFinder (line 56) | public MotifFinder() {
    method getIntersectionOfBEDFiles (line 61) | private static GenomeWideList<GenericLocus> getIntersectionOfBEDFiles(...
    method readJuicerArguments (line 70) | @Override
    method run (line 105) | @Override
    method findInferredMotifs (line 119) | private void findInferredMotifs(ChromosomeHandler handler, Feature2DLi...
    method setUpThreeTieredFiltration (line 167) | private void setUpThreeTieredFiltration() {
    method getThreeTierFilteredProteinTrack (line 181) | private GenomeWideList<GenericLocus> getThreeTierFilteredProteinTrack(...
    method findUniqueMotifs (line 211) | private void findUniqueMotifs(ChromosomeHandler handler, Feature2DList...
    method retrieveFreshMotifs (line 247) | private GenomeWideList<MotifAnchor> retrieveFreshMotifs() {
    method retrieveAllBEDFiles (line 268) | private void retrieveAllBEDFiles(String path) throws IOException {
    method retrieveBEDFilesByExtensionInFolder (line 287) | private List<String> retrieveBEDFilesByExtensionInFolder(String direct...

FILE: src/juicebox/tools/clt/old/AddNorm.java
  class AddNorm (line 43) | public class AddNorm extends JuiceboxCLT {
    method AddNorm (line 52) | public AddNorm() {
    method getBasicUsage (line 66) | public static String getBasicUsage() {
    method defaultHashMapForResToBuildTo (line 70) | public static Map<NormalizationType, Integer> defaultHashMapForResToBu...
    method launch (line 78) | public static void launch(String outputFile, List<NormalizationType> n...
    method readArguments (line 86) | @Override
    method run (line 130) | @Override

FILE: src/juicebox/tools/clt/old/BPToFragment.java
  class BPToFragment (line 40) | public class BPToFragment extends JuiceboxCLT {
    method BPToFragment (line 44) | public BPToFragment() {
    method bpToFrag (line 48) | private static void bpToFrag(String fragmentFile, String inputFile, St...
    method annotateWithSites (line 110) | private static void annotateWithSites(Map<String, int[]> fragmentMap, ...
    method getChrAlias (line 156) | private static String getChrAlias(String token) {
    method readArguments (line 166) | @Override
    method run (line 178) | @Override
    class BedLikeFeature (line 187) | private static class BedLikeFeature implements Locatable {
      method BedLikeFeature (line 195) | BedLikeFeature(String line) {
      method getStart (line 209) | public int getStart() {
      method setStart (line 213) | public void setStart(int start) {
      method getEnd (line 217) | public int getEnd() {
      method setEnd (line 221) | public void setEnd(int end) {
      method getScore (line 225) | public float getScore() {
      method getContig (line 229) | @Override

FILE: src/juicebox/tools/clt/old/BigWig.java
  class BigWig (line 32) | public class BigWig extends JuiceboxCLT {
    method BigWig (line 38) | public BigWig() {
    method readArguments (line 42) | @Override
    method run (line 65) | @Override

FILE: src/juicebox/tools/clt/old/BinToPairs.java
  class BinToPairs (line 32) | public class BinToPairs extends JuiceboxCLT {
    method BinToPairs (line 36) | public BinToPairs() {
    method readArguments (line 40) | @Override
    method run (line 49) | @Override

FILE: src/juicebox/tools/clt/old/CalcKR.java
  class CalcKR (line 42) | public class CalcKR extends JuiceboxCLT {
    method CalcKR (line 46) | public CalcKR() {
    method readArguments (line 50) | @Override
    method calcKR (line 59) | public static void calcKR(String path) throws IOException {
    method run (line 94) | @Override

FILE: src/juicebox/tools/clt/old/CalcMatrixSum.java
  class CalcMatrixSum (line 45) | public class CalcMatrixSum extends JuiceboxCLT {
    method CalcMatrixSum (line 52) | public CalcMatrixSum() {
    method getKeyWithNorm (line 56) | private static String getKeyWithNorm(Chromosome chromosome, HiCZoom zo...
    method readArguments (line 60) | @Override
    method run (line 82) | @Override
    method getNormMatrixSumFactor (line 171) | public Double[] getNormMatrixSumFactor(double[] norm, IteratorContaine...
    method testCode (line 198) | private void testCode(HiCZoom zoom, List<ContactRecord> contactRecordL...

FILE: src/juicebox/tools/clt/old/Dump.java
  class Dump (line 50) | public class Dump extends JuiceboxCLT {
    method Dump (line 68) | public Dump() {
    method getUsage (line 72) | public static String getUsage(){
    method dumpGenomeWideData (line 78) | private void dumpGenomeWideData() {
    method dumpGeneralVector (line 173) | private void dumpGeneralVector() {
    method dumpMatrix (line 226) | private void dumpMatrix() throws IOException {
    method dumpFeature (line 259) | private void dumpFeature() throws IOException {
    method readArguments (line 283) | @Override
    method setQuery (line 401) | public void setQuery(String chr1, String chr2, int binSize) {
    method getBpBinSizes (line 408) | public int[] getBpBinSizes() {
    method extractChromosomeRegionIndices (line 419) | private void extractChromosomeRegionIndices() {
    method run (line 475) | @Override
    method getChromosomeHandler (line 498) | public ChromosomeHandler getChromosomeHandler() {

FILE: src/juicebox/tools/clt/old/Eigenvector.java
  class Eigenvector (line 46) | public class Eigenvector extends JuiceboxCLT {
    method Eigenvector (line 53) | public Eigenvector() {
    method getUsage (line 57) | public static String getUsage(){
    method readArguments (line 61) | @Override
    method run (line 111) | @Override

FILE: src/juicebox/tools/clt/old/FragmentToBed.java
  class FragmentToBed (line 35) | public class FragmentToBed extends JuiceboxCLT {
    method FragmentToBed (line 39) | public FragmentToBed() {
    method fragToBed (line 49) | private static void fragToBed(String filename) throws IOException {
    method readArguments (line 81) | @Override
    method run (line 90) | @Override

FILE: src/juicebox/tools/clt/old/LibraryComplexity.java
  class LibraryComplexity (line 41) | public class LibraryComplexity extends JuiceboxCLT {
    method LibraryComplexity (line 51) | public LibraryComplexity(String command) {
    method getUsage (line 56) | private static String getUsage() {
    method estimateLibrarySize (line 73) | public static long estimateLibrarySize(final long duplicateReadPairs,
    method f (line 113) | private static double f(double x, double c, double n) {
    method readArguments (line 117) | @Override
    method determineCountsFromFile (line 147) | private void determineCountsFromFile(String file) throws IOException {
    method determineCountsFromInput (line 159) | private void determineCountsFromInput(String[] args) throws NumberForm...
    method run (line 165) | @Override

FILE: src/juicebox/tools/clt/old/PairsToBin.java
  class PairsToBin (line 33) | public class PairsToBin extends JuiceboxCLT {
    method PairsToBin (line 37) | public PairsToBin() {
    method readArguments (line 41) | @Override
    method run (line 51) | @Override

FILE: src/juicebox/tools/clt/old/Pearsons.java
  class Pearsons (line 54) | public class Pearsons extends JuiceboxCLT {
    method Pearsons (line 63) | public Pearsons() {
    method getBasicUsage (line 67) | public static String getBasicUsage(){
    method readPearsons (line 71) | public static BasicMatrix readPearsons(String path) throws IOException {
    method getVectorMean (line 102) | private static double getVectorMean(double[] vector) {
    method computePearsons (line 114) | public static BasicMatrix computePearsons(double[][] matrix, int dim, ...
    method computeParallelizedPearsons (line 164) | public static BasicMatrix computeParallelizedPearsons(double[][] matri...
    method inPlaceParallelSubtractRowMeans (line 211) | private static void inPlaceParallelSubtractRowMeans(double[][] matrix,...
    method readArguments (line 238) | @Override
    method run (line 283) | @Override
    method writeHeader (line 373) | private void writeHeader(LittleEndianOutputStream les, int dim, float ...

FILE: src/juicebox/tools/clt/old/PreProcessing.java
  class PreProcessing (line 44) | public class PreProcessing extends JuiceboxCLT {
    method PreProcessing (line 78) | public PreProcessing() {
    method getBasicUsage (line 82) | public static String getBasicUsage() {
    method readArguments (line 86) | @Override
    method run (line 167) | @Override

FILE: src/juicebox/tools/clt/old/SQLDatabase.java
  class SQLDatabase (line 34) | public class SQLDatabase extends JuiceboxCLT {
    method SQLDatabase (line 38) | public SQLDatabase() {
    method readArguments (line 42) | @Override
    method run (line 49) | @Override

FILE: src/juicebox/tools/clt/old/Statistics.java
  class Statistics (line 44) | public class Statistics extends JuiceboxCLT {
    method Statistics (line 55) | public Statistics() {
    method getUsage (line 59) | public static String getUsage() {
    method setMndIndex (line 73) | public void setMndIndex() {
    method readSiteFile (line 86) | private FragmentCalculation readSiteFile(String siteFile) {
    method readArguments (line 95) | @Override
    method tryToReadLocalHandler (line 140) | private void tryToReadLocalHandler(String genomeID) {
    method run (line 150) | @Override

FILE: src/juicebox/tools/clt/old/Summation.java
  class Summation (line 43) | public class Summation extends JuiceboxCLT {
    method Summation (line 50) | public Summation() {
    method getBasicUsage (line 54) | public static String getBasicUsage() {
    method readArguments (line 58) | @Override
    method run (line 115) | @Override
    method populateParameters (line 137) | private void populateParameters(String hicFile, String[] genomeId, Lis...
    method cleanUpGenome (line 152) | private String cleanUpGenome(String genomeId) {
    method getRemainingFiles (line 161) | private String getRemainingFiles(String[] args) {

FILE: src/juicebox/tools/clt/old/ValidateFile.java
  class ValidateFile (line 42) | public class ValidateFile extends JuiceboxCLT {
    method ValidateFile (line 46) | public ValidateFile() {
    method getUsage (line 50) | public static String getUsage() {
    method readArguments (line 54) | @Override
    method run (line 62) | @Override

FILE: src/juicebox/tools/dev/APAvsDistance.java
  class APAvsDistance (line 70) | public class APAvsDistance extends JuicerCLT  {
    method APAvsDistance (line 86) | public APAvsDistance() {
    method getBasicUsage (line 93) | public static String getBasicUsage() {
    method initializeDirectly (line 97) | public void initializeDirectly(String inputHiCFileName, String inputPe...
    method readJuicerArguments (line 108) | @Override
    method printResults (line 160) | private static void printResults(String[] windows, double[] results, S...
    method plotChart (line 175) | private static void plotChart(String SaveFolderPath, XYSeries results) {
    method run (line 210) | @Override

FILE: src/juicebox/tools/dev/ChromosomeCalculation.java
  class ChromosomeCalculation (line 41) | public class ChromosomeCalculation {
    method sum (line 43) | public static void sum(int resolution, int slidingWindow, String fileP...
    method slidingAverageAcrossData (line 98) | public static void slidingAverageAcrossData(int slidingWindow, Map<Chr...
    method writeDataToFile (line 119) | private static void writeDataToFile(Map<Chromosome, Map<Integer, Float...
    method sumColumn (line 145) | private static void sumColumn(MatrixZoomData zd,
    method calculateLogEnrichmentOfObservedOverExpected (line 191) | public static void calculateLogEnrichmentOfObservedOverExpected(Map<Ch...

FILE: src/juicebox/tools/dev/CompareVectors.java
  class CompareVectors (line 40) | public class CompareVectors extends JuiceboxCLT {
    method CompareVectors (line 47) | public CompareVectors() {
    method getUsage (line 51) | private static String getUsage() {
    method readArguments (line 55) | @Override
    method run (line 78) | @Override
    method fillInVector (line 103) | private void fillInVector(double[][] array, NormalizationVector nv, in...

FILE: src/juicebox/tools/dev/GeneFinder.java
  class GeneFinder (line 50) | public class GeneFinder extends JuicerCLT {
    method GeneFinder (line 55) | public GeneFinder() {
    method readJuicerArguments (line 59) | @Override
    method run (line 76) | @Override

FILE: src/juicebox/tools/dev/HiCArtMNDWriter.java
  class HiCArtMNDWriter (line 30) | class HiCArtMNDWriter {
    method main (line 32) | public static void main(String[] args) {
    method writeMergedNoDupsFromTimeSeq (line 36) | private static void writeMergedNoDupsFromTimeSeq(String seqPath, Strin...

FILE: src/juicebox/tools/dev/IntraChromTriple.java
  class IntraChromTriple (line 34) | public class IntraChromTriple extends Feature implements Comparable<Intr...
    method IntraChromTriple (line 38) | public IntraChromTriple(int chrIndex, int x1, int x2, int x3) {
    method IntraChromTriple (line 45) | private IntraChromTriple(int chrIndex, List<Integer> ints) {
    method parse (line 57) | public static IntraChromTriple parse(String line, ChromosomeHandler ha...
    method compareTo (line 80) | @Override
    method getKey (line 89) | @Override
    method toString (line 94) | @Override
    method deepClone (line 99) | @Override
    method getX1 (line 104) | public Integer getX1() {
    method getX2 (line 108) | public Integer getX2() {
    method getX3 (line 112) | public Integer getX3() {
    method toTripleCentroid (line 116) | public TripleCentroid toTripleCentroid() {

FILE: src/juicebox/tools/dev/MapSelectionPanel.java
  class MapSelectionPanel (line 43) | class MapSelectionPanel extends JPanel {
    method MapSelectionPanel (line 52) | private MapSelectionPanel(SuperAdapter superAdapter, Dataset reader, D...
    method launchMapSubsetGUI (line 77) | public static void launchMapSubsetGUI(SuperAdapter superAdapter) {
    method generateMapActivationPanel (line 97) | private JPanel generateMapActivationPanel(final SuperAdapter superAdap...
    method createPane (line 125) | private JPanel createPane(String description, List<JCheckBox> checkBox...

FILE: src/juicebox/tools/dev/ParallelizedJuicerTools.java
  class ParallelizedJuicerTools (line 30) | public class ParallelizedJuicerTools {
    method launchParallelizedCode (line 32) | public static void launchParallelizedCode(Runnable runnable) {
    method launchParallelizedCode (line 36) | public static void launchParallelizedCode(int numCPUThreads, Runnable ...

FILE: src/juicebox/tools/dev/Private.java
  class Private (line 32) | public class Private {
    method assessGenomeForRE (line 34) | public static boolean assessGenomeForRE(String genomeId) {
    method assessGenomeForRE2 (line 38) | public static boolean assessGenomeForRE2(String genomeId) {
    method reForDMEL (line 42) | public static String reForDMEL(int sites) {
    method assessGenomeForRE3 (line 47) | public static boolean assessGenomeForRE3(String genomeId) {
    method reForHG18 (line 51) | public static String reForHG18(int sites) {
    method reForHG19 (line 56) | public static String reForHG19(int sites) {
    method reForMM9 (line 80) | public static String reForMM9(int sites) {
    method assessGenomeForRE4 (line 86) | public static boolean assessGenomeForRE4(String genomeId) {
    method launchMapSubsetGUI (line 90) | public static void launchMapSubsetGUI(SuperAdapter superAdapter) {

FILE: src/juicebox/tools/dev/RandomUtils.java
  class RandomUtils (line 37) | class RandomUtils {
    method intersectLoopLists (line 58) | public static void intersectLoopLists(String genomeID, String[] fileNa...

FILE: src/juicebox/tools/dev/TripleCentroid.java
  class TripleCentroid (line 30) | public class TripleCentroid {
    method TripleCentroid (line 40) | public TripleCentroid(Integer chrIndex, Integer x1, Integer x2, Intege...
    method consumeDuplicate (line 50) | public void consumeDuplicate(IntraChromTriple triple) {
    method average (line 59) | private Integer average(Set<Integer> xs) {
    method hasOverlapWithTriple (line 67) | public boolean hasOverlapWithTriple(IntraChromTriple triple, int toler...
    method toIntraChromTriple (line 74) | public IntraChromTriple toIntraChromTriple() {

FILE: src/juicebox/tools/dev/TriplesAPA.java
  class TriplesAPA (line 40) | public class TriplesAPA extends JuicerCLT {
    method TriplesAPA (line 41) | public TriplesAPA() {
    method removeAnchorsThatAreTooCloseTogether (line 45) | private static void removeAnchorsThatAreTooCloseTogether(GenomeWideLis...
    method readInIntraChromTriple (line 61) | private static GenomeWideList<IntraChromTriple> readInIntraChromTriple...
    method readJuicerArguments (line 76) | @Override
    method run (line 81) | @Override
    method threeDimSearching (line 127) | private void threeDimSearching(GenomeWideList<IntraChromTriple> triple...
    method threeDimHandling (line 175) | private void threeDimHandling(GenomeWideList<IntraChromTriple> triples...
    method makeKey (line 241) | private String makeKey(int diff_1, int diff_2, int diff_3) {
    method dedupTriples (line 245) | private void dedupTriples(GenomeWideList<IntraChromTriple> anchors, fi...
    method translateAnchors (line 271) | private void translateAnchors(GenomeWideList<GenericLocus> anchors, fi...

FILE: src/juicebox/tools/utils/Benchmark.java
  class Benchmark (line 40) | public class Benchmark extends JuiceboxCLT {
    method Benchmark (line 47) | public Benchmark() {
    method getUsage (line 51) | private static String getUsage() {
    method readArguments (line 55) | @Override
    method run (line 76) | @Override

FILE: src/juicebox/tools/utils/common/ArrayTools.java
  class ArrayTools (line 37) | public class ArrayTools {
    method deepCopy (line 42) | public static float[][] deepCopy(float[][] original) {
    method mean (line 53) | public static double mean(double[] doubles) {
    method generatePoissonPMF (line 68) | public static double[] generatePoissonPMF(int index, int width) {
    method makeReverseCumulativeArray (line 82) | public static float[] makeReverseCumulativeArray(float[] inputArray) {
    method makeReverseCumulativeArray (line 92) | private static long[] makeReverseCumulativeArray(long[] inputArray) {
    method makeReverse2DCumulativeArray (line 102) | public static long[][] makeReverse2DCumulativeArray(long[][] data) {
    method newValueInitializedFloatArray (line 113) | public static float[] newValueInitializedFloatArray(int n, float val) {
    method scalarMultiplyArray (line 119) | public static float[] scalarMultiplyArray(long scaleFactor, float[] ar...
    method padEndOfArray (line 135) | public static float[] padEndOfArray(float[] original, int length, floa...
    method extractIntegers (line 144) | public static int[] extractIntegers(List<String> stringList) {
    method extractFloats (line 155) | public static float[] extractFloats(List<String> stringList) {
    method preInitializeIntArray (line 166) | public static int[] preInitializeIntArray(int val, int n) {
    method preInitializeFloatArray (line 174) | public static float[] preInitializeFloatArray(float val, int n) {
    method inverseArrayValues (line 182) | public static float[] inverseArrayValues(float[] array) {
    method preInitializeDoubleArray (line 190) | public static double[] preInitializeDoubleArray(double val, int n) {
    method extractDoubles (line 198) | public static double[] extractDoubles(List<String> stringList) {
    method inverseArrayValues (line 209) | public static double[] inverseArrayValues(double[] array) {
    method flipArrayValues (line 217) | public static double[] flipArrayValues(double[] array) {
    method exportChr1DArrayToWigFormat (line 232) | public static void exportChr1DArrayToWigFormat(double[] vector, PrintW...
    method runSlidingAverageOnArray (line 239) | public static float[] runSlidingAverageOnArray(int radius, float[] val...

FILE: src/juicebox/tools/utils/common/HiCFileUtils.java
  class HiCFileUtils (line 45) | class HiCFileUtils {
    method HiCFileUtils (line 49) | private HiCFileUtils(String hicfile) throws IOException {
    method main (line 54) | public static void main(String[] args) throws IOException {
    method dumpNormalizationVectors (line 60) | private void dumpNormalizationVectors(NormalizationType normType, Stri...
    method dumpExpectedVectors (line 79) | private void dumpExpectedVectors(NormalizationType normType, HiC.Unit ...
    method findChromosome (line 112) | private Chromosome findChromosome(String name) {

FILE: src/juicebox/tools/utils/common/MatrixTools.java
  class MatrixTools (line 47) | public class MatrixTools {
    method cleanArray2DMatrix (line 52) | public static RealMatrix cleanArray2DMatrix(int n) {
    method cleanArray2DMatrix (line 59) | public static RealMatrix cleanArray2DMatrix(int rows, int cols) {
    method ones (line 66) | public static RealMatrix ones(int n) {
    method ones (line 73) | private static RealMatrix ones(int rows, int cols) {
    method presetValueMatrix (line 80) | private static RealMatrix presetValueMatrix(int numRows, int numCols, ...
    method randomUnitMatrix (line 91) | public static RealMatrix randomUnitMatrix(int n) {
    method randomUnitMatrix (line 102) | private static RealMatrix randomUnitMatrix(int rows, int cols) {
    method minimumPositive (line 115) | public static double minimumPositive(RealMatrix data) {
    method minimumPositive (line 122) | private static double minimumPositive(double[][] data) {
    method mean (line 138) | public static double mean(RealMatrix matrix) {
    method flattenedRowMajorOrderMatrix (line 148) | public static double[] flattenedRowMajorOrderMatrix(RealMatrix matrix) {
    method flattenedRowMajorOrderMatrix (line 162) | public static double[] flattenedRowMajorOrderMatrix(double[][] matrix) {
    method flattenedRowMajorOrderMatrix (line 177) | public static float[] flattenedRowMajorOrderMatrix(float[][] matrix) {
    method flattenedRowMajorOrderMatrix (line 192) | public static int[] flattenedRowMajorOrderMatrix(int[][] matrix) {
    method saveMatrixText (line 214) | public static void saveMatrixText(String filename, RealMatrix realMatr...
    method reshapeFlatMatrix (line 241) | public static float[][] reshapeFlatMatrix(float[] flatMatrix, int n) {
    method reshapeFlatMatrix (line 253) | private static float[][] reshapeFlatMatrix(float[] flatMatrix, int num...
    method extractLocalMatrixRegion (line 268) | public static float[][] extractLocalMatrixRegion(float[][] matrix, int...
    method extractLocalMatrixRegion (line 287) | public static RealMatrix extractLocalMatrixRegion(RealMatrix matrix, i...
    method extractDiagonal (line 307) | public static RealMatrix extractDiagonal(RealMatrix matrix) {
    method makeSymmetricMatrix (line 322) | public static RealMatrix makeSymmetricMatrix(RealMatrix matrix) {
    method flipAcrossAntiDiagonal (line 339) | public static RealMatrix flipAcrossAntiDiagonal(RealMatrix matrix) {
    method flipLeftRight (line 354) | public static RealMatrix flipLeftRight(RealMatrix matrix) {
    method flipTopBottom (line 368) | public static RealMatrix flipTopBottom(RealMatrix matrix) {
    method elementBasedMultiplication (line 382) | public static RealMatrix elementBasedMultiplication(RealMatrix matrix1...
    method elementBasedDivision (line 400) | public static RealMatrix elementBasedDivision(RealMatrix matrix1, Real...
    method setNaNs (line 418) | public static void setNaNs(RealMatrix matrix, int val) {
    method sign (line 434) | public static RealMatrix sign(RealMatrix matrix) {
    method replaceValue (line 454) | public static void replaceValue(RealMatrix matrix, int initialVal, int...
    method normalizeByMax (line 469) | public static RealMatrix normalizeByMax(RealMatrix matrix) {
    method calculateMax (line 477) | public static double calculateMax(RealMatrix matrix) {
    method calculateMin (line 493) | public static double calculateMin(RealMatrix matrix) {
    method print (line 509) | public static void print(RealMatrix matrix) {
    method print (line 516) | private static void print(double[][] data) {
    method print (line 525) | private static void print(float[][] data) {
    method getSubMatrix (line 534) | public static RealMatrix getSubMatrix(RealMatrix matrix, int[] indices) {
    method fillLowerLeftTriangle (line 544) | public static RealMatrix fillLowerLeftTriangle(RealMatrix matrix) {
    method thresholdValues (line 551) | public static void thresholdValues(RealMatrix matrix, int val) {
    method thresholdValuesDouble (line 561) | public static void thresholdValuesDouble(RealMatrix matrix, double low...
    method normalizeMatrixUsingColumnSum (line 574) | public static int[][] normalizeMatrixUsingColumnSum(int[][] matrix) {
    method normalizeMatrixUsingRowSum (line 592) | public static int[][] normalizeMatrixUsingRowSum(int[][] matrix) {
    method getRowSums (line 605) | public static int[] getRowSums(int[][] matrix) {
    method getRowSums (line 615) | public static double[] getRowSums(double[][] matrix) {
    method getAbsValColSums (line 625) | public static float[] getAbsValColSums(float[][] matrix) {
    method getAbsValColSums (line 635) | public static int[] getAbsValColSums(int[][] matrix) {
    method getRowSums (line 645) | public static float[] getRowSums(float[][] matrix) {
    method getRowSums (line 655) | public static double[] getRowSums(List<ContactRecord> unNormedRecordLi...
    method cleanUpNaNs (line 672) | public static void cleanUpNaNs(RealMatrix matrix) {
    method cleanUpNaNs (line 682) | public static void cleanUpNaNs(double[][] matrix) {
    method cleanUpNaNs (line 692) | public static void cleanUpNaNs(float[][] matrix) {
    method sum (line 702) | public static double sum(double[][] data) {
    method getAverage (line 712) | public static double getAverage(RealMatrix data) {
    method getAverage (line 716) | private static double getAverage(double[][] data) {
    method exportData (line 730) | public static void exportData(double[][] data, File file) {
    method transpose (line 753) | public static double[][] transpose(double[][] matrix) {
    method transpose (line 766) | public static float[][] transpose(float[][] matrix) {
    method convertToDoubleMatrix (line 779) | public static double[][] convertToDoubleMatrix(boolean[][] adjacencyMa...
    method convertToDoubleMatrix (line 791) | public static double[][] convertToDoubleMatrix(int[][] adjacencyMatrix) {
    method convertToFloatMatrix (line 801) | public static float[][] convertToFloatMatrix(double[][] dataMatrix) {
    method copyFromAToBRegion (line 811) | public static void copyFromAToBRegion(double[][] source, double[][] de...
    method copyFromAToBRegion (line 817) | public static void copyFromAToBRegion(float[][] source, float[][] dest...
    method saveMatrixTextV2 (line 823) | public static void saveMatrixTextV2(String filename, RealMatrix realMa...
    method saveMatrixTextV2 (line 827) | public static void saveMatrixTextV2(String filename, double[][] matrix) {
    method saveMatrixTextV2 (line 848) | public static void saveMatrixTextV2(String filename, float[][] matrix) {
    method saveMatrixTextV2 (line 869) | public static void saveMatrixTextV2(String filename, int[][] matrix) {
    method saveMatrixTextNumpy (line 890) | public static void saveMatrixTextNumpy(String filename, double[][] mat...
    method saveMatrixTextNumpy (line 898) | public static void saveMatrixTextNumpy(String filename, float[][] matr...
    method saveMatrixTextNumpy (line 906) | public static void saveMatrixTextNumpy(String filename, int[][] matrix) {
    method saveMatrixTextNumpy (line 914) | public static void saveMatrixTextNumpy(String filename, int[] matrix) {
    method saveMatrixTextNumpy (line 918) | public static void saveMatrixTextNumpy(String filename, double[] matri...
    method generateCompositeMatrixWithNansCleaned (line 922) | public static float[][] generateCompositeMatrixWithNansCleaned(RealMat...
    method generateCompositeMatrixWithNansCleaned (line 929) | private static float[][] generateCompositeMatrixWithNansCleaned(float[...
    method deepClone (line 947) | public static double[][] deepClone(double[][] data) {
    method deepClone (line 955) | public static float[][] deepClone(float[][] data) {
    method labelRegionWithOnes (line 963) | public static void labelRegionWithOnes(int[][] labelsMatrix, int rowLe...
    method labelEnrichedRegionWithOnes (line 971) | public static void labelEnrichedRegionWithOnes(int[][] labelsMatrix, d...
    method stitchMultipleMatricesTogetherByRowDim (line 993) | public static double[][] stitchMultipleMatricesTogetherByRowDim(List<d...
    method takeDerivativeDownColumn (line 1013) | public static double[][] takeDerivativeDownColumn(double[][] data) {
    method smoothAndAppendDerivativeDownColumn (line 1028) | public static double[][] smoothAndAppendDerivativeDownColumn(double[][...
    method getNormalizedThresholdedAndAppendedDerivativeDownColumn (line 1060) | public static float[][] getNormalizedThresholdedAndAppendedDerivativeD...
    method getNormalizedThresholdedByMedian (line 1083) | public static float[][] getNormalizedThresholdedByMedian(float[][] dat...
    method getMedian (line 1100) | public static double getMedian(float[] values) {
    method getMainAppendedDerivativeScaledPosDownColumn (line 1110) | public static float[][] getMainAppendedDerivativeScaledPosDownColumn(f...
    method getMainAppendedDerivativeDownColumnV2 (line 1126) | public static float[][] getMainAppendedDerivativeDownColumnV2(float[][...
    method getMainAppendedDerivativeDownColumn (line 1148) | public static float[][] getMainAppendedDerivativeDownColumn(float[][] ...
    method getRelevantDerivativeScaledPositive (line 1164) | public static float[][] getRelevantDerivativeScaledPositive(float[][] ...
    method getRelevantDerivative (line 1193) | public static float[][] getRelevantDerivative(float[][] data, float sc...
    method getRelevantDiscreteIntDerivativeScaledPositive (line 1222) | public static float[][] getRelevantDiscreteIntDerivativeScaledPositive...

FILE: src/juicebox/tools/utils/common/ShellCommandRunner.java
  class ShellCommandRunner (line 30) | public class ShellCommandRunner {
    method runShellFile (line 31) | public static void runShellFile(String command, String filepath) {

FILE: src/juicebox/tools/utils/common/StatPercentile.java
  class StatPercentile (line 29) | public class StatPercentile {
    method StatPercentile (line 33) | public StatPercentile(double[] data) {
    method evaluate (line 41) | public double evaluate(double val) {
    method internalEvaluate (line 49) | private double internalEvaluate(double val) {

FILE: src/juicebox/tools/utils/common/UNIXTools.java
  class UNIXTools (line 38) | public class UNIXTools {
    method extractElement (line 39) | public static String extractElement(String str, int i) {
    method makeDir (line 44) | public static String makeDir(String path) {
    method makeDir (line 52) | public static File makeDir(File folder) {
    method redirectOutput (line 59) | public static void redirectOutput(List<String> command, String outputF...
    method executeSimpleCommand (line 73) | public static String executeSimpleCommand(String command) {
    method executeComplexCommand (line 91) | private static String executeComplexCommand(List<String> command) {

FILE: src/juicebox/tools/utils/dev/AFAUtils.java
  class AFAUtils (line 40) | class AFAUtils {
    method filterFeaturesByAttribute (line 41) | public static List<Feature2D> filterFeaturesByAttribute(List<Feature2D...
    method extractLocalizedData (line 82) | public static RealMatrix extractLocalizedData(MatrixZoomData zd, Featu...

FILE: src/juicebox/tools/utils/dev/LocalGenomeRegion.java
  class LocalGenomeRegion (line 31) | public class LocalGenomeRegion {
    method LocalGenomeRegion (line 37) | public LocalGenomeRegion(int initialIndex, int maxNumValsToStore) {
    method addNeighbor (line 42) | public synchronized void addNeighbor(int y, float counts) {
    method filterDownValues (line 50) | public synchronized void filterDownValues(int numNeighborsAllowed) {
    method notConnectedWith (line 65) | public synchronized boolean notConnectedWith(int index) {
    method getOutlierContacts (line 74) | public synchronized int getOutlierContacts(boolean isBadUpstream, int ...
    method toString (line 95) | @Override
    class Neighbor (line 106) | private class Neighbor implements Comparable<Neighbor> {
      method Neighbor (line 110) | Neighbor(int index, float value) {
      method compareTo (line 115) | @Override

FILE: src/juicebox/tools/utils/dev/LocationType.java
  type LocationType (line 30) | public enum LocationType {
    method LocationType (line 36) | LocationType(String label) {
    method enumValueFromString (line 40) | public static LocationType enumValueFromString(String text) {
    method getLabel (line 51) | public String getLabel() {

FILE: src/juicebox/tools/utils/dev/PearsonCorrelationMetric.java
  class PearsonCorrelationMetric (line 27) | public class PearsonCorrelationMetric {
    method corr (line 29) | public static double corr(final double[] x, final double[] y) {

FILE: src/juicebox/tools/utils/juicer/GeneTools.java
  class GeneTools (line 48) | public class GeneTools {
    method getStreamToGeneFile (line 51) | public static BufferedReader getStreamToGeneFile(String genomeID) {
    method extractProperGeneFilePath (line 62) | private static String extractProperGeneFilePath(String genomeID) {
    method getLocationMap (line 80) | public static Map<String, GeneLocation> getLocationMap(BufferedReader ...
    method parseGenome (line 103) | public static GenomeWideList<GenericLocus> parseGenome(String genomeID...
    method extractAllGenes (line 109) | private static List<GenericLocus> extractAllGenes(BufferedReader reade...

FILE: src/juicebox/tools/utils/juicer/apa/APADataStack.java
  class APADataStack (line 41) | public class APADataStack {
    method APADataStack (line 70) | public APADataStack(int n, File outputFolder, String customPrefix) {
    method initializeDataSaveFolder (line 88) | public static void initializeDataSaveFolder(File outputFolderDirectory...
    method initializeGenomeWideVariables (line 98) | private static void initializeGenomeWideVariables(int n) {
    method exportGenomeWideData (line 110) | public static void exportGenomeWideData(Integer[] peakNumbers, int cur...
    method retrieveDataStatistics (line 122) | public static APARegionStatistics retrieveDataStatistics(int currentRe...
    method saveDataSet (line 126) | private static void saveDataSet(String prefix,
    method clearAllData (line 162) | public static void clearAllData() {
    method addData (line 173) | public void addData(RealMatrix newData) {
    method updateGenomeWideData (line 182) | public synchronized void updateGenomeWideData() {
    method exportDataSet (line 192) | public void exportDataSet(String subFolderName, Integer[] peakNumbers,...
    method thresholdPlots (line 204) | public void thresholdPlots(int val) {

FILE: src/juicebox/tools/utils/juicer/apa/APAPlotter.java
  class APAPlotter (line 43) | class APAPlotter {
    method plot (line 75) | public static void plot(RealMatrix dataOriginal, int[] axesRange, File...
    method initializeSizes (line 165) | private static void initializeSizes(HeatChart heatMap) {
    method getImageDimensions (line 186) | private static Dimension getImageDimensions(Image image) {
    method calculateIdealNumDivisions (line 197) | private static int calculateIdealNumDivisions(int range) {
    method plotColorScaleBar (line 209) | private static void plotColorScaleBar(Graphics2D g2) {
    method plotColorScaleValues (line 232) | private static void plotColorScaleValues(Graphics2D g2, HeatChart heat...
    method plotSpecialColorScaleValues (line 261) | private static void plotSpecialColorScaleValues(Graphics2D g2, HeatCha...
    method drawHeatMapBorder (line 291) | private static void drawHeatMapBorder(Graphics2D g2, HeatChart heatMap) {
    method drawCornerRegions (line 310) | private static void drawCornerRegions(Graphics2D g2, HeatChart map, Di...
    method drawCenteredDouble (line 349) | private static void drawCenteredDouble(Graphics2D g2, Double value, Po...
    method drawCenteredString (line 361) | private static void drawCenteredString(Graphics2D g2, String text, Poi...

FILE: src/juicebox/tools/utils/juicer/apa/APARegionStatistics.java
  class APARegionStatistics (line 34) | public class APARegionStatistics {
    method APARegionStatistics (line 52) | public APARegionStatistics(RealMatrix data, int regionWidth) {
    method statistics (line 77) | public static DescriptiveStatistics statistics(double[][] x) {
    method mean (line 85) | private static double mean(double[][] x) {
    method getPeak2mean (line 89) | public double getPeak2mean() {
    method getPeak2UL (line 93) | public double getPeak2UL() {
    method getPeak2UR (line 97) | public double getPeak2UR() {
    method getPeak2LL (line 101) | public double getPeak2LL() {
    method getPeak2LR (line 105) | public double getPeak2LR() {
    method getZscoreLL (line 109) | public double getZscoreLL() {
    method getRegionCornerValues (line 113) | public double[] getRegionCornerValues() {
    method getMeanUR (line 117) | public double getMeanUR() {

FILE: src/juicebox/tools/utils/juicer/apa/APAUtils.java
  class APAUtils (line 44) | public class APAUtils {
    method saveMeasures (line 50) | public static void saveMeasures(String filename, RealMatrix matrix, in...
    method saveListText (line 76) | public static void saveListText(String filename, List<Double> array) {
    method standardNormalization (line 96) | public static RealMatrix standardNormalization(RealMatrix matrix) {
    method centerNormalization (line 101) | public static RealMatrix centerNormalization(RealMatrix matrix) {
    method peakEnhancement (line 115) | public static double peakEnhancement(RealMatrix matrix) {
    method rankPercentile (line 129) | public static RealMatrix rankPercentile(RealMatrix data) {
    method filterFeaturesBySize (line 156) | public static ArrayList<Feature2D> filterFeaturesBySize(List<Feature2D...
    method extractLocalizedData (line 174) | public static RealMatrix extractLocalizedData(MatrixZoomData zd, Featu...
    method extractLocalizedDataForAFA (line 186) | public static RealMatrix extractLocalizedDataForAFA(MatrixZoomData zd,...
    method linearInterpolation (line 207) | public static RealMatrix linearInterpolation (RealMatrix original, int...
    method expandWithZeros (line 267) | public static RealMatrix expandWithZeros (RealMatrix original, int tar...
    method boxSampling (line 277) | public static RealMatrix boxSampling (RealMatrix original, int targetN...
    method maxInMatrix (line 299) | public static double maxInMatrix (RealMatrix matrix){
    method lcm (line 311) | static int lcm (int a, int b){
    method gcd (line 314) | static int gcd (int a, int b){
    method matrixScaling (line 320) | public static RealMatrix matrixScaling (RealMatrix original, int targe...

FILE: src/juicebox/tools/utils/juicer/arrowhead/ArrowheadScore.java
  class ArrowheadScore (line 37) | public class ArrowheadScore {
    method ArrowheadScore (line 42) | public ArrowheadScore(long[] indices) {
    method ArrowheadScore (line 51) | public ArrowheadScore(ArrowheadScore arrowheadScore) {
    method updateScore (line 57) | public void updateScore(double score) {
    method isWithin (line 70) | public boolean isWithin(int limStart, int limEnd, int resolution) {
    method equivalentTo (line 79) | public boolean equivalentTo(ArrowheadScore mScore) {
    method toFeature2D (line 83) | public Feature2D toFeature2D(String chrName) {

FILE: src/juicebox/tools/utils/juicer/arrowhead/ArrowheadScoreList.java
  class ArrowheadScoreList (line 39) | public class ArrowheadScoreList {
    method ArrowheadScoreList (line 44) | public ArrowheadScoreList(int resolution) {
    method ArrowheadScoreList (line 48) | public ArrowheadScoreList(Feature2DList features, Chromosome chr, int ...
    method deepCopy (line 57) | public ArrowheadScoreList deepCopy() {
    method updateActiveIndexScores (line 65) | public ArrowheadScoreList updateActiveIndexScores(RealMatrix blockScor...
    method scaleAndTranslateIndices (line 82) | private int[] scaleAndTranslateIndices(long[] indices, int resolution,...
    method setActiveListElements (line 91) | private void setActiveListElements(int limStart, int limEnd) {
    method addAll (line 103) | public void addAll(ArrowheadScoreList arrowheadScoreList) {
    method mergeScores (line 107) | public void mergeScores() {
    method toFeature2DList (line 127) | public Feature2DList toFeature2DList(int chrIndex, String chrName) {

FILE: src/juicebox/tools/utils/juicer/arrowhead/BinnedScore.java
  class BinnedScore (line 37) | class BinnedScore {
    method BinnedScore (line 49) | public BinnedScore(HighScore score) {
    method convertBinnedScoresToHighScores (line 57) | public static List<HighScore> convertBinnedScoresToHighScores(List<Bin...
    method isNear (line 68) | public boolean isNear(HighScore score, int distanceThreshold) {
    method addScoreToBin (line 76) | public void addScoreToBin(HighScore score) {
    method appendDataValues (line 91) | private void appendDataValues(HighScore score) {
    method convertToHighScore (line 102) | private HighScore convertToHighScore() {

FILE: src/juicebox/tools/utils/juicer/arrowhead/BlockBuster.java
  class BlockBuster (line 43) | public class BlockBuster {
    method run (line 57) | public static void run(Chromosome chrom, int resolution, int matrixWid...
    method callSubBlockbuster (line 143) | private static CumulativeBlockResults callSubBlockbuster(MatrixZoomDat...
    method binScoresByDistance (line 199) | private static List<HighScore> binScoresByDistance(List<HighScore> sco...
    method appendNonConflictingBlocks (line 226) | private static void appendNonConflictingBlocks(List<HighScore> mainLis...
    method filterBlocksBySize (line 257) | private static List<HighScore> filterBlocksBySize(List<HighScore> bloc...
    method orderedSetDifference (line 274) | private static List<HighScore> orderedSetDifference(List<HighScore> li...

FILE: src/juicebox/tools/utils/juicer/arrowhead/BlockResults.java
  class BlockResults (line 41) | class BlockResults {
    method BlockResults (line 47) | public BlockResults(RealMatrix observed, double varThreshold, double s...
    method calculateDirectionalityIndexUpstream (line 76) | private RealMatrix calculateDirectionalityIndexUpstream(RealMatrix obs...
    method getResults (line 110) | public List<HighScore> getResults() {
    method getInternalList (line 114) | public ArrowheadScoreList getInternalList() {
    method getInternalControl (line 118) | public ArrowheadScoreList getInternalControl() {
    method offsetResultsIndex (line 122) | public void offsetResultsIndex(int offset) {

FILE: src/juicebox/tools/utils/juicer/arrowhead/CumulativeBlockResults.java
  class CumulativeBlockResults (line 33) | class CumulativeBlockResults {
    method CumulativeBlockResults (line 39) | public CumulativeBlockResults(int resolution) {
    method add (line 45) | public void add(BlockResults blockResults) {
    method getCumulativeInternalControl (line 51) | public ArrowheadScoreList getCumulativeInternalControl() {
    method getCumulativeResults (line 55) | public List<HighScore> getCumulativeResults() {
    method setCumulativeResults (line 59) | public void setCumulativeResults(List<HighScore> cumulativeResults) {
    method getCumulativeInternalList (line 63) | public ArrowheadScoreList getCumulativeInternalList() {
    method mergeScores (line 67) | public void mergeScores() {
    method scaleIndicesByResolution (line 72) | public void scaleIndicesByResolution(int resolution) {

FILE: src/juicebox/tools/utils/juicer/arrowhead/DynamicProgrammingUtils.java
  class DynamicProgrammingUtils (line 33) | class DynamicProgrammingUtils {
    method sum (line 44) | public static RealMatrix sum(RealMatrix matrix, int superDiagonal) {
    method right (line 76) | public static RealMatrix right(RealMatrix matrix, int maxSize) {
    method upper (line 100) | public static RealMatrix upper(RealMatrix matrix, int maxSize) {

FILE: src/juicebox/tools/utils/juicer/arrowhead/HighScore.java
  class HighScore (line 38) | public class HighScore implements Comparable<HighScore> {
    method HighScore (line 47) | public HighScore(int i, int j, double score, double uVarScore, double ...
    method toString (line 58) | public String toString() {
    method offsetIndex (line 62) | public void offsetIndex(int offset) {
    method scaleIndicesByResolution (line 67) | public void scaleIndicesByResolution(int resolution) {
    method getWidth (line 72) | public int getWidth() {
    method getI (line 76) | public int getI() {
    method getJ (line 80) | public int getJ() {
    method getLoSign (line 84) | public double getLoSign() {
    method getScore (line 88) | public double getScore() {
    method getuVarScore (line 92) | public double getuVarScore() {
    method getlVarScore (line 96) | public double getlVarScore() {
    method getUpSign (line 100) | public double getUpSign() {
    method equals (line 104) | @Override
    method hashCode (line 122) | @Override
    method compareTo (line 127) | @Override
    method sortValue (line 132) | private double sortValue() {
    method toFeature2D (line 136) | public Feature2D toFeature2D(String chrName, int res) {

FILE: src/juicebox/tools/utils/juicer/arrowhead/MatrixTriangles.java
  class MatrixTriangles (line 39) | class MatrixTriangles {
    method MatrixTriangles (line 62) | public MatrixTriangles(RealMatrix matrix) {
    method generateBlockScoreCalculations (line 143) | public void generateBlockScoreCalculations() {
    method thresholdScoreValues (line 165) | public void thresholdScoreValues(double varThreshold, double signThres...
    method varThresholdInternalValues (line 186) | private void varThresholdInternalValues(RealMatrix matrix, RealMatrix ...
    method signThresholdInternalValues (line 204) | private void signThresholdInternalValues(RealMatrix matrix, RealMatrix...
    method updateScoresUsingList (line 220) | public ArrowheadScoreList updateScoresUsingList(ArrowheadScoreList sco...
    method extractConnectedComponents (line 229) | public List<Set<Point>> extractConnectedComponents() {
    method calculateResults (line 240) | public List<HighScore> calculateResults(List<Set<Point>> connectedComp...
    method getHighestScoringPoint (line 259) | private Point getHighestScoringPoint(RealMatrix blockScore, Set<Point>...

FILE: src/juicebox/tools/utils/juicer/arrowhead/connectedcomponents/BinaryConnectedComponents.java
  class BinaryConnectedComponents (line 36) | public class BinaryConnectedComponents {
    method detection (line 46) | public synchronized static List<Set<Point>> detection(double[][] image...
    method processLabeledIndices (line 74) | private static List<Set<Point>> processLabeledIndices(List<IndexNode> ...
    method processNeighbors (line 112) | private static void processNeighbors(int[][] labels, List<IndexNode> i...
    method getSubMatrix (line 143) | private static int[][] getSubMatrix(int[][] matrix, int left, int righ...
    method positiveValues (line 151) | private static Set<Integer> positiveValues(int[][] matrix) {

FILE: src/juicebox/tools/utils/juicer/arrowhead/connectedcomponents/IndexNode.java
  class IndexNode (line 35) | class IndexNode {
    method IndexNode (line 41) | public IndexNode(int n) {
    method addConnections (line 45) | public void addConnections(IndexNode node) {
    method addPoint (line 49) | public void addPoint(Point point) {
    method getMatrixIndices (line 53) | public Set<Point> getMatrixIndices() {
    method index (line 57) | public void index() {
    method hasNotBeenIndexed (line 61) | public boolean hasNotBeenIndexed() {
    method getConnectedNodes (line 65) | public Set<IndexNode> getConnectedNodes() {
    method getIndex (line 69) | public int getIndex() {

FILE: src/juicebox/tools/utils/juicer/hiccups/GPUController.java
  class GPUController (line 51) | public class GPUController {
    method GPUController (line 61) | public GPUController(int window, int matrixSize, int peakWidth, boolea...
    method readCuFile (line 85) | private static String readCuFile(String fileName, int window, int matr...
    method process (line 106) | public GPUOutputContainer process(HiCCUPSRegionHandler regionHandler, ...
    method runCPUVersion (line 254) | private GPUOutputContainer runCPUVersion(double[][] c, float[] d,

FILE: src/juicebox/tools/utils/juicer/hiccups/GPUController2.java
  class GPUController2 (line 54) | public class GPUController2 {
    method GPUController2 (line 64) | public GPUController2(int window, int res, int matrixSize, int peakWid...
    method readCuFile (line 93) | private static String readCuFile(String fileName, int window, int matr...
    method process (line 114) | public GPUOutputContainer2 process(HiCCUPSRegionHandler regionHandler,...
    method runCPUVersion (line 279) | private GPUOutputContainer runCPUVersion(double[][] c, float[] d,

FILE: src/juicebox/tools/utils/juicer/hiccups/GPUHelper.java
  class GPUHelper (line 37) | class GPUHelper {
    method allocateOutput (line 39) | public static CUdeviceptr allocateOutput(int size, int typeSize) {
    method allocateInput (line 45) | public static CUdeviceptr allocateInput(float[] input) {
    method freeUpMemory (line 55) | public static void freeUpMemory(CUdeviceptr[] pointers) {
    method GPUArraytoCPUMatrix (line 61) | public static float[][] GPUArraytoCPUMatrix(float[] result, int n, int...

FILE: src/juicebox/tools/utils/juicer/hiccups/GPUOutputContainer.java
  class GPUOutputContainer (line 37) | public class GPUOutputContainer {
    method GPUOutputContainer (line 53) | public GPUOutputContainer(float[][] observed, float[][] peak,
    method cleanUpBinNans (line 75) | public void cleanUpBinNans() {
    method cleanUpPeakNaNs (line 92) | public void cleanUpPeakNaNs() {
    method updateHistograms (line 106) | public synchronized void updateHistograms(long[][] histBL, long[][] hi...
    method processHistogramValue (line 122) | private void processHistogramValue(float potentialRowIndex, int column...
    method cleanUpBinDiagonal (line 137) | public void cleanUpBinDiagonal(int relativeDiagonal) {
    method cleanUpPeakDiagonal (line 158) | public void cleanUpPeakDiagonal(int relativeDiagonal) {
    method extractPeaks (line 172) | public Feature2DList extractPeaks(int chrIndex, String chrName, int w1...
    method extractPeaksListGiven (line 214) | public Feature2DList extractPeaksListGiven(int chrIndex, String chrNam...

FILE: src/juicebox/tools/utils/juicer/hiccups/GPUOutputContainer2.java
  class GPUOutputContainer2 (line 39) | public class GPUOutputContainer2 {
    method GPUOutputContainer2 (line 59) | public GPUOutputContainer2(float[][] observed, float[][] peak,
    method cleanUpBinNans (line 87) | public void cleanUpBinNans() {
    method cleanUpPvalNans (line 104) | public void cleanUpPvalNans() {
    method cleanUpPeakNaNs (line 129) | public void cleanUpPeakNaNs() {
    method updateHistograms (line 143) | public synchronized void updateHistograms(long[][] histBL, long[][] hi...
    method processHistogramValue (line 159) | private void processHistogramValue(float potentialRowIndex, int column...
    method updatePvalLists (line 172) | public synchronized void updatePvalLists(Map<Integer, Map<Long, Intege...
    method processPValue (line 188) | private synchronized void processPValue(float potentialRowIndex, float...
    method cleanUpBinDiagonal (line 211) | public void cleanUpBinDiagonal(int relativeDiagonal) {
    method cleanUpPeakDiagonal (line 232) | public void cleanUpPeakDiagonal(int relativeDiagonal) {
    method extractPeaks (line 246) | public Feature2DList extractPeaks(int chrIndex, String chrName, int w1...
    method extractPeaksListGiven (line 294) | public Feature2DList extractPeaksListGiven(int chrIndex, String chrNam...

FILE: src/juicebox/tools/utils/juicer/hiccups/GPUTesting.java
  class GPUTesting (line 41) | class GPUTesting {
    method test (line 43) | public static void test() {

FILE: src/juicebox/tools/utils/juicer/hiccups/HiCCUPSConfiguration.java
  class HiCCUPSConfiguration (line 38) | public class HiCCUPSConfiguration {
    method HiCCUPSConfiguration (line 60) | public HiCCUPSConfiguration(int resolution, double fdrThreshold, int p...
    method extractConfigurationsFromCommandLine (line 68) | public static List<HiCCUPSConfiguration> extractConfigurationsFromComm...
    method getHiCCUPS2ConfigFor1K (line 138) | public static HiCCUPSConfiguration getHiCCUPS2ConfigFor1K() {
    method getHiCCUPS2ConfigFor2K (line 141) | public static HiCCUPSConfiguration getHiCCUPS2ConfigFor2K() {
    method getHiCCUPS2ConfigFor5K (line 145) | public static HiCCUPSConfiguration getHiCCUPS2ConfigFor5K() {
    method getDefaultConfigFor5K (line 149) | public static HiCCUPSConfiguration getDefaultConfigFor5K() {
    method getDefaultConfigFor10K (line 153) | public static HiCCUPSConfiguration getDefaultConfigFor10K() {
    method getDefaultConfigFor25K (line 157) | public static HiCCUPSConfiguration getDefaultConfigFor25K() {
    method getDefaultBlankConfig (line 161) | private static HiCCUPSConfiguration getDefaultBlankConfig(int res) {
    method getDefaultSetOfConfigsForUsers (line 165) | public static List<HiCCUPSConfiguration> getDefaultSetOfConfigsForUser...
    method getHiCCUPS2DefaultSetOfConfigsForUsers (line 174) | public static List<HiCCUPSConfiguration> getHiCCUPS2DefaultSetOfConfig...
    method isValid (line 184) | private boolean isValid() {
    method divisor (line 188) | public int divisor() {
    method getResolution (line 192) | public int getResolution() {
    method getClusterRadius (line 196) | public int getClusterRadius() {
    method getWindowWidth (line 200) | public int getWindowWidth() {
    method getPeakWidth (line 204) | public int getPeakWidth() {
    method getFDRThreshold (line 208) | public double getFDRThreshold() {
    method toString (line 212) | public String toString() {
    method getFDRPercent (line 217) | private String getFDRPercent() {

FILE: src/juicebox/tools/utils/juicer/hiccups/HiCCUPSRegionContainer.java
  class HiCCUPSRegionContainer (line 29) | public class HiCCUPSRegionContainer {
    method HiCCUPSRegionContainer (line 34) | public HiCCUPSRegionContainer(Chromosome chromosome, int[] rowBounds, ...
    method getRowBounds (line 40) | public int[] getRowBounds() {
    method getColumnBounds (line 44) | public int[] getColumnBounds() {
    method getChromosome (line 48) | public Chromosome getChromosome() {

FILE: src/juicebox/tools/utils/juicer/hiccups/HiCCUPSUtils.java
  class HiCCUPSUtils (line 49) | public class HiCCUPSUtils {
    method generatePeak (line 89) | public static Feature2D generatePeak(String chrName, float observed, f...
    method generatePeak (line 114) | public static Feature2D generatePeak(String chrName, float observed, f...
    method calculateFDR (line 149) | public static void calculateFDR(Feature2D feature, float[][] fdrLogBL,...
    method removeLowMapQFeatures (line 169) | private static void removeLowMapQFeatures(Feature2DList list, final in...
    method coalesceFeaturesToCentroid (line 196) | private static void coalesceFeaturesToCentroid(Feature2DList list, fin...
    method filterOutFeaturesByEnrichment (line 205) | public static void filterOutFeaturesByEnrichment(Feature2DList list, f...
    method enrichmentThreshold (line 214) | private static List<Feature2D> enrichmentThreshold(List<Feature2D> fea...
    method doFinalCleanUp (line 223) | private static void doFinalCleanUp(Feature2DList list) {
    method finalCleanUp (line 232) | private static List<Feature2D> finalCleanUp(List<Feature2D> feature2DL...
    method filterOutFeaturesByFDR (line 241) | private static void filterOutFeaturesByFDR(Feature2DList list, int ver...
    method fdrThreshold (line 250) | private static List<Feature2D> fdrThreshold(List<Feature2D> feature2DL...
    method removeLowMapQ (line 264) | private static List<Feature2D> removeLowMapQ(int res, int chrIndex, Da...
    method nearbyValuesClear (line 285) | private static boolean nearbyValuesClear(double[] normalizationVector,...
    method coalescePixelsToCentroid (line 296) | private static List<Feature2D> coalescePixelsToCentroid(int resolution...
    method setPixelColor (line 357) | private static void setPixelColor(Feature2D pixel) {
    method fdrThresholdsSatisfied (line 368) | private static boolean fdrThresholdsSatisfied(Feature2D pixel) {
    method fdrThresholds2Satisfied (line 395) | private static boolean fdrThresholds2Satisfied(Feature2D pixel) {
    method finalCleanSatisfied (line 427) | private static boolean finalCleanSatisfied(Feature2D pixel) {
    method enrichmentThresholdSatisfied (line 454) | private static boolean enrichmentThresholdSatisfied(Feature2D pixel, f...
    method mean (line 472) | private static int mean(List<Feature2D> pixelList, int i) {
    method hypotenuse (line 484) | public static double hypotenuse(double x, double y) {
    method mergeHighResolutions (line 493) | public static Feature2DList mergeHighResolutions(Map<Integer, Feature2...
    method mergeAllResolutions (line 530) | public static Feature2DList mergeAllResolutions(Map<Integer, Feature2D...
    method handleExistingGenericMerger (line 594) | private static void handleExistingGenericMerger(Feature2DList mergedLi...
    method handleExistingMergerWithTwentyFiveKB (line 601) | private static void handleExistingMergerWithTwentyFiveKB(Feature2DList...
    method handleGenericTwoListMerger (line 608) | private static Feature2DList handleGenericTwoListMerger(Feature2DList ...
    method handleGenericThreeListMerger (line 633) | private static Feature2DList handleGenericThreeListMerger(Feature2DLis...
    method handleFiveAndTenKBMerger (line 681) | private static Feature2DList handleFiveAndTenKBMerger(Feature2DList fi...
    method extractIntegerValues (line 705) | public static int[] extractIntegerValues(List<String> valList, int n) {
    method extractFDRValues (line 721) | public static double[] extractFDRValues(List<String> fdrStrings, int n...
    method extractDoubleValues (line 729) | public static double[] extractDoubleValues(List<String> valList, int n...
    method postProcess (line 752) | public static void postProcess(Map<Integer, Feature2DList> looplists, ...
    method calculateThresholdAndFDR (line 778) | public static void calculateThresholdAndFDR(int index, int width, doub...
    method histogramPvals (line 808) | public static long histogramPvals(Map<Long, Integer> kHist, long total...
    method filterOutFeaturelistByEnrichment (line 823) | public static Feature2DList filterOutFeaturelistByEnrichment(List<HiCC...
    method getEnrichedPixelFileName (line 835) | public static String getEnrichedPixelFileName(int resolution) {
    method getPostprocessedLoopsFileName (line 839) | private static String getPostprocessedLoopsFileName(int resolution, bo...
    method getRequestedLoopsFileName (line 847) | public static String getRequestedLoopsFileName(int resolution) {
    method getMergedLoopsFileName (line 851) | public static String getMergedLoopsFileName() {
    method getMergedRequestedLoopsFileName (line 855) | public static String getMergedRequestedLoopsFileName() {
    method getFDRThresholdsFilename (line 859) | public static String getFDRThresholdsFilename(int resolution) {

FILE: src/juicebox/tools/utils/juicer/localizer/LocalizerUtils.java
  class LocalizerUtils (line 50) | public class LocalizerUtils {
    method filterFeaturesBySize (line 60) | public static ArrayList<Feature2D> filterFeaturesBySize(List<Feature2D...
    method extractLocalizedData (line 78) | public static RealMatrix extractLocalizedData(MatrixZoomData zd, Featu...
    method extractNormParts (line 90) | public static List<List<Double>> extractNormParts(Dataset ds, MatrixZo...
    method localMax (line 115) | public static List<List<Double>> localMax(RealMatrix rawSource, List<D...
    method calculateNormMatrix (line 211) | public static RealMatrix calculateNormMatrix(RealMatrix inputData, Lis...
    method setNormExpected (line 231) | public static RealMatrix setNormExpected(RealMatrix rawSummedData, Rea...
    method matrixSum (line 256) | public static double matrixSum(RealMatrix inputData, int rowBound1, in...
    method nonZeroEntries (line 266) | public static int nonZeroEntries(RealMatrix inputData, int rowBound1, ...
    method multiplyInPlace (line 278) | public static void multiplyInPlace(RealMatrix inputData, double scaleR...
    method multiplyInPlaceRound (line 288) | public static void multiplyInPlaceRound(RealMatrix inputData, double s...
    method gaussBlur (line 300) | public static RealMatrix gaussBlur(RealMatrix inputData, int window) {
    method boxesForGauss (line 331) | public static int[] boxesForGauss(int sigma, int numBoxes) {
    method boxBlur (line 346) | public static void boxBlur(RealMatrix inputData, RealMatrix outputData...
    method boxBlurH (line 358) | public static void boxBlurH(RealMatrix source, RealMatrix target, int ...
    method boxBlurT (line 393) | public static void boxBlurT(RealMatrix source, RealMatrix target, int ...
    method localGradient (line 428) | public static RealMatrix localGradient(RealMatrix inputData, int windo...
    method nonmaxsuppress (line 447) | public static RealMatrix nonmaxsuppress(RealMatrix inputData, int wind...
    method nonmaxsuppressPoissonZ (line 487) | public static RealMatrix nonmaxsuppressPoissonZ(RealMatrix observedDat...
    method orderPeaks (line 528) | public static List<List<Double>> orderPeaks(RealMatrix inputData, doub...
    method orderPeaksPoissonZ (line 599) | public static List<List<Double>> orderPeaksPoissonZ(RealMatrix inputDa...

FILE: src/juicebox/tools/utils/norm/CustomNormVectorFileHandler.java
  class CustomNormVectorFileHandler (line 47) | public class CustomNormVectorFileHandler extends NormVectorUpdater {
    method updateHicFile (line 50) | public static void updateHicFile(String path, String vectorPath, int n...
    method unsafeHandleUpdatingOfNormalizations (line 63) | public static void unsafeHandleUpdatingOfNormalizations(SuperAdapter s...
    method completeCalculationsNecessaryForUpdatingCustomNormalizations (line 94) | private static NormVectorInfo completeCalculationsNecessaryForUpdating...
    method handleLoadedVector (line 208) | private static void handleLoadedVector(NormalizationType customNormTyp...
    method readVectorFile (line 239) | private static Map<NormalizationType, Map<String, NormalizationVector>...
    method skipLinesUntilTextEncountered (line 319) | private static String skipLinesUntilTextEncountered(BufferedReader vec...

FILE: src/juicebox/tools/utils/norm/ExternalNormalizationVectorLoader.java
  class ExternalNormalizationVectorLoader (line 27) | class ExternalNormalizationVectorLoader {

FILE: src/juicebox/tools/utils/norm/GenomeWideNormalizationVectorUpdater.java
  class GenomeWideNormalizationVectorUpdater (line 43) | public class GenomeWideNormalizationVectorUpdater extends NormVectorUpda...
    method updateHicFileForGWfromPreAddNormOnly (line 121) | public static void updateHicFileForGWfromPreAddNormOnly(Dataset ds, Hi...
    method getWGVectors (line 158) | private static Pair<Map<Chromosome, NormalizationVector>, ExpectedValu...

FILE: src/juicebox/tools/utils/norm/MultithreadedNormalizationVectorUpdater.java
  class MultithreadedNormalizationVectorUpdater (line 45) | public class MultithreadedNormalizationVectorUpdater extends Normalizati...
    method MultithreadedNormalizationVectorUpdater (line 59) | public MultithreadedNormalizationVectorUpdater(int numCPUThreads) {
    method updateHicFile (line 63) | @Override
    method updateExpectedValueCalculationForChr (line 225) | protected static void updateExpectedValueCalculationForChr(final int c...
    method buildVCOrVCSQRT (line 235) | protected void buildVCOrVCSQRT(boolean weShouldBuildVC, boolean weShou...
    method buildKR (line 258) | protected void buildKR(Chromosome chr, NormalizationCalculations nc, H...
    method buildScale (line 284) | protected void buildScale(Chromosome chr, NormalizationCalculations nc...
    method runIndividualChromosomeCode (line 310) | protected void runIndividualChromosomeCode(AtomicInteger chromosomeIndex,

FILE: src/juicebox/tools/utils/norm/NormVectorInfo.java
  class NormVectorInfo (line 35) | class NormVectorInfo {
    method NormVectorInfo (line 42) | NormVectorInfo(Map<NormalizationType, Map<String, NormalizationVector>...
    method getNormVectorBuffers (line 51) | public List<BufferedByteWriter> getNormVectorBuffers() {
    method getNormVectorIndices (line 55) | public List<NormalizationVectorIndexEntry> getNormVectorIndices() {
    method getExpectedValueFunctionMap (line 59) | public Map<String, ExpectedValueFunction> getExpectedValueFunctionMap() {
    method getNormalizationVectorsMap (line 63) | public Map<NormalizationType, Map<String, NormalizationVector>> getNor...

FILE: src/juicebox/tools/utils/norm/NormVectorUpdater.java
  class NormVectorUpdater (line 45) | public class NormVectorUpdater {
    method updateNormVectorIndexWithVector (line 47) | static void updateNormVectorIndexWithVector(List<NormalizationVectorIn...
    method isValidNormValue (line 64) | public static boolean isValidNormValue(float v) {
    method putFloatArraysIntoBufferList (line 68) | static void putFloatArraysIntoBufferList(List<BufferedByteWriter> buff...
    method putMapValuesIntoBuffer (line 85) | private static void putMapValuesIntoBuffer(List<BufferedByteWriter> bu...
    method writeExpectedToBuffer (line 100) | private static void writeExpectedToBuffer(RandomAccessFile raf, List<B...
    method handleVersionSix (line 108) | private static void handleVersionSix(RandomAccessFile raf, int version...
    method writeNormIndex (line 126) | static void writeNormIndex(BufferedByteWriter buffer, List<Normalizati...
    method writeNormsToUpdateFile (line 138) | static void writeNormsToUpdateFile(DatasetReaderV2 reader, String path...
    method writeExpectedValues (line 166) | private static void writeExpectedValues(List<BufferedByteWriter> expec...
    method writeExpectedValues (line 179) | private static void writeExpectedValues(List<BufferedByteWriter> expec...
    method appendExpectedValuesToBuffer (line 192) | private static void appendExpectedValuesToBuffer(List<BufferedByteWrit...
    method getBufferWithEnoughSpace (line 213) | private static BufferedByteWriter getBufferWithEnoughSpace(List<Buffer...
    method writeNormsToBuffer (line 228) | private static void writeNormsToBuffer(RandomAccessFile raf, List<Norm...

FILE: src/juicebox/tools/utils/norm/NormalizationCalculations.java
  class NormalizationCalculations (line 50) | public class NormalizationCalculations {
    method NormalizationCalculations (line 56) | public NormalizationCalculations(IteratorContainer ic) {
    method sparseMultiplyFromContactRecords (line 62) | private static ListOfDoubleArrays sparseMultiplyFromContactRecords(Lis...
    method computeKRNormVector (line 106) | private ListOfDoubleArrays computeKRNormVector(ListOfIntArrays offset,...
    method getIterator (line 253) | private Iterator<ContactRecord> getIterator() {
    method isEnoughMemory (line 257) | boolean isEnoughMemory() {
    method getNorm (line 261) | public ListOfFloatArrays getNorm(NormalizationType normOption) {
    method computeVC (line 288) | ListOfFloatArrays computeVC() {
    method getSumFactor (line 313) | public double getSumFactor(ListOfFloatArrays norm) {
    method getNormMatrixSumFactor (line 318) | public double[] getNormMatrixSumFactor(ListOfFloatArrays norm) {
    method getNumberOfValidEntriesInVector (line 345) | public int getNumberOfValidEntriesInVector(double[] norm) {
    method computeKR (line 356) | ListOfFloatArrays computeKR() {
    method getOffset (line 434) | private ListOfIntArrays getOffset(double percent) {
    method computeMMBA (line 492) | public ListOfFloatArrays computeMMBA() {
    method getRandomWithExclusion (line 739) | public int getRandomWithExclusion(Random rnd, int end, List<Integer> e...

FILE: src/juicebox/tools/utils/norm/NormalizationTools.java
  class NormalizationTools (line 41) | public class NormalizationTools {
    method parCreateNormVectorMap (line 42) | public static Map<Chromosome, NormalizationVector> parCreateNormVector...
    method createOffsets (line 70) | private static long[] createOffsets(Chromosome[] chromosomes, int reso...

FILE: src/juicebox/tools/utils/norm/NormalizationVectorIndexEntry.java
  class NormalizationVectorIndexEntry (line 27) | class NormalizationVectorIndexEntry {
    method NormalizationVectorIndexEntry (line 35) | NormalizationVectorIndexEntry(String type, int chrIdx, String unit, in...
    method toString (line 44) | @Override

FILE: src/juicebox/tools/utils/norm/NormalizationVectorUpdater.java
  class NormalizationVectorUpdater (line 47) | public class NormalizationVectorUpdater extends NormVectorUpdater {
    method printNormTiming (line 65) | protected static void printNormTiming(String norm, Chromosome chr, HiC...
    method updateExpectedValueCalculationForChr (line 71) | protected static void updateExpectedValueCalculationForChr(final int c...
    method reEvaluateWhichIntraNormsToBuild (line 81) | protected void reEvaluateWhichIntraNormsToBuild(List<NormalizationType...
    method buildVCOrVCSQRT (line 88) | protected void buildVCOrVCSQRT(boolean weShouldBuildVC, boolean weShou...
    method buildKR (line 108) | protected void buildKR(Chromosome chr, NormalizationCalculations nc, H...
    method updateHicFile (line 125) | public void updateHicFile(String path, List<NormalizationType> normali...
    method buildScale (line 228) | protected void buildScale(Chromosome chr, NormalizationCalculations nc...

FILE: src/juicebox/tools/utils/norm/NormalizedSum.java
  class NormalizedSum (line 27) | class NormalizedSum {
    method NormalizedSum (line 35) | public NormalizedSum(String type, int chr1Idx, int chr2Idx, String uni...

FILE: src/juicebox/tools/utils/norm/UnusedFunctions.java
  class UnusedFunctions (line 39) | class UnusedFunctions {
    method internalTest (line 47) | public static void internalTest(String[] args) throws IOException {
    method dumpNormalizationVectorIndex (line 145) | static private void dumpNormalizationVectorIndex(String path, String o...

FILE: src/juicebox/tools/utils/norm/ZeroScale.java
  class ZeroScale (line 35) | public class ZeroScale {
    method scale (line 36) | public static ListOfFloatArrays scale(IteratorContainer ic, ListOfFloa...
    method normalizeVectorByScaleFactor (line 45) | public static ListOfFloatArrays normalizeVectorByScaleFactor(ListOfFlo...
    method mmbaScaleToVector (line 86) | public static ListOfFloatArrays mmbaScaleToVector(IteratorContainer ic...

FILE: src/juicebox/tools/utils/norm/final2/FinalScale.java
  class FinalScale (line 36) | public class FinalScale {
    method scaleToTargetVector (line 51) | public static ListOfFloatArrays scaleToTargetVector(IteratorContainer ...
    method setRowSums (line 340) | private static void setRowSums(ListOfIntArrays numNonZero, IteratorCon...
    method setBadValues (line 353) | private static void setBadValues(ListOfIntArrays bad, IteratorContaine...
    method dealWithSorting (line 365) | private static double[] dealWithSorting(double[] vector, int length) {
    method sparseMultiplyGetRowSums (line 372) | private static ListOfFloatArrays sparseMultiplyGetRowSums(IteratorCont...

FILE: src/juicebox/tools/utils/norm/final2/ScaleThreadObject.java
  class ScaleThreadObject (line 27) | public class ScaleThreadObject {
    method ScaleThreadObject (line 34) | public ScaleThreadObject(int[] iIndexes, int[] jIndexes, float[] xValu...
    method execute (line 42) | public void execute() {

FILE: src/juicebox/tools/utils/original/BigWigUtils.java
  class BigWigUtils (line 40) | public class BigWigUtils {
    method computeBins (line 42) | public static void computeBins(String path, int windowSize) throws IOE...
    method computeBins (line 52) | public static void computeBins(String path, String chr, int start, int...
    method computeBins (line 79) | private static void computeBins(BBFileReader reader, String chr, int s...
    method main (line 142) | public static void main(String[] args) throws Exception {

FILE: src/juicebox/tools/utils/original/BlockPP.java
  class BlockPP (line 34) | class BlockPP {
    method BlockPP (line 42) | BlockPP(int number) {
    method BlockPP (line 47) | BlockPP(int number, Map<Point, ContactCount> contactRecordMap) {
    method getNumber (line 53) | int getNumber() {
    method getNumRecords (line 57) | int getNumRecords() {return contactRecordMap.size();}
    method incrementCount (line 59) | void incrementCount(int col, int row, float score) {
    method getContactRecordMap (line 71) | Map<Point, ContactCount> getContactRecordMap() {
    method merge (line 75) | void merge(BlockPP other) {
    method clear (line 92) | void clear() {

FILE: src/juicebox/tools/utils/original/BlockQueue.java
  type BlockQueue (line 29) | interface BlockQueue {
    method advance (line 31) | void advance() throws IOException;
    method getBlock (line 33) | BlockPP getBlock();

FILE: src/juicebox/tools/utils/original/BlockQueueFB.java
  class BlockQueueFB (line 34) | class BlockQueueFB implements BlockQueue {
    method BlockQueueFB (line 41) | BlockQueueFB(File file) {
    method advance (line 51) | public void advance() throws IOException {
    method getBlock (line 92) | public BlockPP getBlock() {
    method readFully (line 99) | void readFully(byte[] b, InputStream is) throws IOException {

FILE: src/juicebox/tools/utils/original/BlockQueueMem.java
  class BlockQueueMem (line 32) | class BlockQueueMem implements BlockQueue {
    method BlockQueueMem (line 37) | BlockQueueMem(Collection<BlockPP> blockCollection) {
    method advance (line 48) | public void advance() {
    method getBlock (line 52) | public BlockPP getBlock() {

FILE: src/juicebox/tools/utils/original/Chunk.java
  class Chunk (line 27) | public class Chunk {
    method Chunk (line 31) | public Chunk(long mndIndex, int mndChunk) {
    method Chunk (line 36) | public Chunk(String s1, String s2) {

FILE: src/juicebox/tools/utils/original/ContactCount.java
  class ContactCount (line 27) | class ContactCount {
    method ContactCount (line 30) | ContactCount(float value) {
    method incrementCount (line 34) | void incrementCount(float increment) {
    method getCounts (line 38) | float getCounts() {

FILE: src/juicebox/tools/utils/original/ExpectedValueCalculation.java
  class ExpectedValueCalculation (line 59) | public class ExpectedValueCalculation {
    method ExpectedValueCalculation (line 101) | public ExpectedValueCalculation(ChromosomeHandler chromosomeHandler, i...
    method getGridSize (line 146) | public int getGridSize() {
    method addDistance (line 158) | public synchronized void addDistance(Integer chrIdx, int bin1, int bin...
    method merge (line 178) | public void merge(ExpectedValueCalculation otherEVCalc) {
    method hasData (line 197) | public boolean hasData() {
    method computeDensity (line 210) | public synchronized void computeDensity() {
    method getChrScaleFactors (line 313) | public Map<Integer, Double> getChrScaleFactors() {
    method getDensityAvg (line 322) | public ListOfDoubleArrays getDensityAvg() {
    method getType (line 331) | public NormalizationType getType() {
    method getExpectedValueFunction (line 335) | public ExpectedValueFunctionImpl getExpectedValueFunction() {
    method addDistancesFromIterator (line 341) | public void addDistancesFromIterator(int chrIndx, IteratorContainer ic...
    method addDistancesFromZD (line 357) | public void addDistancesFromZD(MatrixZoomData zd, Map<String, Integer>...

FILE: src/juicebox/tools/utils/original/FragmentCalculation.java
  class FragmentCalculation (line 39) | public class FragmentCalculation {
    method FragmentCalculation (line 43) | private FragmentCalculation(Map<String, int[]> sitesMap) {
    method readFragments (line 47) | private static FragmentCalculation readFragments(InputStream is, Chrom...
    method readFragments (line 75) | public static FragmentCalculation readFragments(String filename, Chrom...
    method binarySearch (line 103) | public static int binarySearch(int[] sites, int position) {
    method getSites (line 117) | public int[] getSites(String chrName) {
    method getNumberFragments (line 121) | public int getNumberFragments(String chrName) {
    method getSitesMap (line 128) | public Map<String, int[]> getSitesMap() {

FILE: src/juicebox/tools/utils/original/HiCDBUtils.java
  class HiCDBUtils (line 44) | public class HiCDBUtils {
    method main (line 51) | public static void main(String[] args) throws IOException, SQLException {
    method insertAnnotationList (line 73) | private static void insertAnnotationList(String annotListFile) throws ...
    method insertAnnotations (line 93) | private static void insertAnnotations(String line) throws IOException,...
    method insertFragments (line 175) | private static void insertFragments(String fragmentFile) throws IOExce...
    method updateFragmentAnnotations (line 234) | private static void updateFragmentAnnotations() throws SQLException {
    method getDBConnection (line 317) | private static Connection getDBConnection() {
    method getChrAlias (line 354) | private static String getChrAlias(String token) {

FILE: src/juicebox/tools/utils/original/IndexEntry.java
  class IndexEntry (line 27) | public class IndexEntry {
    method IndexEntry (line 32) | public IndexEntry(int id, long position, int size) {
    method IndexEntry (line 38) | public IndexEntry(long position, int size) {

FILE: src/juicebox/tools/utils/original/LargeIndexEntry.java
  class LargeIndexEntry (line 27) | public class LargeIndexEntry {
    method LargeIndexEntry (line 32) | LargeIndexEntry(int id, long position, long size) {
    method LargeIndexEntry (line 38) | public LargeIndexEntry(long position, long size) {

FILE: src/juicebox/tools/utils/original/MTIndexHandler.java
  class MTIndexHandler (line 39) | public class MTIndexHandler {
    method readMndIndex (line 40) | public static Map<Integer, List<Chunk>> readMndIndex(String mndIndexFile,
    method populateChromosomeIndexes (line 91) | public static Map<String, Integer> populateChromosomeIndexes(Chromosom...
    method populateChromosomePairIndexes (line 99) | public static int populateChromosomePairIndexes(ChromosomeHandler chro...

FILE: src/juicebox/tools/utils/original/MatrixPP.java
  class MatrixPP (line 37) | public class MatrixPP {
    method MatrixPP (line 58) | public MatrixPP(int chr1Idx, int chr2Idx, ChromosomeHandler chromosome...
    method getNumColumnsFromNumBins (line 109) | private int getNumColumnsFromNumBins(int nBins, int binSize, int cutof...
    method MatrixPP (line 127) | MatrixPP(int chr1Idx, int chr2Idx, int binSize, int blockColumnCount, ...
    method getKey (line 138) | String getKey() {
    method incrementCount (line 143) | void incrementCount(int pos1, int pos2, int frag1, int frag2, float sc...
    method incrementCount (line 153) | public void incrementCount(ContactRecord cr, Map<String, ExpectedValue...
    method parsingComplete (line 163) | public void parsingComplete() {
    method getChr1Idx (line 170) | int getChr1Idx() {
    method getChr2Idx (line 174) | int getChr2Idx() {
    method getZoomData (line 178) | MatrixZoomDataPP[] getZoomData() {
    method mergeMatrices (line 185) | public void mergeMatrices(MatrixPP otherMatrix) {

FILE: src/juicebox/tools/utils/original/MatrixZoomDataPP.java
  class MatrixZoomDataPP (line 48) | public class MatrixZoomDataPP {
    method MatrixZoomDataPP (line 81) | MatrixZoomDataPP(Chromosome chr1, Chromosome chr2, int binSize, int bl...
    method MatrixZoomDataPP (line 107) | MatrixZoomDataPP(Chromosome chr1, Chromosome chr2, int binSize, int bl...
    method getUnit (line 134) | HiC.Unit getUnit() {
    method getSum (line 138) | double getSum() {
    method getOccupiedCellCount (line 142) | double getOccupiedCellCount() {
    method getPercent95 (line 146) | double getPercent95() {
    method getPercent5 (line 150) | double getPercent5() {
    method getBinSize (line 155) | int getBinSize() {
    method getChr1 (line 160) | Chromosome getChr1() {
    method getChr2 (line 165) | Chromosome getChr2() {
    method getZoom (line 169) | int getZoom() {
    method getBlockBinCount (line 173) | int getBlockBinCount() {
    method getBlockColumnCount (line 177) | int getBlockColumnCount() {
    method getBlocks (line 181) | Map<Integer, BlockPP> getBlocks() {
    method incrementCount (line 188) | void incrementCount(int pos1, int pos2, float score, Map<String, Expec...
    method incrementCount (line 254) | public void  incrementCount(ContactRecord cr, Map<String, ExpectedValu...
    method dumpBlocks (line 354) | private void dumpBlocks(File file) throws IOException {
    method mergeAndWriteBlocks (line 420) | protected List<IndexEntry> mergeAndWriteBlocks(LittleEndianOutputStrea...
    method mergeAndWriteBlocks (line 497) | protected List<IndexEntry> mergeAndWriteBlocks(LittleEndianOutputStrea...
    method writeBlockChunk (line 597) | private void writeBlockChunk(Integer[] threadBlocks, Map<Integer, Bloc...
    method readAndMerge (line 641) | private void readAndMerge(BlockPP currentBlock, Map.Entry<File, Long> ...
    method readTmpBlock (line 648) | private BlockPP readTmpBlock(File file, long filePosition) throws IOEx...
    method computeStats (line 692) | private void computeStats(DownsampledDoubleArrayList sampledData) {
    method parsingComplete (line 700) | void parsingComplete() {
    method mergeMatrices (line 719) | void mergeMatrices(MatrixZoomDataPP otherMatrixZoom) {
    method writeBlock (line 763) | protected void writeBlock(BlockPP block, DownsampledDoubleArrayList sa...
    method incrementSum (line 948) | private synchronized void incrementSum(float counts) {
    method incrementCellCount (line 952) | private synchronized void incrementCellCount(int nRecords) {
    method compress (line 963) | protected byte[] compress(byte[] data, Deflater compressor) {

FILE: src/juicebox/tools/utils/original/MultithreadedPreprocessor.java
  class MultithreadedPreprocessor (line 45) | public class MultithreadedPreprocessor extends Preprocessor {
    method MultithreadedPreprocessor (line 74) | public MultithreadedPreprocessor(File outputFile, String genomeId, Chr...
    method setMndIndex (line 87) | public void setMndIndex(String mndIndexFile, Map<Integer, String> chro...
    method preprocess (line 95) | @Override
    method getGenomicPosition (line 133) | private int getGenomicPosition(int chr, int pos, ChromosomeHandler loc...
    method processIndividualMatrixChunk (line 144) | private Pair<Pair<Integer,Integer>, MatrixPP> processIndividualMatrixC...
    method writeBody (line 253) | @Override
    method WriteIndividualMatrix (line 423) | void WriteIndividualMatrix(Integer chromosomePair, int numOfNeededThre...
    method writeMatrix (line 452) | @Override

FILE: src/juicebox/tools/utils/original/MultithreadedPreprocessorHic.java
  class MultithreadedPreprocessorHic (line 48) | public class MultithreadedPreprocessorHic extends Preprocessor {
    method MultithreadedPreprocessorHic (line 61) | public MultithreadedPreprocessorHic(File outputFile, String genomeId, ...
    method preprocess (line 73) | @Override
    method writeBody (line 112) | @Override
    method writeIndividualMatrix (line 145) | void writeIndividualMatrix(Integer chromosomePair, int numOfNeededThre...
    method writeZoomHeader (line 270) | protected void writeZoomHeader(MatrixZoomData zd, LittleEndianOutputSt...

FILE: src/juicebox/tools/utils/original/Preprocessor.java
  class Preprocessor (line 53) | public class Preprocessor {
    method Preprocessor (line 116) | public Preprocessor(File outputFile, String genomeId, ChromosomeHandle...
    method setCountThreshold (line 137) | public void setCountThreshold(int countThreshold) {
    method setV9DepthBase (line 141) | public void setV9DepthBase(int v9DepthBase) {
    method setMapqThreshold (line 147) | public void setMapqThreshold(int mapqThreshold) {
    method setDiagonalsOnly (line 151) | public void setDiagonalsOnly(boolean diagonalsOnly) {
    method setIncludedChromosomes (line 155) | public void setIncludedChromosomes(Set<String> includedChromosomes) {
    method setFragmentFile (line 164) | public void setFragmentFile(String fragmentFileName) {
    method setExpectedVectorFile (line 168) | public void setExpectedVectorFile(String expectedVectorFile) {
    method setGraphFile (line 172) | public void setGraphFile(String graphFileName) {
    method setGenome (line 176) | public void setGenome(String genome) {
    method setResolutions (line 182) | public void setResolutions(List<String> resolutions) {
    method setAlignmentFilter (line 240) | public void setAlignmentFilter(Alignment al) {
    method setRandomizeFragMaps (line 244) | public void setRandomizeFragMaps(Set<String> fragMaps) {
    method setSubsampler (line 248) | public void setSubsampler(double subsampleFraction) {
    method randomizePos (line 257) | protected static int randomizePos(FragmentCalculation fragmentCalculat...
    method setRandomizePosition (line 273) | public void setRandomizePosition(boolean allowPositionsRandomization) {
    method setThrowOutIntraFragOption (line 277) | public void setThrowOutIntraFragOption(boolean throwOutIntraFrag) {
    method findFragMap (line 281) | protected static FragmentCalculation findFragMap(List<FragmentCalculat...
    method setFromHIC (line 320) | public void setFromHIC(boolean fromHIC) {
    method preprocess (line 324) | public void preprocess(final String inputFile, final String headerFile...
    method writeHeader (line 472) | protected void writeHeader(StringBuilder stats, StringBuilder graphs, ...
    method setPositionRandomizerSeed (line 567) | public void setPositionRandomizerSeed(long randomSeed) {
    method getInitialGenomeWideMatrixPP (line 571) | protected MatrixPP getInitialGenomeWideMatrixPP(ChromosomeHandler chro...
    method computeWholeGenomeMatrix (line 585) | private MatrixPP computeWholeGenomeMatrix(String file) throws IOExcept...
    method alignmentsAreEqual (line 642) | protected boolean alignmentsAreEqual(Alignment alignment, Alignment al...
    method getGenomicPosition (line 654) | protected int getGenomicPosition(int chr, int pos) {
    method calculateAlignment (line 665) | protected static Alignment calculateAlignment(AlignmentPair pair) {
    method writeBody (line 688) | protected void writeBody(String inputFile, Map<Integer, List<Chunk>> m...
    method ensureFitInChromosomeBounds (line 782) | protected int ensureFitInChromosomeBounds(int bp, int chrom) {
    method getRandomizedPositions (line 793) | protected Pair<Integer, Integer> getRandomizedPositions(int chr1, int ...
    method shouldSkipContact (line 824) | protected boolean shouldSkipContact(AlignmentPair pair) {
    method updateMasterIndex (line 851) | protected void updateMasterIndex(String headerFile) throws IOException {
    method updateNormVectorIndexInfo (line 868) | private void updateNormVectorIndexInfo() throws IOException {
    method writeFooter (line 892) | protected void writeFooter(LittleEndianOutputStream[] los) throws IOEx...
    method getDefaultCompressor (line 999) | protected Deflater getDefaultCompressor() {
    method writeMatrix (line 1005) | protected Pair<Map<Long, List<IndexEntry>>, Long> writeMatrix(MatrixPP...
    method updateIndexPositions (line 1064) | protected void updateIndexPositions(List<IndexEntry> blockIndex, Littl...
    method writeZoomHeader (line 1102) | private void writeZoomHeader(MatrixZoomDataPP zd, LittleEndianOutputSt...
    method setTmpdir (line 1127) | public void setTmpdir(String tmpDirName) {
    method createTempFolder (line 1133) | private File createTempFolder(String newPath) {
    method setStatisticsFile (line 1142) | public void setStatisticsFile(String statsOption) {

FILE: src/juicebox/tools/utils/original/merge/HiCMergeTools.java
  class HiCMergeTools (line 38) | public class HiCMergeTools {
    method mergeStatsAndGraphs (line 40) | public static void mergeStatsAndGraphs(List<String> dsPaths, Preproces...
    method addToListIfValidString (line 69) | private static void addToListIfValidString(String info, List<String> i...
    method confirmAllSingleAlignment (line 75) | private static boolean confirmAllSingleAlignment(List<String> statsLis...

FILE: src/juicebox/tools/utils/original/merge/StatsUtils.java
  class StatsUtils (line 31) | public class StatsUtils {
    method merge (line 32) | public static void merge(List<String> statsList, Merger merger, String...

FILE: src/juicebox/tools/utils/original/merge/merger/GraphsMerger.java
  class GraphsMerger (line 32) | public class GraphsMerger extends Merger {
    method parse (line 39) | @Override
    method printToMergedFile (line 68) | @Override
    method addTo1DArray (line 93) | private void addTo1DArray(long[] arr, Scanner scanner) {
    method write1DArray (line 99) | private void write1DArray(long[] arr, BufferedWriter histWriter) throw...
    method addTo2DArray (line 105) | private void addTo2DArray(long[][] arr, Scanner scanner) {
    method write2DArray (line 120) | private void write2DArray(long[][] arr, BufferedWriter histWriter) thr...
    method skipUntilNextArray (line 132) | private void skipUntilNextArray(Scanner scanner) {

FILE: src/juicebox/tools/utils/original/merge/merger/Merger.java
  class Merger (line 27) | public abstract class Merger {
    method containsIgnoreCase (line 28) | public static boolean containsIgnoreCase(String main, String word) {
    method parse (line 32) | public abstract void parse(String s);
    method printToMergedFile (line 34) | public abstract void printToMergedFile(String filename);

FILE: src/juicebox/tools/utils/original/merge/merger/PairedAlignmentStatsMerger.java
  class PairedAlignmentStatsMerger (line 31) | public class PairedAlignmentStatsMerger extends StatsMerger {
    method printToMergedFile (line 32) | @Override
    method parseLabel (line 70) | @Override

FILE: src/juicebox/tools/utils/original/merge/merger/SingleAlignmentStatsMerger.java
  class SingleAlignmentStatsMerger (line 31) | public class SingleAlignmentStatsMerger extends StatsMerger {
    method printToMergedFile (line 32) | @Override
    method parseLabel (line 75) | @Override

FILE: src/juicebox/tools/utils/original/merge/merger/StatsMerger.java
  class StatsMerger (line 33) | public abstract class StatsMerger extends Merger {
    method parse (line 38) | public void parse(String s) {
    method getStatistic (line 46) | protected long getStatistic(STATS_LABEL label) {
    method processLine (line 50) | protected void processLine(String current) {
    method checkAll25 (line 84) | private boolean checkAll25(String s) {
    method hasNA (line 90) | private boolean hasNA(String s) {
    method parseLabel (line 95) | protected STATS_LABEL parseLabel(String s) {
    method write (line 118) | protected void write(BufferedWriter statsOut, String description, STAT...
    method percent (line 134) | private String percent(long num, long total) {
    method commify (line 138) | private String commify(long value) {
    type STATS_LABEL (line 142) | public enum STATS_LABEL {

FILE: src/juicebox/tools/utils/original/mnditerator/AlignmentPair.java
  class AlignmentPair (line 31) | public class AlignmentPair {
    method AlignmentPair (line 47) | public AlignmentPair(boolean strand1, int chr1, int pos1, int frag1, i...
    method AlignmentPair (line 61) | public AlignmentPair() {
    method AlignmentPair (line 67) | public AlignmentPair(boolean ignore) {
    method AlignmentPair (line 73) | public AlignmentPair(int chr1, int pos1, int chr2, int pos2) {
    method AlignmentPair (line 81) | public AlignmentPair(boolean strand1, int chr1, int pos1, int frag1, b...
    method getChr1 (line 93) | public int getChr1() {
    method getPos1 (line 97) | public int getPos1() {
    method getChr2 (line 101) | public int getChr2() {
    method getPos2 (line 105) | public int getPos2() {
    method getMapq1 (line 109) | public int getMapq1() {
    method getMapq2 (line 113) | public int getMapq2() {
    method getStrand1 (line 117) | public boolean getStrand1() {
    method getStrand1AsInt (line 121) | private int getStrand1AsInt() {
    method getStrand2AsInt (line 125) | private int getStrand2AsInt() {
    method getStrand2 (line 129) | public boolean getStrand2() {
    method getFrag1 (line 133) | public int getFrag1() {
    method getFrag2 (line 137) | public int getFrag2() {
    method getScore (line 141) | public float getScore() {
    method setScore (line 145) | public void setScore(float score1) {
    method toString (line 149) | public String toString() {
    method isContigPair (line 156) | public boolean isContigPair() {
    method isValid (line 160) | public boolean isValid() {
    method isShort (line 164) | public boolean isShort() {
    method updateFragments (line 168) | public void updateFragments(int frag1, int frag2) {
    method updateStrands (line 173) | public void updateStrands(boolean strand1, boolean strand2) {
    method updateMAPQs (line 178) | public void updateMAPQs(int mapq1, int mapq2) {

FILE: src/juicebox/tools/utils/original/mnditerator/AlignmentPairLong.java
  class AlignmentPairLong (line 27) | public class AlignmentPairLong extends AlignmentPair {
    method AlignmentPairLong (line 32) | public AlignmentPairLong(boolean strand1, int chr1, int pos1, int frag...
    method AlignmentPairLong (line 39) | public AlignmentPairLong(AlignmentPair np, String seq1, String seq2) {
    method getSeq1 (line 44) | public String getSeq1() {
    method getSeq2 (line 48) | public String getSeq2() {

FILE: src/juicebox/tools/utils/original/mnditerator/AsciiPairIterator.java
  class AsciiPairIterator (line 38) | public class AsciiPairIterator extends GenericPairIterator implements Pa...
    method AsciiPairIterator (line 44) | public AsciiPairIterator(String path, Map<String, Integer> chromosomeO...
    method AsciiPairIterator (line 58) | public AsciiPairIterator(String path, Map<String, Integer> chromosomeO...
    method validateLine (line 75) | @Override

FILE: src/juicebox/tools/utils/original/mnditerator/AsciiToBinConverter.java
  class AsciiToBinConverter (line 44) | public class AsciiToBinConverter {
    method convert (line 51) | public static void convert(String inputPath, String outputFile, Chromo...
    method writeOutShortBinaryFormat (line 79) | private static void writeOutShortBinaryFormat(AsciiPairIterator iter, ...
    method writeOutStandardBinaryFormat (line 90) | private static void writeOutStandardBinaryFormat(AsciiPairIterator ite...
    method convertBack (line 104) | public static void convertBack(String inputPath, String outputFile) th...

FILE: src/juicebox/tools/utils/original/mnditerator/BAMPairIterator.java
  class BAMPairIterator (line 43) | public class BAMPairIterator implements PairIterator {
    method BAMPairIterator (line 52) | public BAMPairIterator(String path) throws IOException {
    method advance (line 60) | private void advance() {
    method hasNext (line 92) | public boolean hasNext() {
    method next (line 96) | public AlignmentPair next() {
    method remove (line 108) | public void remove() {
    method close (line 112) | public void close() {

FILE: src/juicebox/tools/utils/original/mnditerator/BinPairIterator.java
  class BinPairIterator (line 38) | public class BinPairIterator implements PairIterator {
    method BinPairIterator (line 52) | public BinPairIterator(String path) throws IOException {
    method hasNext (line 57) | public boolean hasNext() {
    method next (line 61) | public AlignmentPair next() {
    method remove (line 74) | public void remove() {
    method close (line 77) | public void close() {
    method advance (line 85) | protected void advance() {

FILE: src/juicebox/tools/utils/original/mnditerator/ComplexLineParser.java
  class ComplexLineParser (line 31) | public class ComplexLineParser extends MNDLineParser {
    method ComplexLineParser (line 38) | ComplexLineParser(Map<String, Integer> chromosomeOrdinals, ChromosomeH...
    method getChromosomeOrdinal (line 48) | @Override
    method generateBasicPair (line 53) | @Override
    method getChromosomeNameFromIndex (line 63) | @Override
    method updateOrdinalsMap (line 68) | private void updateOrdinalsMap(String chrom) {
    method updateChromCounter (line 74) | private void updateChromCounter() {
    method isValid (line 81) | private boolean isValid(String chrom1, String chrom2) {

FILE: src/juicebox/tools/utils/original/mnditerator/GenericPairIterator.java
  class GenericPairIterator (line 30) | public abstract class GenericPairIterator implements PairIterator {
    method GenericPairIterator (line 36) | public GenericPairIterator(MNDFileParser mndFileParser) {
    method hasNext (line 40) | public boolean hasNext() {
    method next (line 44) | public AlignmentPair next() {
    method advance (line 50) | protected void advance() {
    method validateLine (line 65) | protected String validateLine(String nextLine) {
    method remove (line 69) | public void remove() {
    method close (line 73) | public void close() {

FILE: src/juicebox/tools/utils/original/mnditerator/MNDFileParser.java
  class MNDFileParser (line 31) | public class MNDFileParser {
    method MNDFileParser (line 39) | MNDFileParser(MNDLineParser pg) {
    method getFileFormat (line 43) | public static Format getFileFormat(int nTokens, String nextLine) throw...
    method parse (line 65) | public AlignmentPair parse(String nextLine) throws IOException {
    method updateDCICIndicesIfApplicable (line 91) | public void updateDCICIndicesIfApplicable(String nextLine, String[] to...
    method parseShortFormat (line 103) | public AlignmentPair parseShortFormat(String[] tokens, boolean include...
    method parseSuperShortFormat (line 111) | public AlignmentPair parseSuperShortFormat(String[] tokens, boolean in...
    method parseDCICFormat (line 117) | public AlignmentPair parseDCICFormat(String[] tokens) {
    method parseLongFormat (line 129) | public AlignmentPair parseLongFormat(String[] tokens) {
    method parseMediumFormat (line 135) | public AlignmentPair parseMediumFormat(String[] tokens) {
    method getChromosomeNameFromIndex (line 140) | public String getChromosomeNameFromIndex(int chrIndex) {
    type Format (line 144) | enum Format {SUPER_SHORT, SUPER_SHORT_WITH_SCORE, SHORT, LONG, MEDIUM,...

FILE: src/juicebox/tools/utils/original/mnditerator/MNDLineParser.java
  class MNDLineParser (line 30) | public abstract class MNDLineParser {
    method getChromosomeOrdinal (line 38) | abstract protected int getChromosomeOrdinal(String chrom);
    method getChromosomeNameFromIndex (line 40) | abstract public String getChromosomeNameFromIndex(int chrIndex);
    method generateBasicPair (line 42) | public abstract AlignmentPair generateBasicPair(String[] tokens, int c...
    method createPair (line 44) | protected AlignmentPair createPair(String[] tokens, String chrom1, Str...
    method generateMediumPair (line 52) | public AlignmentPair generateMediumPair(String[] tokens, int chrom1Ind...
    method updateStrandsForPair (line 62) | public void updateStrandsForPair(AlignmentPair nextPair, String[] toke...
    method updateDCICStrandsForPair (line 68) | public void updateDCICStrandsForPair(AlignmentPair nextPair, String[] ...
    method updateMAPQsForPair (line 74) | public void updateMAPQsForPair(AlignmentPair nextPair, String[] tokens...
    method updateFragmentsForPair (line 80) | public void updateFragmentsForPair(AlignmentPair nextPair, String[] to...
    method updatePairScoreIfNeeded (line 86) | public void updatePairScoreIfNeeded(boolean includeScore, AlignmentPai...
    method getInternedString (line 96) | protected String getInternedString(String aString) {

FILE: src/juicebox/tools/utils/original/mnditerator/PairIterator.java
  type PairIterator (line 38) | public interface PairIterator extends Iterator<AlignmentPair> {
    method hasNext (line 40) | boolean hasNext();
    method next (line 42) | AlignmentPair next();
    method remove (line 44) | void remove();
    method close (line 46) | void close();
    method getIterator (line 48) | static PairIterator getIterator(String file, Map<String, Integer> chro...

FILE: src/juicebox/tools/utils/original/mnditerator/RandomAccessAsciiPairIterator.java
  class RandomAccessAsciiPairIterator (line 38) | public class RandomAccessAsciiPairIterator extends AsciiPairIterator {
    method RandomAccessAsciiPairIterator (line 39) | public RandomAccessAsciiPairIterator(String path, Map<String, Integer>...

FILE: src/juicebox/tools/utils/original/mnditerator/ShortBinPairIterator.java
  class ShortBinPairIterator (line 30) | public class ShortBinPairIterator extends BinPairIterator {
    method ShortBinPairIterator (line 32) | public ShortBinPairIterator(String path) throws IOException {
    method advance (line 36) | @Override

FILE: src/juicebox/tools/utils/original/mnditerator/SimpleAsciiPairIterator.java
  class SimpleAsciiPairIterator (line 34) | public class SimpleAsciiPairIterator extends GenericPairIterator impleme...
    method SimpleAsciiPairIterator (line 36) | public SimpleAsciiPairIterator(String path) throws IOException {
    method getChromosomeNameFromIndex (line 48) | public String getChromosomeNameFromIndex(int chrIndex) {

FILE: src/juicebox/tools/utils/original/mnditerator/SimpleLineParser.java
  class SimpleLineParser (line 30) | public class SimpleLineParser extends MNDLineParser {
    method getChromosomeOrdinal (line 36) | @Override
    method generateBasicPair (line 49) | @Override
    method getChromosomeNameFromIndex (line 56) | @Override

FILE: src/juicebox/tools/utils/original/stats/LoneStatisticsWorker.java
  class LoneStatisticsWorker (line 33) | public class LoneStatisticsWorker extends StatisticsWorker {
    method LoneStatisticsWorker (line 37) | public LoneStatisticsWorker(String siteFile, List<String> statsFiles, ...
    method infileStatistics (line 42) | public void infileStatistics() {
    method getChromosomeNameFromIndex (line 53) | protected String getChromosomeNameFromIndex(int chr) {

FILE: src/juicebox/tools/utils/original/stats/ParallelStatistics.java
  class ParallelStatistics (line 36) | public class ParallelStatistics {
    method ParallelStatistics (line 51) | public ParallelStatistics(int numThreads, StatisticsContainer mergedCo...
    method launchThreads (line 67) | public void launchThreads() {
    method runParallelizedStatistics (line 78) | public void runParallelizedStatistics(final StatisticsContainer merged...

FILE: src/juicebox/tools/utils/original/stats/ParallelStatisticsWorker.java
  class ParallelStatisticsWorker (line 38) | public class ParallelStatisticsWorker extends StatisticsWorker {
    method ParallelStatisticsWorker (line 42) | public ParallelStatisticsWorker(String siteFile, List<String> statsFil...
    method infileStatistics (line 49) | public void infileStatistics(Chunk chunk) {
    method getChromosomeNameFromIndex (line 76) | protected String getChromosomeNameFromIndex(int chr) {

FILE: src/juicebox/tools/utils/original/stats/StatisticsContainer.java
  class StatisticsContainer (line 33) | public class StatisticsContainer {
    method StatisticsContainer (line 84) | public StatisticsContainer() {
    method add (line 97) | public void add(StatisticsContainer individualContainer, int numberOfM...
    method commify (line 146) | private String commify(long value) {
    method percentify (line 150) | private String percentify(long num, long total) {
    method wholePercentify (line 154) | private String wholePercentify(long num, long total) {
    method outputStatsFile (line 158) | public void outputStatsFile(List<String> statsFiles) {
    method isUTLibrary (line 194) | private boolean isUTLibrary(boolean[] valsWereFound, long[] valsFound,...
    method writeLibComplexityIfNeeded (line 200) | private void writeLibComplexityIfNeeded(boolean[] valsWereFound, long[...
    method attempReadingDataFromExistingFile (line 239) | private void attempReadingDataFromExistingFile(boolean[] valsWereFound...
    method isSingleAlignment (line 276) | private boolean isSingleAlignment(String text) {
    method populateFoundVals (line 283) | private void populateFoundVals(String statsData, boolean[] valsWereFou...
    method attemptMapqCorrection (line 295) | private void attemptMapqCorrection(boolean[] valsWereGiven, long[] val...
    method appendPairTypeStatsOutputToFile (line 301) | void appendPairTypeStatsOutputToFile(int i, BufferedWriter statsOut) t...
    method writeOut (line 319) | private void writeOut(BufferedWriter statsOut, String description, boo...
    method writeHistFile (line 332) | public void writeHistFile(List<String> statsFiles) {
    method calculateConvergence (line 383) | public void calculateConvergence(int numMapQs) {
    method confirmConvergenceMaintained (line 398) | private boolean confirmConvergenceMaintained(int q, int startIndex, in...
    method getConvergenceError (line 407) | private double getConvergenceError(int q, int i) {

FILE: src/juicebox/tools/utils/original/stats/StatisticsWorker.java
  class StatisticsWorker (line 34) | public abstract class StatisticsWorker {
    method StatisticsWorker (line 51) | public StatisticsWorker(String siteFile, List<String> statsFiles, List...
    method getResultsContainer (line 63) | public StatisticsContainer getResultsContainer() {
    method processSingleEntry (line 67) | protected boolean processSingleEntry(AlignmentPair pair, String blockK...
    method populateDist (line 226) | private void populateDist(long[] array, long[] arrayDangling, int ind,...
    method populateLIOR (line 233) | private void populateLIOR(boolean distGT20KB, long[] array, List<Map<I...
    method distHindIII (line 267) | private int distHindIII(boolean strand, int chrIndex, int pos, int fra...
    method getChromosomeNameFromIndex (line 305) | protected abstract String getChromosomeNameFromIndex(int chr);
    method bSearch (line 307) | private static int bSearch(int distance) {

FILE: src/juicebox/track/CategoryPanel.java
  class CategoryPanel (line 52) | class CategoryPanel extends JPanel {
    method CategoryPanel (line 60) | public CategoryPanel(String name, List<ResourceLocator> locatorList, S...
    method getSelectedTracks (line 108) | public Collection<String> getSelectedTracks() {
    method getPreferredSize (line 132) | @Override
    method getMinimumSize (line 157) | @Override
    method doLayout (line 162) | @Override

FILE: src/juicebox/track/EigenvectorTrack.java
  class EigenvectorTrack (line 51) | public class EigenvectorTrack extends HiCTrack {
    method EigenvectorTrack (line 66) | public EigenvectorTrack(String id, String name, HiC hic, boolean isCon...
    method loadData (line 73) | private double[] loadData(int chrIdxPreCtrlInt, int zoomBinSize) {
    method getCacheKey (line 111) | private String getCacheKey(int chrIdx, int zoomBinSize) {
    method getToolTipText (line 119) | @Override
    method getPopupMenu (line 132) | @Override
    method flipEigenvector (line 156) | protected void flipEigenvector(int chrIdx, int zoomBinSize) {
    method render (line 172) | @Override
    method getAppropriateZD (line 243) | private MatrixZoomData getAppropriateZD() {
    method getName (line 255) | public String getName() {
    method setName (line 259) | @Override
    method getRenderer (line 264) | public Renderer<?> getRenderer() {
    method forceRefreshCache (line 268) | public void forceRefreshCache() {
    method drawRotatedString (line 275) | private void drawRotatedString(Graphics2D g2, String string, float x, ...

FILE: src/juicebox/track/HiCCoverageDataSource.java
  class HiCCoverageDataSource (line 48) | public class HiCCoverageDataSource implements HiCDataSource {
    method HiCCoverageDataSource (line 57) | public HiCCoverageDataSource(HiC hic, NormalizationType no, boolean is...
    method initDataRange (line 68) | private void initDataRange() {
    method getDataRange (line 91) | public DataRange getDataRange() {
    method setDataRange (line 98) | public void setDataRange(DataRange dataRange) {
    method getName (line 102) | public String getName() {
    method setName (line 106) | public void setName(String name) {
    method getPosColor (line 110) | public Color getPosColor() {
    method setColor (line 114) | public void setColor(Color color) {
    method getNegColor (line 118) | public Color getNegColor() {
    method setNegColor (line 122) | public void setNegColor(Color color) {
    method isLog (line 126) | public boolean isLog() {
    method getAvailableWindowFunctions (line 130) | public Collection<WindowFunction> getAvailableWindowFunctions() {
    method getData (line 134) | public HiCDataPoint[] getData(Chromosome chr, int startBin, int endBin...
    class CoverageDataPoint (line 169) | public static class CoverageDataPoint implements HiCDataPoint {
      method CoverageDataPoint (line 177) | public CoverageDataPoint(int binNumber, long genomicStart, long geno...
      method getBinNumber (line 184) | @Override
      method getWithInBins (line 189) | @Override
      method getGenomicStart (line 194) | @Override
      method getValue (line 199) | @Override
      method getGenomicEnd (line 205) | @Override

FILE: src/juicebox/track/HiCDataAdapter.java
  class HiCDataAdapter (line 40) | public abstract class HiCDataAdapter implements HiCDataSource {
    method HiCDataAdapter (line 47) | HiCDataAdapter(HiC hic) {
    method isLog (line 52) | @Override
    method getData (line 57) | @Override
    method setName (line 164) | @Override
    method getLocusScores (line 169) | protected abstract List<LocusScore> getLocusScores(String chr,
    class DataAccumulator (line 175) | public static class DataAccumulator implements HiCDataPoint {
      method DataAccumulator (line 186) | public DataAccumulator(double binNumber) {
      method DataAccumulator (line 190) | public DataAccumulator(double binNumber, double delta, long genomicS...
      method getBinNumber (line 197) | @Override
      method getWithInBins (line 202) | @Override
      method getGenomicEnd (line 207) | @Override
      method getGenomicStart (line 212) | @Override
      method getValue (line 217) | @Override
      method addScore (line 223) | void addScore(LocusScore ls) {
    class LoadedDataInterval (line 239) | class LoadedDataInterval {
      method LoadedDataInterval (line 250) | LoadedDataInterval(String zoom, int scaleFactor, String axisType, Wi...
      method contains (line 262) | boolean contains(String zoom, int scaleFactor, String axisType, Wind...
      method getData (line 273) | DataAccumulator[] getData() {

FILE: src/juicebox/track/HiCDataPoint.java
  type HiCDataPoint (line 34) | public interface HiCDataPoint {
    method getBinNumber (line 36) | double getBinNumber();
    method getGenomicStart (line 38) | long getGenomicStart();
    method getGenomicEnd (line 40) | long getGenomicEnd();
    method getValue (line 42) | double getValue(WindowFunction windowFunction);
    method getWithInBins (line 44) | double getWithInBins();

FILE: src/juicebox/track/HiCDataSource.java
  type HiCDataSource (line 39) | public interface HiCDataSource {
    method getName (line 41) | String getName();
    method setName (line 43) | void setName(String text);
    method getPosColor (line 45) | Color getPosColor();
    method setColor (line 47) | void setColor(Color selectedColor);
    method getNegColor (line 49) | Color getNegColor();
    method setNegColor (line 51) | void setNegColor(Color selectedColor);
    method getDataRange (line 53) | DataRange getDataRange();
    method setDataRange (line 55) | void setDataRange(DataRange dataRange);
    method isLog (line 57) | boolean isLog();
    method getData (line 59) | HiCDataPoint[] getData(Chromosome chr, int startBin, int endBin, HiCGr...
    method getAvailableWindowFunctions (line 61) | Collection<WindowFunction> getAvailableWindowFunctions();

FILE: src/juicebox/track/HiCDataTrack.java
  class HiCDataTrack (line 50) | public class HiCDataTrack extends HiCTrack {
    method HiCDataTrack (line 64) | public HiCDataTrack(HiC hic, ResourceLocator locator, HiCDataSource da) {
    method render (line 71) | @Override
    method getWindowFunction (line 184) | public WindowFunction getWindowFunction() {
    method setWindowFunction (line 188) | public void setWindowFunction(WindowFunction windowFunction) {
    method getName (line 192) | public String getName() {
    method setName (line 196) | @Override
    method getToolTipText (line 203) | @Override
    method getPopupMenu (line 265) | @Override
    method getDataRange (line 286) | public DataRange getDataRange() {
    method setDataRange (line 290) | public void setDataRange(DataRange dataRange) {
    method getPosColor (line 294) | @Override
    method setPosColor (line 299) | @Override
    method getNegColor (line 304) | @Override
    method setNegColor (line 309) | @Override
    method getAvailableWindowFunctions (line 314) | public Collection<WindowFunction> getAvailableWindowFunctions() {

FILE: src/juicebox/track/HiCFeatureTrack.java
  class HiCFeatureTrack (line 54) | public class HiCFeatureTrack extends HiCTrack {
    method HiCFeatureTrack (line 64) | public HiCFeatureTrack(HiC hic, ResourceLocator locator, FeatureSource...
    method getFractionalBin (line 71) | public static double getFractionalBin(int position, double scaleFactor...
    method render (line 81) | @Override
    method getToolTipText (line 202) | @Override
    method getFeatureAtPixel (line 222) | private IGVFeature getFeatureAtPixel(int x, Context context, TrackPane...
    method getName (line 279) | @Override
    method setName (line 284) | public void setName(String name) {
    method drawStrandArrows (line 288) | protected void drawStrandArrows(Strand strand, int startX, int endX, i...
    method mouseClicked (line 309) | public void mouseClicked(int x, int y, Context context, TrackPanel.Ori...

FILE: src/juicebox/track/HiCFixedGridAxis.java
  class HiCFixedGridAxis (line 32) | public class HiCFixedGridAxis implements HiCGridAxis {
    method HiCFixedGridAxis (line 40) | public HiCFixedGridAxis(long binCount, int binSize, int[] sites) {
    method getBinSize (line 51) | @Override
    method getGenomicStart (line 56) | @Override
    method getGenomicEnd (line 61) | @Override
    method getGenomicMid (line 66) | @Override
    method getIGVZoom (line 71) | @Override
    method getBinNumberForGenomicPosition (line 76) | @Override
    method getBinNumberForFragment (line 81) | @Override
    method getBinCount (line 91) | @Override

FILE: src/juicebox/track/HiCFragmentAxis.java
  class HiCFragmentAxis (line 32) | public class HiCFragmentAxis implements HiCGridAxis {
    method HiCFragmentAxis (line 45) | public HiCFragmentAxis(int binSize, int[] sites, long chrLength) {
    method getGenomicStart (line 56) | @Override
    method getGenomicEnd (line 68) | @Override
    method getGenomicMid (line 113) | @Override
    method getIGVZoom (line 119) | @Override
    method getBinNumberForGenomicPosition (line 132) | @Override
    method getFragmentNumberForGenomicPosition (line 145) | private int getFragmentNumberForGenomicPosition(int position) {
    method getBinNumberForFragment (line 172) | @Override
    method getBinCount (line 181) | @Override
    method getBinSize (line 186) | @Override

FILE: src/juicebox/track/HiCGridAxis.java
  type HiCGridAxis (line 32) | public interface HiCGridAxis {
    method getGenomicStart (line 34) | long getGenomicStart(double binNumber);
    method getGenomicEnd (line 36) | long getGenomicEnd(double binNumber);
    method getGenomicMid (line 38) | long getGenomicMid(double binNumber);
    method getIGVZoom (line 40) | int getIGVZoom();
    method getBinCount (line 42) | long getBinCount();
    method getBinSize (line 44) | int getBinSize();
    method getBinNumberForGenomicPosition (line 46) | int getBinNumberForGenomicPosition(long genomePosition);
    method getBinNumberForFragment (line 48) | int getBinNumberForFragment(int fragmentX);

FILE: src/juicebox/track/HiCIGVDataAdapter.java
  class HiCIGVDataAdapter (line 42) | public class HiCIGVDataAdapter extends HiCDataAdapter {
    method HiCIGVDataAdapter (line 47) | public HiCIGVDataAdapter(HiC hic, DataTrack igvTrack) {
    method getMax (line 52) | public double getMax() {
    method getName (line 56) | public String getName() {
    method setName (line 60) | @Override
    method getPosColor (line 65) | public Color getPosColor() {
    method setColor (line 69) | @Override
    method isLogScale (line 74) | public boolean isLogScale() {
    method getNegColor (line 78) | public Color getNegColor() {
    method setNegColor (line 82) | @Override
    method getDataRange (line 87) | public DataRange getDataRange() {
    method setDataRange (line 91) | @Override
    method getAvailableWindowFunctions (line 96) | @Override
    method getLocusScores (line 101) | protected List<LocusScore> getLocusScores(String chr, long gStart, lon...

FILE: src/juicebox/track/HiCLoadDialog.java
  class HiCLoadDialog (line 43) | class HiCLoadDialog extends JDialog {
    method HiCLoadDialog (line 50) | public HiCLoadDialog(Frame parent, Map<String, List<ResourceLocator>> ...
    method initComponents (line 57) | private void initComponents(Map<String, List<ResourceLocator>> locator...
    method isCanceled (line 134) | public boolean isCanceled() {
    method getSelectedTracks (line 138) | public Collection<String> getSelectedTracks() {

FILE: src/juicebox/track/HiCTrack.java
  class HiCTrack (line 42) | public abstract class HiCTrack{
    method HiCTrack (line 49) | HiCTrack(ResourceLocator locator) {
    method getHeight (line 53) | public int getHeight() {
    method setHeight (line 57) | public void setHeight(int height) {
    method getLocator (line 61) | public ResourceLocator getLocator() {
    method mouseClicked (line 65) | public void mouseClicked(int x, int y, Context context, TrackPanel.Ori...
    method getPopupMenu (line 69) | public JPopupMenu getPopupMenu(final TrackPanel trackPanel, final Supe...
    method getName (line 110) | public abstract String getName();
    method setName (line 112) | public abstract void setName(String text);
    method getPosColor (line 114) | public Color getPosColor() {
    method setPosColor (line 118) | public void setPosColor(Color posColor) {
    method getNegColor (line 122) | public Color getNegColor() {
    method setNegColor (line 126) | public void setNegColor(Color negColor) {
    method render (line 130) | public abstract void render(Graphics g2d,
    method getToolTipText (line 136) | public abstract String getToolTipText(int x, int y, TrackPanel.Orienta...

FILE: src/juicebox/track/HiCTrackManager.java
  class HiCTrackManager (line 48) | public class HiCTrackManager {
    method HiCTrackManager (line 59) | public HiCTrackManager(SuperAdapter superAdapter, HiC hic) {
    method unsafeLoadTrackDirectPath (line 66) | public void unsafeLoadTrackDirectPath(final String path) {
    method loadCoverageTrack (line 71) | public void loadCoverageTrack(NormalizationType no, boolean isControl) {
    method unsafeTrackLoad (line 90) | public void unsafeTrackLoad(final List<ResourceLocator> locators) {
    method add (line 103) | public void add(HiCTrack track) {
    method unsafeLoadTrackDirect (line 108) | private void unsafeLoadTrackDirect(final ResourceLocator locator) {
    method removeTrack (line 203) | public void removeTrack(HiCTrack track) {
    method removeTrack (line 230) | public void removeTrack(ResourceLocator locator) {
    method moveTrackUp (line 244) | public void moveTrackUp(HiCTrack track) {
    method moveTrackDown (line 252) | public void moveTrackDown(HiCTrack track) {
    method getLoadedTracks (line 260) | public List<HiCTrack> getLoadedTracks() {
    method clearTracks (line 264) | public void clearTracks() {
    method loadGenome (line 287) | private Genome loadGenome() {
    method loadTribbleFile (line 317) | private void loadTribbleFile(ResourceLocator locator, List<HiCTrack> n...

FILE: src/juicebox/track/HiCWigAdapter.java
  class HiCWigAdapter (line 46) | public class HiCWigAdapter extends HiCDataAdapter {
    method HiCWigAdapter (line 55) | public HiCWigAdapter(HiC hic, String path) {
    method init (line 61) | private void init(String path) {
    method getLocusScores (line 105) | protected java.util.List<LocusScore> getLocusScores(String chr, long g...
    method getName (line 136) | @Override
    method setName (line 141) | @Override
    method getPosColor (line 146) | @Override
    method setColor (line 151) | @Override
    method getNegColor (line 156) | @Override
    method setNegColor (line 161) | @Override
    method getDataRange (line 166) | @Override
    method setDataRange (line 171) | @Override
    method getAvailableWindowFunctions (line 176) | @Override

FILE: src/juicebox/track/LoadAction.java
  class LoadAction (line 56) | public class LoadAction extends AbstractAction {
    method LoadAction (line 65) | public LoadAction(String s, MainWindow mainWindow, HiC hic, Runnable r...
    method createMasterDocument (line 73) | private static Document createMasterDocument(String xmlUrl, JFrame par...
    method readXMLDocument (line 102) | private static Document readXMLDocument(String url, StringBuffer error...
    method resolveIncludes (line 137) | private static Document resolveIncludes(Document document, StringBuffe...
    method getXmlUrl (line 178) | private String getXmlUrl() {
    method actionPerformed (line 187) | @Override
    method safeLoadNodes (line 203) | private void safeLoadNodes(final String xmlFile) {
    method checkBoxesForReload (line 220) | public void checkBoxesForReload(String track) {
    method getAvaliableXmlResourses (line 235) | private ArrayList<String> getAvaliableXmlResourses() throws Exception {
    method unsafeLoadNodes (line 277) | private List<ResourceLocator> unsafeLoadNodes(String xmlFile) {

FILE: src/juicebox/track/LoadEncodeAction.java
  class LoadEncodeAction (line 47) | public class LoadEncodeAction extends AbstractAction {
    method LoadEncodeAction (line 70) | public LoadEncodeAction(String s, MainWindow mainWindow, HiC hic, Runn...
    method checkEncodeBoxes (line 79) | public void checkEncodeBoxes(String track) {
    method actionPerformed (line 92) | @Override
    method safeLoadENCODETracks (line 129) | private void safeLoadENCODETracks(final List<EncodeFileRecord> records...
    method unsafeLoadENCODETracks (line 143) | private void unsafeLoadENCODETracks(List<EncodeFileRecord> records, St...
    method remove (line 181) | public void remove(ResourceLocator locator) {

FILE: src/juicebox/track/ResourceTree.java
  class ResourceTree (line 55) | public class ResourceTree {
    method ResourceTree (line 72) | public ResourceTree(final HiC hic, Document document) {
    method getAttribute (line 124) | private static String getAttribute(Element element, String key) {
    method getLocators (line 135) | public LinkedHashSet<ResourceLocator> getLocators() {
    method getDeselectedLocators (line 139) | public LinkedHashSet<ResourceLocator> getDeselectedLocators() {
    method showResourceTreeDialog (line 149) | public void showResourceTreeDialog(JFrame parent) {
    method addLocalButtonActionPerformed (line 243) | public boolean addLocalButtonActionPerformed(final SuperAdapter superA...
    method containsDuplicate (line 301) | private boolean containsDuplicate(DefaultMutableTreeNode treeNode) {
    method setSelectionForMatchingChildNodes (line 305) | private void setSelectionForMatchingChildNodes(DefaultMutableTreeNode ...
    method removeResourceFromLeaf (line 314) | private void removeResourceFromLeaf(CheckableResource resource, List<C...
    method removeChildNodeFromFeatureRoot (line 323) | private void removeChildNodeFromFeatureRoot(DefaultMutableTreeNode tre...
    method removeChildNodeFromAddedNodes (line 344) | private void removeChildNodeFromAddedNodes(DefaultMutableTreeNode tree...
    method getMatchingChildNodesFromAddedNodes (line 351) | private List<DefaultMutableTreeNode> getMatchingChildNodesFromAddedNod...
    method removeFeature (line 367) | private void removeFeature(DefaultMutableTreeNode node) {
    method createTreeFromDataset (line 392) | private void createTreeFromDataset(HiC hic, ResourceTree resourceTree) {
    method createTreeFromDOM (line 458) | private DefaultMutableTreeNode createTreeFromDOM(Document document) {
    method buildLocatorTree (line 489) | private void buildLocatorTree(DefaultMutableTreeNode treeNode, Element...
    method remove (line 569) | public void remove(ResourceLocator locator) {
    method addBack (line 591) | private void addBack(ResourceLocator locator) {
    method getSelectedResourceLocators (line 608) | private LinkedHashSet<ResourceLocator> getSelectedResourceLocators() {
    method checkTrackBoxesForReloadState (line 621) | public void checkTrackBoxesForReloadState(String track) {
    method expandTree (line 649) | private void expandTree() {
    type SelectableResource (line 667) | interface SelectableResource extends DataResource {
      method isSelected (line 669) | boolean isSelected();
      method setSelected (line 671) | void setSelected(boolean newValue);
    type DataResource (line 677) | interface DataResource {
      method getResourceLocator (line 679) | ResourceLocator getResourceLocator();
      method getText (line 681) | String getText();
      method setText (line 683) | void setText(String newValue);
      method isEnabled (line 685) | boolean isEnabled();
      method setEnabled (line 687) | void setEnabled(boolean value);
    class NodeRenderer (line 693) | static class NodeRenderer implements TreeCellRenderer {
      method NodeRenderer (line 701) | NodeRenderer() {
      method getTreeCellRendererComponent (line 720) | public Component getTreeCellRendererComponent(JTree tree, Object value,
      method getRendereringComponent (line 775) | LinkCheckBox getRendereringComponent() {
    class ResourceEditor (line 783) | static class ResourceEditor extends AbstractCellEditor
      method ResourceEditor (line 790) | ResourceEditor(JTree tree) {
      method checkOrUncheckParentNodesRecursively (line 798) | static void checkOrUncheckParentNodesRecursively(TreeNode node,
      method hasSelectedDescendants (line 842) | static boolean hasSelectedDescendants(TreeNode treeNode) {
      method doesNotHaveSelectedChildren (line 869) | static boolean doesNotHaveSelectedChildren(TreeNode treeNode) {
      method getCellEditorValue (line 889) | public Object getCellEditorValue() {
      method uncheckCurrentNodeIfAllowed (line 967) | private void uncheckCurrentNodeIfAllowed(CheckableResource resource,
      method checkOrUncheckChildNodesRecursively (line 987) | private void checkOrUncheckChildNodesRecursively(TreeNode currentNode,
      method hasLockedDescendants (line 1030) | boolean hasLockedDescendants(TreeNode treeNode) {
      method hasSelectedAndLockedDescendants (line 1131) | boolean hasSelectedAndLockedDescendants(TreeNode treeNode) {
      method isCellEditable (line 1170) | @Override
      method getTreeCellEditorComponent (line 1198) | public Component getTreeCellEditorComponent(JTree tree, Object value,
    class CheckableResource (line 1221) | public static class CheckableResource implements SelectableResource {
      method CheckableResource (line 1231) | CheckableResource(String text, boolean selected,
      method isSelected (line 1239) | public boolean isSelected() {
      method setSelected (line 1243) | public void setSelected(boolean newValue) {
      method isEnabled (line 1247) | public boolean isEnabled() {
      method setEnabled (line 1251) | public void setEnabled(boolean value) {
      method getText (line 1255) | public String getText() {
      method setText (line 1259) | public void setText(String newValue) {
      method getResourceLocator (line 1263) | public ResourceLocator getResourceLocator() {
      method isParentOfPartiallySelectedChildren (line 1267) | public boolean isParentOfPartiallySelectedChildren() {
      method toString (line 1271) | @Override

FILE: src/juicebox/track/TrackConfigDialog.java
  class TrackConfigDialog (line 43) | class TrackConfigDialog extends JDialog {
    method TrackConfigDialog (line 58) | public TrackConfigDialog(Frame owner, HiCTrack track) {
    method minYFieldFocusLost (line 106) | private void minYFieldFocusLost(FocusEvent e) {
    method maxYFieldFocusLost (line 115) | private void maxYFieldFocusLost(FocusEvent e) {
    method isNotCanceled (line 124) | public boolean isNotCanceled() {
    method okButtonActionPerformed (line 129) | private void okButtonActionPerformed(ActionEvent e) {
    method cancelButtonActionPerformed (line 154) | private void cancelButtonActionPerformed(ActionEvent e) {
    method initComponents (line 183) | private void initComponents() {
    method validateNumeric (line 421) | private boolean validateNumeric(String text) {

FILE: src/juicebox/track/TrackConfigPanel.java
  class TrackConfigPanel (line 43) | public class TrackConfigPanel extends JPanel {
    method TrackConfigPanel (line 57) | public TrackConfigPanel(SuperAdapter superAdapter, HiCTrack track) {
    method minYFieldFocusLost (line 101) | private void minYFieldFocusLost(FocusEvent e) {
    method maxYFieldFocusLost (line 110) | private void maxYFieldFocusLost(FocusEvent e) {
    method initComponents (line 119) | private void initComponents(final SuperAdapter superAdapter) {
    method dataActionDocument (line 261) | private DocumentListener dataActionDocument(final JTextField field, fi...
    method performDataAction (line 288) | private void performDataAction(SuperAdapter superAdapter) {
    method isReasonableText (line 306) | private boolean isReasonableText(String text) {
    method validateNumeric (line 310) | private boolean validateNumeric(String text) {

FILE: src/juicebox/track/TrackLabelPanel.java
  class TrackLabelPanel (line 46) | public class TrackLabelPanel extends JPanel {
    method TrackLabelPanel (line 55) | public TrackLabelPanel(HiC hic) {
    method setBounds (line 60) | @Override
    method updateLabels (line 73) | public void updateLabels() {
    method getTrackLabel (line 100) | private JLabel getTrackLabel(String name, boolean addToolTip) {

FILE: src/juicebox/track/TrackPanel.java
  class TrackPanel (line 53) | public class TrackPanel extends JPanel {
    method TrackPanel (line 63) | public TrackPanel(SuperAdapter superAdapter, HiC hiC, Orientation orie...
    method removeTrack (line 79) | public void removeTrack(HiCTrack track) {
    method moveTrackUp (line 86) | public void moveTrackUp(HiCTrack track) {
    method moveTrackDown (line 93) | public void moveTrackDown(HiCTrack track) {
    method getTrackList (line 101) | public List<HiCTrack> getTrackList() {
    method addMouseAdapter (line 105) | private void addMouseAdapter(final SuperAdapter superAdapter) {
    method getHeight (line 187) | @Override
    method getWidth (line 201) | @Override
    method getPreferredSize (line 226) | @Override
    method paintComponent (line 231) | protected void paintComponent(Graphics g) {
    method getContext (line 347) | private Context getContext() {
    method tooltipText (line 351) | public String tooltipText(int mx, int my, boolean isMouseDirectlyOnTra...
    type Orientation (line 399) | public enum Orientation {X, Y}

FILE: src/juicebox/track/feature/AnnotationLayer.java
  class AnnotationLayer (line 43) | public class AnnotationLayer {
    method AnnotationLayer (line 58) | public AnnotationLayer() {
    method AnnotationLayer (line 64) | public AnnotationLayer(Feature2DList inputList) {
    method AnnotationLayer (line 69) | public AnnotationLayer(Feature2DHandler feature2DHandler, LayerType la...
    method reset (line 75) | private void reset() {
    method clearAnnotations (line 85) | public void clearAnnotations() {
    method getLayerType (line 90) | public LayerType getLayerType() {
    method setLayerType (line 94) | public void setLayerType(LayerType layerType) {
    method add (line 99) | public void add(int chr1Idx, int chr2Idx, Feature2D feature) {
    method makeTempFile (line 129) | private void makeTempFile() {
    method deleteTempFile (line 141) | private void deleteTempFile() {
    method getLayerVisibility (line 154) | public boolean getLayerVisibility() {
    method setLayerVisibility (line 159) | public void setLayerVisibility(boolean newStatus) {
    method getIdentifier (line 164) | private String getIdentifier(Feature2D feature) {
    method undo (line 169) | public void undo() {
    method updateAutoSave (line 176) | private void updateAutoSave() {
    method reSaveAll (line 185) | private void reSaveAll() {
    method hasLoop (line 191) | public boolean hasLoop(MatrixZoomData zd, int chrIdx1, int chrIdx2, in...
    method removeRecentFromList (line 200) | private void removeRecentFromList(int idx1, int idx2, Feature2D featur...
    method removeFromList (line 223) | public void removeFromList(MatrixZoomData zd, int chrIdx1, int chrIdx2...
    method exportAnnotations (line 248) | public boolean exportAnnotations(String outputFilePath) {
    method exportOverlap (line 256) | public boolean exportOverlap(Feature2DList otherAnnotations, String ou...
    method getAndAddAttributes (line 264) | private void getAndAddAttributes(List<String> featureKeys) {
    method addAllAttributeValues (line 274) | public void addAllAttributeValues(String key, String newValue) {
    method getNearbyFeatures (line 279) | public List<Feature2D> getNearbyFeatures(MatrixZoomData zd, int chrIdx...
    method getIntersectingFeatures (line 285) | public List<Feature2D> getIntersectingFeatures(int chrIdx1, int chrIdx...
    method getFeatureHandler (line 289) | public Feature2DHandler getFeatureHandler() {
    method getId (line 293) | public int getId() {
    method resetCounter (line 297) | public void resetCounter() {
    method getNumberOfFeatures (line 301) | public int getNumberOfFeatures() {
    method setColorOfAllAnnotations (line 305) | public void setColorOfAllAnnotations(Color color) {
    method getIsSparse (line 309) | public boolean getIsSparse() {
    method setIsSparse (line 313) | public void setIsSparse(boolean isSparse) {
    method createMergedLoopLists (line 317) | public void createMergedLoopLists(List<Feature2DList> lists) {
    method createMergedLoopLists (line 321) | public void createMergedLoopLists(Feature2DList list) {
    method getFeatureList (line 327) | public Feature2DList getFeatureList() {
    method getAutosaveFilename (line 331) | private String getAutosaveFilename() {
    method getAutosaveFile (line 335) | private File getAutosaveFile() {
    type LayerType (line 339) | public enum LayerType {DEFAULT, EDIT, SCAFFOLD, SUPERSCAFFOLD}

FILE: src/juicebox/track/feature/AnnotationLayerHandler.java
  class AnnotationLayerHandler (line 50) | public class AnnotationLayerHandler {
    method AnnotationLayerHandler (line 73) | public AnnotationLayerHandler() {
    method AnnotationLayerHandler (line 79) | public AnnotationLayerHandler(Feature2DList feature2DList) {
    method resetSelection (line 85) | private void resetSelection() {
    method doPeak (line 91) | public void doPeak() {
    method doDomain (line 95) | private void doDomain() {
    method setStationaryStart (line 99) | public void setStationaryStart(long start1, long start2) {
    method setStationaryEnd (line 104) | public void setStationaryEnd(long end1, long end2) {
    method updateSelectionRegion (line 110) | public void updateSelectionRegion(Rectangle newRegion) {
    method setLastItem (line 140) | public void setLastItem(int idx1, int idx2, Feature2D lastLoop) {
    method clearLastItem (line 146) | private void clearLastItem() {
    method generateFeature (line 160) | public Feature2D generateFeature(HiC hic) {
    method addFeature (line 235) | public Feature2D addFeature(HiC hic) {
    method generateTempSelectedGroup (line 242) | private Feature2D generateTempSelectedGroup(List<Feature2D> selectedFe...
    method addTempSelectedGroup (line 261) | public Feature2D addTempSelectedGroup(List<Feature2D> selectedFeatures...
    method getTempSelectedGroups (line 267) | private List<Feature2D> getTempSelectedGroups(int chr1Idx, int chr2Idx) {
    method filterTempSelectedGroup (line 280) | public void filterTempSelectedGroup(int chr1Idx, int chr2Idx) {
    method regionsOverlapSignificantly (line 287) | private boolean regionsOverlapSignificantly(long start1, long end1, lo...
    method pointsShouldSnapToDiagonal (line 300) | private boolean pointsShouldSnapToDiagonal(HiC hic, int x, int y, int ...
    method allPointsAreOnSameSideOfDiagonal (line 315) | private boolean allPointsAreOnSameSideOfDiagonal(HiC hic, int x, int y...
    method undo (line 360) | public void undo(JButton undoButton) {
    method nearDiagonal (line 369) | private boolean nearDiagonal(HiC hic, int x, int y) {
    method geneXPos (line 390) | private long geneXPos(HiC hic, int x, int displacement) {
    method geneYPos (line 403) | private long geneYPos(HiC hic, int y, int displacement) {
    method getXBin (line 415) | private int getXBin(HiC hic, int x) {
    method getYBin (line 419) | private int getYBin(HiC hic, int y) {
    method getLayerVisibility (line 423) | public boolean getLayerVisibility() {
    method setLayerVisibility (line 427) | public void setLayerVisibility(boolean showCustom) {
    method getAnnotationLayerType (line 431) | public AnnotationLayer.LayerType getAnnotationLayerType() {
    method clearAnnotations (line 435) | public void clearAnnotations() {
    method getAnnotationLayer (line 439) | public AnnotationLayer getAnnotationLayer() {
    method setAnnotationLayer (line 443) | private void setAnnotationLayer(AnnotationLayer annotationLayer) {
    method getNearbyFeatures (line 447) | public List<Feature2D> getNearbyFeatures(MatrixZoomData zd, int chr1Id...
    method getIntersectingFeatures (line 454) | private List<Feature2D> getIntersectingFeatures(int chr1Idx, int chr2I...
    method getSelectedFeatures (line 462) | public List<Feature2D> getSelectedFeatures(HiC hic, int lastX, int las...
    method selectSingleRegion (line 523) | private List<Feature2D> selectSingleRegion(int chr1Idx, int chr2Idx, i...
    method removeFromList (line 545) | public void removeFromList(MatrixZoomData zd, int chr1Idx, int chr2Idx...
    method hasLoop (line 551) | public boolean hasLoop(MatrixZoomData zd, int chr1Idx, int chr2Idx, in...
    method getLayerName (line 557) | public String getLayerName() {
    method setLayerNameAndOtherField (line 561) | public void setLayerNameAndOtherField(String layerName) {
    method setLayerNameAndField (line 569) | public void setLayerNameAndField(String layerName) {
    method getFeatureHandler (line 576) | public Feature2DHandler getFeatureHandler() {
    method getIsTransparent (line 580) | public boolean getIsTransparent() {
    method setIsTransparent (line 584) | public void setIsTransparent(boolean isTransparent) {
    method getIsEnlarged (line 588) | public boolean getIsEnlarged() {
    method setIsEnlarged (line 592) | public void setIsEnlarged(boolean isEnlarged) {
    method getPlottingStyle (line 596) | public FeatureRenderer.PlottingOption getPlottingStyle() {
    method setPlottingStyle (line 600) | public void setPlottingStyle(FeatureRenderer.PlottingOption plottingSt...
    method exportAnnotations (line 607) | public void exportAnnotations() {
    method getImportAnnotationsEnabled (line 611) | private boolean getImportAnnotationsEnabled() {
    method setImportAnnotationsEnabled (line 615) | public void setImportAnnotationsEnabled(boolean status) {
    method loadLoopList (line 622) | public void loadLoopList(String path, ChromosomeHandler chromosomeHand...
    method getAllVisibleLoops (line 632) | public Feature2DList getAllVisibleLoops() {
    method setExportAbility (line 637) | public void setExportAbility(boolean allowed) {
    method setExportButton (line 647) | public void setExportButton(JButton exportButton) {
    method setCensorButton (line 651) | public void setCensorButton(JButton censorButton) {
    method getExportCapability (line 655) | public boolean getExportCapability() {
    method setUndoAbility (line 659) | public void setUndoAbility(boolean allowed) {
    method setUndoButton (line 666) | public void setUndoButton(JButton undoButton) {
    method getUndoCapability (line 670) | public boolean getUndoCapability() {
    method isActiveLayer (line 674) | public boolean isActiveLayer(SuperAdapter superAdapter) {
    method setActiveLayerButtonStatus (line 678) | public void setActiveLayerButtonStatus(boolean status) {
    method setActiveLayerButton (line 685) | public void setActiveLayerButton(JToggleButton activeLayerButton) {
    method getNumberOfFeatures (line 689) | public int getNumberOfFeatures() {
    method setColorOfAllAnnotations (line 693) | public void setColorOfAllAnnotations(Color color) {
    method getDefaultColor (line 698) | public Color getDefaultColor() {
    method setDefaultColor (line 702) | private void setDefaultColor(Color defaultColor) {
    method setDeleteLayerButtonStatus (line 710) | public void setDeleteLayerButtonStatus(boolean status) {
    method setDeleteLayerButton (line 717) | public void setDeleteLayerButton(JButton deleteLayerButton) {
    method getIsSparse (line 721) | public boolean getIsSparse() {
    method setIsSparse (line 725) | public void setIsSparse(boolean isSparse) {
    method getLineStyle (line 729) | public FeatureRenderer.LineStyle getLineStyle() {
    method setLineStyle (line 733) | public void setLineStyle(FeatureRenderer.LineStyle lineStyle) {
    method duplicateDetailsFrom (line 737) | public void duplicateDetailsFrom(AnnotationLayerHandler handlerOrigina...
    method mergeDetailsFrom (line 755) | public void mergeDetailsFrom(Collection<AnnotationLayerHandler> origin...
    method togglePlottingStyle (line 774) | public void togglePlottingStyle() {
    method setPlottingStyleButton (line 782) | public void setPlottingStyleButton(PlottingStyleButton plottingStyleBu...
    method setColorChooserPanel (line 786) | public void setColorChooserPanel(ColorChooserPanel colorChooserPanel) {
    method setNameTextField (line 790) | public void setNameTextField(JTextField nameTextField) {
    method setMiniNameLabelField (line 794) | public void setMiniNameLabelField(JLabel miniNameLabel) {
    method setProperties (line 798) | public void setProperties(AnnotationLayer scaffoldLayer, String name, ...
    method convertToFeaturePairs (line 804) | public List<Feature2DGuiContainer> convertToFeaturePairs(AnnotationLay...

FILE: src/juicebox/track/feature/CustomAnnotationRTree2DHandler.java
  class CustomAnnotationRTree2DHandler (line 37) | class CustomAnnotationRTree2DHandler extends Feature2DHandler {
    method CustomAnnotationRTree2DHandler (line 39) | public CustomAnnotationRTree2DHandler(Feature2DList inputList) {
    method add (line 44) | public void add(int chr1Idx, int chr2Idx, Feature2D feature) {
    method getNumberOfFeatures (line 50) | public int getNumberOfFeatures() {
    method addAttributeFieldToAll (line 54) | public void addAttributeFieldToAll(String key, String aNull) {
    method autoSaveNew (line 63) | public void autoSaveNew(PrintWriter outputFile, Feature2D feature) {
    method autoSaveAll (line 72) | public void autoSaveAll(PrintWriter outputFile) {
    method checkAndRemoveFeature (line 76) | public boolean checkAndRemoveFeature(int idx1, int idx2, Feature2D fea...
    method getOverlap (line 85) | public Feature2DList getOverlap(Feature2DList inputList) {
    method extractSingleFeature (line 91) | public Feature2D extractSingleFeature() {
    method get (line 96) | public List<Feature2D> get(int chrIdx1, int chrIdx2) {
    method exportFeatureList (line 101) | public boolean exportFeatureList(File file, boolean b, Feature2DList.L...

FILE: src/juicebox/track/feature/Feature2D.java
  class Feature2D (line 48) | public class Feature2D implements Comparable<Feature2D> {
    method Feature2D (line 69) | public Feature2D(FeatureType featureType, String chr1, long start1, lo...
    method getDefaultOutputFileHeader (line 83) | public static String getDefaultOutputFileHeader() {
    method getFeatureType (line 91) | public FeatureType getFeatureType() {
    method getFeatureName (line 95) | private String getFeatureName() {
    method getChr1 (line 105) | public String getChr1() {
    method getChr2 (line 109) | public String getChr2() {
    method getStart1 (line 113) | public long getStart1() {
    method getStart2 (line 117) | public long getStart2() {
    method getEnd1 (line 121) | public long getEnd1() {
    method setEnd1 (line 125) | public void setEnd1(int end1) {
    method getEnd2 (line 131) | public long getEnd2() {
    method setEnd2 (line 135) | public void setEnd2(int end2) {
    method getWidth1 (line 141) | public long getWidth1() {
    method getWidth2 (line 145) | public long getWidth2() {
    method getMidPt1 (line 149) | public long getMidPt1() {
    method getMidPt2 (line 153) | public long getMidPt2() {
    method midPoint (line 157) | private long midPoint(long start, long end) {
    method getColor (line 161) | public Color getColor() {
    method setColor (line 170) | public void setColor(Color color) {
    method getTranslucentColor (line 177) | public Color getTranslucentColor() {
    method setTranslucentColor (line 185) | private void setTranslucentColor() {
    method tooltipText (line 191) | public String tooltipText() {
    method getOutputFileHeader (line 301) | public String getOutputFileHeader() {
    method simpleString (line 314) | private String simpleString() {
    method justColorString (line 318) | private String justColorString() {
    method simpleStringWithColor (line 322) | public String simpleStringWithColor() {
    method toString (line 332) | @Override
    method getAttributeKeys (line 345) | public ArrayList<String> getAttributeKeys() {
    method getAttribute (line 351) | public String getAttribute(String key) {
    method setAttribute (line 355) | public void setAttribute(String key, String newVal) {
    method getFloatAttribute (line 362) | public float getFloatAttribute(String key) {
    method addIntAttribute (line 366) | public void addIntAttribute(String key, int value) {
    method addFloatAttribute (line 370) | public void addFloatAttribute(String key, Float value) {
    method addStringAttribute (line 374) | public void addStringAttribute(String key, String value) {
    method overlapsWith (line 382) | public boolean overlapsWith(Feature2D otherFeature) {
    method compareTo (line 393) | @Override
    method isOnDiagonal (line 415) | public boolean isOnDiagonal() {
    method reflectionAcrossDiagonal (line 419) | public Feature2D reflectionAcrossDiagonal() {
    method isInLowerLeft (line 427) | public boolean isInLowerLeft() {
    method isInUpperRight (line 431) | public boolean isInUpperRight() {
    method doesNotContainAttributeKey (line 435) | public boolean doesNotContainAttributeKey(String attribute) {
    method containsAttributeValue (line 439) | public boolean containsAttributeValue(String attribute) {
    method containsAttributeKey (line 443) | public boolean containsAttributeKey(String attribute) {
    method getLocationKey (line 447) | public String getLocationKey() {
    method toArrowheadScore (line 451) | public ArrowheadScore toArrowheadScore() {
    method equals (line 456) | @Override
    method hashCode (line 484) | @Override
    method clearAttributes (line 489) | public void clearAttributes() {
    method getAnchors (line 493) | public List<MotifAnchor> getAnchors(boolean onlyUninitializedFeatures,...
    method deepCopy (line 509) | public Feature2D deepCopy() {
    method setSetIsSelectedColorUpdate (line 517) | public void setSetIsSelectedColorUpdate(boolean setIsSelectedColorUpda...
    method toFeature2DWithMotif (line 521) | public Feature2DWithMotif toFeature2DWithMotif() {
    method containsPoint (line 525) | public boolean containsPoint(float x, float y) {
    method containsPoint (line 529) | public boolean containsPoint(Point point) {
    type FeatureType (line 533) | public enum FeatureType {

FILE: src/juicebox/track/feature/Feature2DGuiContainer.java
  class Feature2DGuiContainer (line 33) | public class Feature2DGuiContainer {
    method Feature2DGuiContainer (line 39) | public Feature2DGuiContainer(Rectangle rectangle, Feature2D feature2D,...
    method getRectangle (line 45) | public Rectangle getRectangle() {
    method getFeature2D (line 49) | public Feature2D getFeature2D() {
    method getAnnotationLayerHandler (line 53) | public AnnotationLayerHandler getAnnotationLayerHandler() {

FILE: src/juicebox/track/feature/Feature2DList.java
  class Feature2DList (line 49) | public class Feature2DList {
    method parallelizedProcessLists (line 58) | public void parallelizedProcessLists(FeatureFunction featureFunction) {
    method filterLists (line 81) | public synchronized void filterLists(FeatureFilter filter) {
    method Feature2DList (line 89) | public Feature2DList() {
    method Feature2DList (line 92) | public Feature2DList(Feature2DList list) {
    method getKey (line 104) | public static String getKey(int chr1Idx, int chr2Idx) {
    method getKey (line 126) | public static String getKey(Chromosome chr1, Chromosome chr2) {
    method getIntersection (line 137) | public static Feature2DList getIntersection(final Feature2DList listA,...
    method addAllUnique (line 163) | private synchronized static void addAllUnique(List<Feature2D> inputFea...
    method get (line 179) | public List<Feature2D> get(int chr1Idx, int chr2Idx) {
    method get (line 195) | public List<Feature2D> get(String key) {
    method add (line 210) | public synchronized void add(int chr1Idx, int chr2Idx, Feature2D featu...
    method addByKey (line 223) | public synchronized void addByKey(String key, Feature2D feature) {
    method addByKey (line 242) | public synchronized void addByKey(String key, List<Feature2D> features) {
    method updateAttributeForFeature (line 252) | private synchronized Feature2D updateAttributeForFeature(Feature2D fea...
    method updateAttributes (line 272) | private synchronized List<Feature2D> updateAttributes(List<Feature2D> ...
    method putFeature (line 284) | private synchronized void putFeature(String key, List<Feature2D> loops) {
    method exportFeatureList (line 294) | public boolean exportFeatureList(File outputFile, boolean formattedOut...
    method exportFeatureList (line 312) | private boolean exportFeatureList(final PrintWriter outputFilePrintWri...
    method autoSaveNew (line 398) | public void autoSaveNew(PrintWriter outputFile, Feature2D feature) {
    method autoSaveAll (line 409) | public void autoSaveAll(PrintWriter outputFile) {
    method extractSingleFeature (line 424) | public Feature2D extractSingleFeature() {
    method setColor (line 438) | public void setColor(final Color color) {
    method add (line 456) | public synchronized void add(Feature2DList inputList) {
    method addUnique (line 480) | public synchronized void addUnique(Feature2DList inputList) {
    method getOverlap (line 498) | public Feature2DList getOverlap(Feature2DList inputList) {
    method setDefaultAttributes (line 516) | public synchronized void setDefaultAttributes(Map<String, String> defa...
    method addDefaultAttribute (line 521) | public synchronized void addDefaultAttribute(String attribute, String ...
    method addAttributeFieldToAll (line 527) | public synchronized void addAttributeFieldToAll(final String newAttrib...
    method removeDuplicates (line 543) | public void removeDuplicates() {
    method getKeySet (line 557) | private Set<String> getKeySet() {
    method getFeatureList (line 567) | List<Feature2D> getFeatureList(String key) {
    type ListFormat (line 571) | public enum ListFormat {ENRICHED, FINAL, LOCALIZED, ARROWHEAD, NA}
    method processLists (line 578) | public synchronized void processLists(FeatureFunction function) {
    method containsKey (line 589) | public boolean containsKey(String key) {
    method getIndex (line 593) | public int getIndex(Chromosome chrX, Chromosome chrY, Feature2D featur...
    method getNumTotalFeatures (line 607) | public int getNumTotalFeatures() {
    method checkAndRemoveFeature (line 615) | public synchronized boolean checkAndRemoveFeature(int idx1, int idx2, ...
    method searchForFeature (line 631) | public Feature2D searchForFeature(final int c1, final int start1, fina...
    method clearAllAttributes (line 649) | public void clearAllAttributes() {
    method deepCopy (line 660) | public Feature2DList deepCopy() {
    method printChromosomeRegionKeys (line 672) | public String printChromosomeRegionKeys() {

FILE: src/juicebox/track/feature/Feature2DParser.java
  class Feature2DParser (line 51) | public class Feature2DParser {
    method loadFeatures (line 53) | public static Feature2DList loadFeatures(String path, String genomeID,...
    method loadFeatures (line 58) | public static Feature2DList loadFeatures(String path, ChromosomeHandle...
    method parseTitleForFeatureType (line 105) | private static Feature2D.FeatureType parseTitleForFeatureType(String p...
    method parseHighScoreList (line 115) | public static Feature2DList parseHighScoreList(int chrIndex, String ch...
    method parseArrowheadScoreList (line 125) | public static Feature2DList parseArrowheadScoreList(int chrIndex, Stri...
    method parseGeneralFile (line 133) | private static Feature2DList parseGeneralFile(String path, ChromosomeH...
    method getHeaders (line 185) | private static String[] getHeaders(String line) {
    class SpecificParser (line 211) | private static abstract class SpecificParser {
      method SpecificParser (line 215) | SpecificParser() {
      method parseAttributes (line 219) | private static Map<String, String> parseAttributes(boolean loadAttri...
      method addToList (line 229) | private static void addToList(String chr1Name, String chr2Name, Chro...
      method addToList (line 255) | private static void addToList(String chrAName, Feature2D feature, Ch...
      method handleError (line 265) | private static void handleError(String nextLine) {
      method parseAndAddToList (line 276) | abstract void parseAndAddToList(String path, String[] headers, Strin...
      method parseDomainsAndAddToList (line 279) | void parseDomainsAndAddToList(String path, String[] headers, String[...
      method parseBEDPEAndAddToList (line 304) | void parseBEDPEAndAddToList(String path, String[] headers, String[] ...
      method parseLegacyLoopsAndAddToList (line 344) | void parseLegacyLoopsAndAddToList(String path, String[] headers, Str...
      method parsePxLoopsAndAddToList (line 375) | void parsePxLoopsAndAddToList(String path, String[] headers, String[...

FILE: src/juicebox/track/feature/Feature2DTools.java
  class Feature2DTools (line 38) | public class Feature2DTools {
    method extractPeaksNearCentroids (line 41) | public static Feature2DList extractPeaksNearCentroids(final Feature2DL...
    method extractPeaksNotNearCentroids (line 72) | public static Feature2DList extractPeaksNotNearCentroids(final Feature...
    method calculateFDR (line 111) | public static void calculateFDR(Feature2DList features, final float[][...
    method extractReproducibleCentroids (line 124) | public static Feature2DList extractReproducibleCentroids(final Feature...
    method extractReproducibleCentroids (line 151) | public static Feature2DList extractReproducibleCentroids(final Feature...
    method getPeaksNearDiagonal (line 188) | public static Feature2DList getPeaksNearDiagonal(Feature2DList feature...
    method getStrongPeaks (line 208) | public static Feature2DList getStrongPeaks(Feature2DList feature2DList...
    method compareLists (line 230) | public static Feature2DList compareLists(final Feature2DList listA, fi...
    method subtract (line 271) | public static Feature2DList subtract(final Feature2DList listA, final ...
    method loopIsUpstreamOfDomain (line 287) | public static boolean loopIsUpstreamOfDomain(Feature2D loop, Feature2D...
    method loopIsDownstreamOfDomain (line 292) | public static boolean loopIsDownstreamOfDomain(Feature2D loop, Feature...
    method domainContainsLoopWithinExpandedTolerance (line 297) | public static boolean domainContainsLoopWithinExpandedTolerance(Featur...
    method doesOverlap (line 311) | public static boolean doesOverlap(Feature2D feature, List<Feature2D> e...
    method isResolutionPresent (line 321) | public static boolean isResolutionPresent(final Feature2DList feature2...

FILE: src/juicebox/track/feature/Feature2DWithMotif.java
  class Feature2DWithMotif (line 39) | public class Feature2DWithMotif extends Feature2D {
    method Feature2DWithMotif (line 73) | public Feature2DWithMotif(FeatureType featureType, String chr1, long s...
    method updateMotifData (line 80) | public void updateMotifData(boolean strand, boolean unique, String seq...
    method importAttributesForMotifInformation (line 134) | private void importAttributesForMotifInformation() {
    method getOutputFileHeader (line 205) | @Override
    method toString (line 219) | @Override
    method getAnchors (line 258) | @Override
    method equals (line 288) | @Override
    method hashCode (line 356) | @Override
    method getConvergenceStatus (line 361) | public int getConvergenceStatus() {
    method deepCopy (line 388) | @Override

FILE: src/juicebox/track/feature/FeatureFilter.java
  type FeatureFilter (line 32) | public interface FeatureFilter {
    method filter (line 33) | List<Feature2D> filter(String chr, List<Feature2D> feature2DList);

FILE: src/juicebox/track/feature/FeatureFunction.java
  type FeatureFunction (line 32) | public interface FeatureFunction {
    method process (line 33) | void process(String chr, List<Feature2D> feature2DList);

FILE: src/juicebox/windowui/DisabledGlassPane.java
  class DisabledGlassPane (line 46) | public class DisabledGlassPane extends JComponent implements KeyListener {
    method DisabledGlassPane (line 51) | public DisabledGlassPane(int cursor) {
    method paintComponent (line 84) | @Override
    method setBackground (line 94) | @Override
    method keyPressed (line 105) | public void keyPressed(KeyEvent e) {
    method keyTyped (line 109) | public void keyTyped(KeyEvent e) {
    method keyReleased (line 112) | public void keyReleased(KeyEvent e) {
    method activate (line 121) | public void activate(String text) {
    method deactivate (line 136) | public void deactivate() {

FILE: src/juicebox/windowui/DumpDialog.java
  class DumpDialog (line 40) | public class DumpDialog extends JFileChooser {
    method DumpDialog (line 51) | public DumpDialog(MainWindow mainWindow, HiC hic) {
    method createDialog (line 129) | protected JDialog createDialog(Component component) throws HeadlessExc...

FILE: src/juicebox/windowui/EditFeatureAttributesDialog.java
  class EditFeatureAttributesDialog (line 46) | public class EditFeatureAttributesDialog extends JDialog implements Acti...
    method EditFeatureAttributesDialog (line 62) | public EditFeatureAttributesDialog(MainWindow mainWindow, Feature2D fe...
    method getValidatedText (line 142) | public String getValidatedText() {
    method actionPerformed (line 149) | public void actionPerformed(ActionEvent e) {
    method propertyChange (line 156) | public void propertyChange(PropertyChangeEvent e) {
    method clearAndHide (line 211) | private void clearAndHide() {

FILE: src/juicebox/windowui/FileDropTargetListener.java
  class FileDropTargetListener (line 41) | public class FileDropTargetListener implements DropTargetListener {
    method FileDropTargetListener (line 45) | public FileDropTargetListener(SuperAdapter superAdapter) {
    method dragEnter (line 49) | public void dragEnter(DropTargetDragEvent event) {
    method dragExit (line 56) | public void dragExit(DropTargetEvent event) {
    method dragOver (line 59) | public void dragOver(DropTargetDragEvent event) {
    method dropActionChanged (line 63) | public void dropActionChanged(DropTargetDragEvent event) {
    method drop (line 69) | public void drop(DropTargetDropEvent event) {
    method isDragNotAcceptable (line 104) | private boolean isDragNotAcceptable(DropTargetDragEvent event) {
    method isDropAcceptable (line 110) | private boolean isDropAcceptable(DropTargetDropEvent event) {

FILE: src/juicebox/windowui/GoToPanel.java
  class GoToPanel (line 55) | public class GoToPanel extends JPanel implements ActionListener, FocusLi...
    method GoToPanel (line 65) | public GoToPanel(SuperAdapter superAdapter) {
    method initializeGoToTextField (line 107) | private JTextField initializeGoToTextField() {
    method setEnabled (line 116) | public void setEnabled(boolean enabled) {
    method actionPerformed (line 123) | public void actionPerformed(ActionEvent event) {
    method setPositionChrLeft (line 135) | public void setPositionChrLeft(String newPositionDate) {
    method setPositionChrTop (line 139) | public void setPositionChrTop(String newPositionDate) {
    method parsePositionText (line 143) | private void parsePositionText() {
    method parse (line 243) | private List<String[]> parse(JTextField textField) {
    method extractResolutionParametersFromTokens (line 276) | private int[] extractResolutionParametersFromTokens(String[] chrTokens...
    method extractParametersFromTokens (line 294) | private int[] extractParametersFromTokens(String[] chrTokens, String[]...
    method getEstimationOfAppropriateZoomLevel (line 325) | private int getEstimationOfAppropriateZoomLevel(int diff0) {
    method cleanUpNumber (line 337) | private int cleanUpNumber(String number) {
    method parseGenePositionText (line 344) | private void parseGenePositionText() {
    method initializeGeneHashMap (line 356) | private void initializeGeneHashMap(String genomeID) {
    method unsafeInitializeGeneHashMap (line 381) | private void unsafeInitializeGeneHashMap(String genomeID) {
    method goToScaffoldName (line 406) | private void goToScaffoldName(String scafName1, String scafName2) {
    method extractGeneLocation (line 432) | private void extractGeneLocation() {
    method focusGained (line 464) | public void focusGained(FocusEvent event) {
    method focusLost (line 469) | public void focusLost(FocusEvent event) {

FILE: src/juicebox/windowui/HiCChromosomeFigPanel.java
  class HiCChromosomeFigPanel (line 52) | public class HiCChromosomeFigPanel extends JComponent {
    method HiCChromosomeFigPanel (line 63) | public HiCChromosomeFigPanel(final HiC hic) {
    method getHiCScale (line 148) | private Point2D.Double getHiCScale(int width, int height) {
    method setContext (line 157) | public void setContext(Context frame, Orientation orientation) {
    method paintComponent (line 162) | @Override
    method drawChr (line 194) | private void drawChr(Graphics2D g) {
    method genomeLength (line 239) | private long genomeLength() {
    method drawRegion (line 243) | private void drawRegion(Graphics2D g, int w, int h) {
    method isHorizontal (line 328) | private boolean isHorizontal() {
    type Orientation (line 332) | public enum Orientation {HORIZONTAL, VERTICAL}

FILE: src/juicebox/windowui/HiCKeyDispatcher.java
  class HiCKeyDispatcher (line 41) | public class HiCKeyDispatcher implements KeyEventDispatcher {
    method HiCKeyDispatcher (line 48) | public HiCKeyDispatcher(SuperAdapter superAdapter, HiC hic, JComboBox<...
    method dispatchKeyEvent (line 55) | @Override

FILE: src/juicebox/windowui/HiCLayout.java
  class HiCLayout (line 33) | public class HiCLayout implements LayoutManager2 {
    method addLayoutComponent (line 69) | public void addLayoutComponent(Component comp, Object constraints) {
    method addLayoutComponent (line 79) | public void addLayoutComponent(String name, Component comp) {
    method removeLayoutComponent (line 116) | public void removeLayoutComponent(Component comp) {
    method minimumLayoutSize (line 150) | public Dimension minimumLayoutSize(Container target) {
    method preferredLayoutSize (line 207) | public Dimension preferredLayoutSize(Container target) {
    method maximumLayoutSize (line 257) | public Dimension maximumLayoutSize(Container target) {
    method getLayoutAlignmentX (line 268) | public float getLayoutAlignmentX(Container parent) {
    method getLayoutAlignmentY (line 279) | public float getLayoutAlignmentY(Container parent) {
    method invalidateLayout (line 287) | public void invalidateLayout(Container target) {
    method layoutContainer (line 310) | public void layoutContainer(Container target) {
    method getChild (line 368) | private Component getChild(String key, boolean ltr) {
    method toString (line 396) | public String toString() {

FILE: src/juicebox/windowui/HiCRulerPanel.java
  class HiCRulerPanel (line 45) | public class HiCRulerPanel extends JPanel {
    method HiCRulerPanel (line 56) | public HiCRulerPanel(HiC hic) {
    method formatNumber (line 65) | private static String formatNumber(double position) {
    method findSpacing (line 81) | private static TickSpacing findSpacing(long maxValue, int width, boole...
    method getShowOnlyEndPts (line 130) | public static boolean getShowOnlyEndPts() {
    method setShowOnlyEndPts (line 134) | public static void setShowOnlyEndPts(boolean toggled) {
    method getShowChromosomeFigure (line 138) | public static boolean getShowChromosomeFigure() {
    method setShowChromosomeFigure (line 142) | public static void setShowChromosomeFigure(boolean toggled) {
    method setContext (line 146) | public void setContext(Context frame, Orientation orientation) {
    method paintComponent (line 151) | @Override
    method drawChr (line 187) | private void drawChr(Graphics g) {
    method isHorizontal (line 221) | private boolean isHorizontal() {
    method drawTicks (line 225) | private void drawTicks(Graphics g) {
    type Orientation (line 395) | public enum Orientation {HORIZONTAL, VERTICAL}
    class TickSpacing (line 397) | static class TickSpacing {
      method TickSpacing (line 404) | TickSpacing(double majorTick, String majorUnit, int unitMultiplier) {
      method getMajorTick (line 411) | double getMajorTick() {
      method getMinorTick (line 415) | public double getMinorTick() {
      method getMajorUnit (line 419) | String getMajorUnit() {
      method setMajorUnit (line 423) | public void setMajorUnit(String majorUnit) {
      method getUnitMultiplier (line 427) | int getUnitMultiplier() {
      method setUnitMultiplier (line 431) | public void setUnitMultiplier(int unitMultiplier) {
    class ClickLink (line 438) | class ClickLink {
      method ClickLink (line 444) | ClickLink(Rectangle region, String value, String tooltipText) {

FILE: src/juicebox/windowui/HiCZoom.java
  class HiCZoom (line 37) | public class HiCZoom implements Comparable<HiCZoom> {
    method HiCZoom (line 42) | public HiCZoom(HiC.Unit unit, int binSize) {
    method clone (line 47) | @SuppressWarnings("MethodDoesntCallSuperMethod")
    method getUnit (line 52) | public HiC.Unit getUnit() {
    method getBinSize (line 56) | public int getBinSize() {
    method getKey (line 60) | public String getKey() {
    method toString (line 64) | public String toString() {
    method equals (line 68) | @Override
    method hashCode (line 78) | @Override
    method compareTo (line 83) | @Override

FILE: src/juicebox/windowui/JBTreeCellRenderer.java
  class JBTreeCellRenderer (line 31) | public class JBTreeCellRenderer extends DefaultTreeCellRenderer {
    method JBTreeCellRenderer (line 37) | public JBTreeCellRenderer(String[] parts, String[] colors) {
    method getTreeCellRendererComponent (line 42) | @Override

FILE: src/juicebox/windowui/JSplitButton.java
  class JSplitButton (line 43) | class JSplitButton extends AbstractButton implements Accessible {
    method JSplitButton (line 74) | private JSplitButton() {
    method JSplitButton (line 83) | public JSplitButton(String text) {
    method JSplitButton (line 130) | public JSplitButton(Action action) {
    method createDefaultPopupIcon (line 135) | private Icon createDefaultPopupIcon() {
    method resetComponents (line 156) | private void resetComponents() {
    method isAlwaysShowPopup (line 174) | public boolean isAlwaysShowPopup() {
    method setAlwaysShowPopup (line 185) | public void setAlwaysShowPopup(boolean alwaysShowPopup) {
    method getSplitGap (line 202) | public int getSplitGap() {
    method setSplitGap (line 212) | public void setSplitGap(int splitGap) {
    method getPopupIcon (line 230) | private Icon getPopupIcon() {
    method setPopupIcon (line 243) | public void setPopupIcon(Icon icon) {
    method getDisabledPopupIcon (line 264) | private Icon getDisabledPopupIcon() {
    method setDisabledPopupIcon (line 277) | public void setDisabledPopupIcon(Icon icon) {
    method getDisabledSelectedPopupIcon (line 298) | private Icon getDisabledSelectedPopupIcon() {
    method setDisabledSelectedPopupIcon (line 310) | public void setDisabledSelectedPopupIcon(Icon icon) {
    method getPressedPopupIcon (line 328) | private Icon getPressedPopupIcon() {
    method setPressedPopupIcon (line 339) | public void setPressedPopupIcon(Icon icon) {
    method getRolloverPopupIcon (line 356) | private Icon getRolloverPopupIcon() {
    method setRolloverPopupIcon (line 367) | public void setRolloverPopupIcon(Icon icon) {
    method getRolloverSelectedPopupIcon (line 384) | private Icon getRolloverSelectedPopupIcon() {
    method setRolloverSelectedPopupIcon (line 395) | public void setRolloverSelectedPopupIcon(Icon icon) {
    method getSelectedPopupIcon (line 412) | private Icon getSelectedPopupIcon() {
    method setSelectedPopupIcon (line 423) | public void setSelectedPopupIcon(Icon icon) {
    method getMainText (line 441) | private String getMainText() {
    method setMainText (line 451) | public void setMainText(String text) {
    method addActionListener (line 463) | @Override
    method removeActionListener (line 472) | @Override
    method addChangeListener (line 481) | @Override
    method removeChangeListener (line 490) | @Override
    method addItemListener (line 499) | @Override
    method removeItemListener (line 508) | @Override
    method getAction (line 517) | @Override
    method setAction (line 525) | @Override
    method getAccessibleContext (line 535) | @Override
    method getComponentPopupMenu (line 547) | @Override
    method setComponentPopupMenu (line 555) | @Override
    method getPopupLocation (line 578) | @Override
    method getSelectedObjects (line 586) | @Override
    method getMnemonic (line 604) | @Override
    method setMnemonic (line 612) | @Override
    method getDisplayedMnemonicIndex (line 622) | @Override
    method setDisplayedMnemonicIndex (line 630) | @Override
    method setHideActionText (line 641) | @Override
    method getUIClassID (line 650) | @Override
    method updateUI (line 658) | @Override
    method getPopupLocationRelativeTo (line 663) | private Point getPopupLocationRelativeTo(Component comp) {
    class AccessibleJSplitButton (line 680) | private class AccessibleJSplitButton extends AccessibleAbstractButton {
      method getAccessibleRole (line 684) | @Override
    class PopupAction (line 691) | private class PopupAction implements ActionListener {
      method PopupAction (line 695) | PopupAction(JPopupMenu popupMenu) {
      method actionPerformed (line 703) | @Override
      method getPopupMenu (line 710) | JPopupMenu getPopupMenu() {

FILE: src/juicebox/windowui/LoadAssemblyAnnotationsDialog.java
  class LoadAssemblyAnnotationsDialog (line 63) | public class LoadAssemblyAnnotationsDialog extends JDialog implements Tr...
    method LoadAssemblyAnnotationsDialog (line 74) | public LoadAssemblyAnnotationsDialog(final SuperAdapter superAdapter) {
    method getPath (line 164) | public static TreePath getPath(TreeNode treeNode) {
    method closeWindow (line 178) | private void closeWindow() {
    method addLocalButtonActionPerformed (line 189) | private void addLocalButtonActionPerformed(final SuperAdapter superAda...
    method expandTree (line 243) | private void expandTree() {
    method safeLoadAssemblyFiles (line 259) | private void safeLoadAssemblyFiles(final TreePath[] paths, final Layer...
    method unsafeLoadAssemblyFiles (line 269) | private void unsafeLoadAssemblyFiles(TreePath[] paths, LayersPanel lay...
    method expandToWantedNode (line 375) | private void expandToWantedNode(DefaultMutableTreeNode dNode) {
    method createNodes (line 384) | private boolean createNodes(DefaultMutableTreeNode top, HiC hic) {
    method valueChanged (line 438) | public void valueChanged(TreeSelectionEvent e) {
    method collapseAll (line 447) | private void collapseAll(JTree tree) {
    class ItemInfo (line 455) | private class ItemInfo {
      method ItemInfo (line 459) | ItemInfo(String itemName, String itemURL) {
      method ItemInfo (line 464) | ItemInfo(String itemName) {
      method toString (line 469) | public String toString() {

FILE: src/juicebox/windowui/LoadDialog.java
  class LoadDialog (line 47) | public class LoadDialog extends JDialog implements TreeSelectionListener...
    method LoadDialog (line 64) | public LoadDialog(MainWindow mainWindow, Properties properties, SuperA...
    method getTreePath (line 183) | @Nullable
    method createMAPQ0Button (line 198) | private JSplitButton createMAPQ0Button(String buttonText) {
    method createMAPQ30Menu (line 204) | private JMenuItem createMAPQ30Menu(JSplitButton button, String button3...
    method getPathToRoot (line 215) | public static TreeNode[] getPathToRoot(TreeNode aNode, int depth) {
    method expandToWantedNode (line 230) | private void expandToWantedNode(TreeNode dNode) {
    method colorSearchStrings (line 240) | private void colorSearchStrings(final String[] parts) {
    method setControl (line 244) | public void setControl(boolean control) {
    method getSuccess (line 248) | public boolean getSuccess() {
    method createNodes (line 252) | private boolean createNodes(DefaultMutableTreeNode top, Properties pro...
    method valueChanged (line 295) | public void valueChanged(TreeSelectionEvent e) {
    method actionPerformed (line 312) | public void actionPerformed(ActionEvent e) {
    method loadFiles (line 337) | private void loadFiles(TreePath[] paths, String ext) {
    method collapseAll (line 371) | private void collapseAll(JTree tree) {
    class ItemInfo (line 380) | private class ItemInfo {
      method ItemInfo (line 386) | ItemInfo(String uid, String parentKey, String itemName, String itemU...
      method ItemInfo (line 393) | ItemInfo(String uid, String parentKey, String itemName) {
      method toString (line 399) | public String toString() {

FILE: src/juicebox/windowui/LoadModifiedAssemblyAnnotationsDialog.java
  class LoadModifiedAssemblyAnnotationsDialog (line 60) | public class LoadModifiedAssemblyAnnotationsDialog extends JDialog imple...
    method LoadModifiedAssemblyAnnotationsDialog (line 72) | public LoadModifiedAssemblyAnnotationsDialog(final SuperAdapter superA...
    method getPath (line 162) | public static TreePath getPath(TreeNode treeNode) {
    method closeWindow (line 176) | private void closeWindow() {
    method addLocalButtonActionPerformed (line 187) | private void addLocalButtonActionPerformed(final SuperAdapter superAda...
    method expandTree (line 241) | private void expandTree() {
    method safeLoadAssemblyFiles (line 257) | private void safeLoadAssemblyFiles(final TreePath[] paths, final Layer...
    method unsafeLoadAssemblyFiles (line 267) | private void unsafeLoadAssemblyFiles(TreePath[] paths, LayersPanel lay...
    method expandToWantedNode (line 310) | private void expandToWantedNode(DefaultMutableTreeNode dNode) {
    method createNodes (line 319) | private boolean createNodes(DefaultMutableTreeNode top, HiC hic) {
    method valueChanged (line 373) | public void valueChanged(TreeSelectionEvent e) {
    method collapseAll (line 382) | private void collapseAll(JTree tree) {
    class ItemInfo (line 390) | private class ItemInfo {
      method ItemInfo (line 394) | ItemInfo(String itemName, String itemURL) {
      method ItemInfo (line 399) | ItemInfo(String itemName) {
      method toString (line 404) | public String toString() {

FILE: src/juicebox/windowui/MatrixType.java
  type MatrixType (line 28) | public enum MatrixType {
    method MatrixType (line 109) | MatrixType(String value) {
    method enumValueFromString (line 113) | public static MatrixType enumValueFromString(String text) {
    method isObservedOrControl (line 130) | public static boolean isObservedOrControl(MatrixType option) {
    method isColorScaleType (line 137) | public static boolean isColorScaleType(MatrixType option) {
    method isValidGenomeWideOption (line 144) | public static boolean isValidGenomeWideOption(MatrixType option) {
    method isSimpleControlType (line 151) | public static boolean isSimpleControlType(MatrixType option) {
    method isOEColorScaleType (line 159) | public static boolean isOEColorScaleType(MatrixType option) {
    method isSubtactType (line 167) | public static boolean isSubtactType(MatrixType option) {
    method isOnlyIntrachromosomalType (line 174) | public static boolean isOnlyIntrachromosomalType(MatrixType option) {
    method isExpectedValueType (line 181) | public static boolean isExpectedValueType(MatrixType option) {
    method isPearsonType (line 188) | public static boolean isPearsonType(MatrixType option) {
    method isDumpVectorType (line 195) | public static boolean isDumpVectorType(MatrixType option) {
    method isDumpMatrixType (line 202) | public static boolean isDumpMatrixType(MatrixType option) {
    method isVSTypeDisplay (line 206) | public static boolean isVSTypeDisplay(MatrixType option) {
    method isControlPearsonType (line 210) | public static boolean isControlPearsonType(MatrixType option) {
    method getOptions (line 214) | public static MatrixType[] getOptions(boolean withControl) {
    method toggleAdvancedViews (line 228) | public static void toggleAdvancedViews() {
    method getAdvancedViewEnabled (line 232) | public static boolean getAdvancedViewEnabled() {
    method toString (line 236) | public String toString() {

FILE: src/juicebox/windowui/NormalizationHandler.java
  class NormalizationHandler (line 30) | public class NormalizationHandler {
    method NormalizationHandler (line 56) | public NormalizationHandler() {
    method getAllNormTypes (line 70) | public static List<NormalizationType> getAllNormTypes() {
    method isGenomeWideNorm (line 74) | public static boolean isGenomeWideNorm(NormalizationType norm) {
    method getAllGWNormTypes (line 78) | public static NormalizationType[] getAllGWNormTypes(boolean isUseOnlyS...
    method isGenomeWideNormIntra (line 85) | public static boolean isGenomeWideNormIntra(NormalizationType norm) {
    method isGenomeWideNormInter (line 89) | public static boolean isGenomeWideNormInter(NormalizationType norm) {
    method getIdealResolutionLimit (line 93) | public static Integer getIdealResolutionLimit(NormalizationType normal...
    method getNormTypeFromString (line 101) | public NormalizationType getNormTypeFromString(String text) {
    method getDefaultSetForHiCFileBuilding (line 114) | public List<NormalizationType> getDefaultSetForHiCFileBuilding() {

FILE: src/juicebox/windowui/NormalizationType.java
  class NormalizationType (line 33) | public class NormalizationType {
    method NormalizationType (line 38) | public NormalizationType(String label, String description) {
    method getLabel (line 49) | public String getLabel() {
    method getDescription (line 53) | public String getDescription() {
    method toString (line 57) | @Override
    method equals (line 62) | @Override
    method hashCode (line 73) | @Override
    method usesKR (line 78) | public boolean usesKR() {
    method usesVC (line 82) | public boolean usesVC() {
    method usesSCALE (line 86) | public boolean usesSCALE() {
    method isNONE (line 90) | public boolean isNONE() {

FILE: src/juicebox/windowui/QCDialog.java
  class QCDialog (line 49) | public class QCDialog extends JDialog {
    method QCDialog (line 63) | public QCDialog(MainWindow mainWindow, HiC hic, String title, boolean ...

FILE: src/juicebox/windowui/RecentMenu.java
  class RecentMenu (line 55) | public abstract class RecentMenu extends JMenu {
    method RecentMenu (line 67) | public RecentMenu(String name, int count, String prefEntry, HiCGlobals...
    method addClearItem (line 93) | private void addClearItem() {
    method encodeSafeDelimeterSplit (line 129) | public static String[] encodeSafeDelimeterSplit(String path) {
    method addEntry (line 146) | public void addEntry(String savedEntryOriginal, boolean updateFile) {
    method onSelectPosition (line 207) | protected abstract void onSelectPosition(String mapPath);
    method updateNamesFromImport (line 210) | public void updateNamesFromImport(String importedFile) {
    method checkForDuplicateNames (line 269) | public String checkForDuplicateNames(String savedNameOriginal) {

FILE: src/juicebox/windowui/SaveAssemblyDialog.java
  class SaveAssemblyDialog (line 41) | public class SaveAssemblyDialog extends JFileChooser {
    method SaveAssemblyDialog (line 47) | public SaveAssemblyDialog(AssemblyScaffoldHandler assemblyScaffoldHand...
    method menuOptions (line 56) | private void menuOptions() {

FILE: src/juicebox/windowui/SaveImageDialog.java
  class SaveImageDialog (line 43) | public class SaveImageDialog extends JFileChooser {
    method SaveImageDialog (line 49) | public SaveImageDialog(String saveImagePath, final HiC hic, final Main...
    method createDialog (line 99) | protected JDialog createDialog(Component parent) {
    method exportAsPDF (line 116) | private void exportAsPDF(File file, MainWindow mainWindow, HiC hic, fi...
    method exportAsSVG (line 127) | private void exportAsSVG(File file, MainWindow mainWindow, HiC hic, fi...
    method writeGraphicsToFile (line 138) | private void writeGraphicsToFile(ProcessingPipeline g, File file) thro...
    method plotDataOnGraphics (line 144) | private void plotDataOnGraphics(Graphics g, final MainWindow mainWindo...

FILE: src/juicebox/windowui/layers/LayerPanelButtons.java
  class LayerPanelButtons (line 40) | class LayerPanelButtons {
    method createColorChooserButton (line 44) | public static ColorChooserPanel createColorChooserButton(final SuperAd...
    method createCensorButton (line 62) | public static JButton createCensorButton(final LayersPanel lp, final S...
    method createVisibleButton (line 77) | public static JToggleButton createVisibleButton(final Object lp, final...
    method createTransparencyButton (line 100) | public static JToggleButton createTransparencyButton(final LayersPanel...
    method createToggleSparseButton (line 118) | public static JToggleButton createToggleSparseButton(final LayersPanel...
    method createCopyButton (line 134) | public static JButton createCopyButton(final LayersPanel lp, final Sup...
    method createMoveDownButton (line 148) | public static JButton createMoveDownButton(final LayersPanel layersPan...
    method createMoveUpButton (line 168) | public static JButton createMoveUpButton(final LayersPanel layersPanel...
    method createDeleteButton (line 188) | public static JButton createDeleteButton(final LayersPanel layersPanel...
    method createToggleEnlargeButton (line 214) | public static JToggleButton createToggleEnlargeButton(final LayersPane...
    method createTogglePlottingStyleButton (line 233) | public static JButton createTogglePlottingStyleButton(final SuperAdapt...
    method createExportButton (line 243) | public static JButton createExportButton(final LayersPanel layersPanel...
    method createUndoButton (line 260) | public static JButton createUndoButton(final LayersPanel lp, final Sup...
    method createEraseButton (line 279) | public static JButton createEraseButton(final LayersPanel lp, final Su...
    method createWritingButton (line 302) | public static JToggleButton createWritingButton(final Object lp, final...
    method createTogglePlottingStyleIconButton (line 322) | private static PlottingStyleButton createTogglePlottingStyleIconButton...
    method createIconButton (line 344) | private static JButton createIconButton(Object ls, String url) throws ...
    method createToggleIconButton (line 364) | private static JToggleButton createToggleIconButton(Object lp, String ...
    method translucentImage (line 396) | public static Image translucentImage(BufferedImage originalImage, floa...

FILE: src/juicebox/windowui/layers/LayersPanel.java
  class LayersPanel (line 52) | public class LayersPanel extends JDialog {
    method LayersPanel (line 66) | public LayersPanel(final SuperAdapter superAdapter) {
    method getEncodeAction (line 121) | public LoadEncodeAction getEncodeAction() {
    method generate1DAnnotationsLayerSelectionPanel (line 125) | private JPanel generate1DAnnotationsLayerSelectionPanel(final SuperAda...
    method redraw1DLayerPanels (line 211) | public void redraw1DLayerPanels(SuperAdapter superAdapter) {
    method generate2DAnnotationsLayerSelectionPanel (line 230) | private JPanel generate2DAnnotationsLayerSelectionPanel(final SuperAda...
    method generateLayers2DScrollPane (line 316) | private JScrollPane generateLayers2DScrollPane(SuperAdapter superAdapt...
    method createNewLayerAndAddItToPanels (line 337) | public AnnotationLayerHandler createNewLayerAndAddItToPanels(SuperAdap...
    method merge2DAnnotationsAction (line 355) | private void merge2DAnnotationsAction(SuperAdapter superAdapter) {
    method createLayerPanel (line 394) | private JPanel createLayerPanel(final AnnotationLayerHandler handler, ...
    method anyTextChangeListener (line 443) | private DocumentListener anyTextChangeListener(final AnnotationLayerHa...
    method updateLayers2DPanel (line 466) | public void updateLayers2DPanel(SuperAdapter superAdapter) {
    method updateBothLayersPanels (line 474) | public void updateBothLayersPanels(SuperAdapter superAdapter) {
    method getTrackLoadAction (line 479) | public LoadAction getTrackLoadAction() {

FILE: src/juicebox/windowui/layers/Load2DAnnotationsDialog.java
  class Load2DAnnotationsDialog (line 55) | public class Load2DAnnotationsDialog extends JDialog implements TreeSele...
    method Load2DAnnotationsDialog (line 66) | public Load2DAnnotationsDialog(final LayersPanel layersPanel, final Su...
    method addLocalButtonActionPerformed (line 225) | public void addLocalButtonActionPerformed(final Component parentCompon...
    method expandTree (line 277) | private void expandTree() {
    method safeLoadAnnotationFiles (line 292) | private void safeLoadAnnotationFiles(final TreePath[] paths, final Lay...
    method unsafeLoadAnnotationFiles (line 303) | private void unsafeLoadAnnotationFiles(TreePath[] paths, LayersPanel l...
    method expandToWantedNode (line 323) | private void expandToWantedNode(TreeNode dNode) {
    method colorSearchStrings (line 334) | private void colorSearchStrings(final String[] parts) {
    method createNodes (line 338) | private boolean createNodes(DefaultMutableTreeNode top, HiC hic) {
    method valueChanged (line 392) | public void valueChanged(TreeSelectionEvent e) {
    method collapseAll (line 401) | private void collapseAll(JTree tree) {
    class ItemInfo (line 409) | private class ItemInfo {
      method ItemInfo (line 413) | ItemInfo(String itemName, String itemURL) {
      method ItemInfo (line 418) | ItemInfo(String itemName) {
      method toString (line 423) | public String toString() {

FILE: src/juicebox/windowui/layers/MiniAnnotationsLayerPanel.java
  class MiniAnnotationsLayerPanel (line 39) | public class MiniAnnotationsLayerPanel extends JPanel {
    method MiniAnnotationsLayerPanel (line 50) | public MiniAnnotationsLayerPanel(SuperAdapter superAdapter, int width,...
    method shortenedName (line 69) | public static String shortenedName(final String text) {
    method setRows (line 80) | private void setRows(SuperAdapter superAdapter) {
    method createMiniLayerPanel (line 108) | private JPanel createMiniLayerPanel(final AnnotationLayerHandler handl...
    method getDynamicHeight (line 139) | public int getDynamicHeight() {
    method updateRows (line 143) | public void updateRows(SuperAdapter superAdapter) {

FILE: src/juicebox/windowui/layers/PlottingStyleButton.java
  class PlottingStyleButton (line 34) | public class PlottingStyleButton extends JButton {
    method PlottingStyleButton (line 40) | public PlottingStyleButton() throws IOException {
    method setCurrentState (line 65) | public void setCurrentState(FeatureRenderer.PlottingOption state) {

FILE: src/juicebox/windowui/layers/SaveAnnotationsDialog.java
  class SaveAnnotationsDialog (line 41) | public class SaveAnnotationsDialog extends JFileChooser {
    method SaveAnnotationsDialog (line 48) | public SaveAnnotationsDialog(AnnotationLayer annotationsLayer, String ...
    method menuOptions (line 55) | private void menuOptions() {

FILE: src/juicebox/windowui/layers/UnsavedAnnotationWarning.java
  class UnsavedAnnotationWarning (line 37) | public class UnsavedAnnotationWarning {
    method UnsavedAnnotationWarning (line 41) | public UnsavedAnnotationWarning(SuperAdapter adapter) {
    method checkAndDelete (line 45) | public boolean checkAndDelete(boolean isCurrentSession) {
    method initPopup (line 54) | private boolean initPopup(boolean isCurrentSession) {
    method removeAllOldAnnotationFiles (line 96) | private void removeAllOldAnnotationFiles() {
    method moveOldAnnotationFiles (line 105) | private String moveOldAnnotationFiles() {

FILE: src/org/tc33/jheatchart/HeatChart.java
  class HeatChart (line 141) | public class HeatChart {
    method HeatChart (line 233) | public HeatChart(double[][] zValues) {
    method HeatChart (line 249) | private HeatChart(double[][] zValues, double low, double high) {
    method max (line 299) | private static double max(double[][] values) {
    method min (line 314) | private static double min(double[][] values) {
    method getLowValue (line 330) | public double getLowValue() {
    method getHighValue (line 340) | public double getHighValue() {
    method getPermissiveIntRange (line 350) | public int getPermissiveIntRange() {
    method getDataRange (line 360) | public double getDataRange() {
    method getZValues (line 372) | public double[][] getZValues() {
    method setZValues (line 385) | public void setZValues(double[][] zValues) {
    method setZValues (line 444) | private void setZValues(double[][] zValues, double low, double high) {
    method setXValues (line 468) | public void setXValues(double xOffset, double xInterval) {
    method setYValues (line 494) | public void setYValues(double yOffset, double yInterval) {
    method getXValues (line 511) | public Object[] getXValues() {
    method setXValues (line 524) | public void setXValues(Object[] xValues) {
    method getYValues (line 537) | public Object[] getYValues() {
    method setYValues (line 550) | public void setYValues(Object[] yValues) {
    method isXValuesHorizontal (line 561) | public boolean isXValuesHorizontal() {
    method setXValuesHorizontal (line 572) | public void setXValuesHorizontal(boolean xValuesHorizontal) {
    method isYValuesHorizontal (line 583) | public boolean isYValuesHorizontal() {
    method setYValuesHorizontal (line 594) | public void setYValuesHorizontal(boolean yValuesHorizontal) {
    method getCellWidth (line 605) | @Deprecated
    method setCellWidth (line 619) | @Deprecated
    method getCellHeight (line 631) | @Deprecated
    method setCellHeight (line 645) | @Deprecated
    method getCellSize (line 657) | public Dimension getCellSize() {
    method setCellSize (line 670) | private void setCellSize(Dimension cellSize) {
    method getChartWidth (line 681) | @Deprecated
    method getChartHeight (line 693) | @Deprecated
    method getChartSize (line 705) | public Dimension getChartSize() {
    method getTitle (line 715) | public String getTitle() {
    method setTitle (line 732) | public void setTitle(String title) {
    method getXAxisLabel (line 742) | public String getXAxisLabel() {
    method setXAxisLabel (line 760) | public void setXAxisLabel(String xAxisLabel) {
    method getYAxisLabel (line 770) | public String getYAxisLabel() {
    method setYAxisLabel (line 788) | public void setYAxisLabel(String yAxisLabel) {
    method getChartMargin (line 799) | public int getChartMargin() {
    method setChartMargin (line 815) | public void setChartMargin(int margin) {
    method getBackgroundColour (line 825) | public Color getBackgroundColour() {
    method setBackgroundColour (line 840) | public void setBackgroundColour(Color backgroundColour) {
    method getTitleFont (line 854) | public Font getTitleFont() {
    method setTitleFont (line 868) | public void setTitleFont(Font titleFont) {
    method getTitleColour (line 878) | public Color getTitleColour() {
    method setTitleColour (line 891) | public void setTitleColour(Color titleColour) {
    method getAxisThickness (line 901) | public int getAxisThickness() {
    method setAxisThickness (line 915) | public void setAxisThickness(int axisThickness) {
    method getAxisColour (line 925) | public Color getAxisColour() {
    method setAxisColour (line 938) | public void setAxisColour(Color axisColour) {
    method getAxisLabelsFont (line 948) | public Font getAxisLabelsFont() {
    method setAxisLabelsFont (line 962) | public void setAxisLabelsFont(Font axisLabelsFont) {
    method getAxisLabelColour (line 972) | public Color getAxisLabelColour() {
    method setAxisLabelColour (line 985) | public void setAxisLabelColour(Color axisLabelColour) {
    method getAxisValuesFont (line 996) | public Font getAxisValuesFont() {
    method setAxisValuesFont (line 1010) | public void setAxisValuesFont(Font axisValuesFont) {
    method getAxisValuesColour (line 1020) | public Color getAxisValuesColour() {
    method setAxisValuesColour (line 1033) | public void setAxisValuesColour(Color axisValuesColour) {
    method getXAxisValuesFrequency (line 1046) | public int getXAxisValuesFrequency() {
    method setXAxisValuesFrequency (line 1062) | public void setXAxisValuesFrequency(int axisValuesFrequency) {
    method getYAxisValuesFrequency (line 1074) | public int getYAxisValuesFrequency() {
    method setYAxisValuesFrequency (line 1090) | public void setYAxisValuesFrequency(int axisValuesFrequency) {
    method isShowXAxisValues (line 1103) | public boolean isShowXAxisValues() {
    method setShowXAxisValues (line 1121) | public void setShowXAxisValues(boolean showXAxisValues) {
    method isShowYAxisValues (line 1134) | public boolean isShowYAxisValues() {
    method setShowYAxisValues (line 1151) | public void setShowYAxisValues(boolean showYAxisValues) {
    method getHighValueColour (line 1165) | public Color getHighValueColour() {
    method setHighValueColour (line 1183) | public void setHighValueColour(Color highValueColour) {
    method getLowValueColour (line 1199) | public Color getLowValueColour() {
    method setLowValueColour (line 1217) | public void setLowValueColour(Color lowValueColour) {
    method getColourScale (line 1235) | public double getColourScale() {
    method setColourScale (line 1255) | public void setColourScale(double colourScale) {
    method updateColourDistance (line 1265) | private void updateColourDistance() {
    method saveToFile (line 1303) | public void saveToFile(File outputFile) throws IOException {
    method saveGraphicJpeg (line 1328) | private void saveGraphicJpeg(BufferedImage chart, File outputFile, flo...
    method getChartImage (line 1360) | private Image getChartImage(boolean alpha) {
    method getChartImage (line 1415) | public Image getChartImage() {
    method measureComponents (line 1422) | private void measureComponents() {
    method updateCoordinates (line 1520) | private void updateCoordinates() {
    method drawTitle (line 1541) | private void drawTitle(Graphics2D chartGraphics) {
    method drawHeatMap (line 1557) | private void drawHeatMap(Graphics2D chartGraphics, double[][] data) {
    method drawXLabel (line 1587) | private void drawXLabel(Graphics2D chartGraphics) {
    method drawYLabel (line 1603) | private void drawYLabel(Graphics2D chartGraphics) {
    method drawAxisBars (line 1629) | private void drawAxisBars(Graphics2D chartGraphics) {
    method drawXValues (line 1652) | private void drawXValues(Graphics2D chartGraphics) {
    method drawYValues (line 1700) | private void drawYValues(Graphics2D chartGraphics) {
    method getCellColour (line 1748) | private Color getCellColour(double data, double min, double max) {
    method getColourPosition (line 1789) | private int getColourPosition(double percentPosition) {
    method changeColourValue (line 1793) | private int changeColourValue(int colourValue, int colourDistance) {
    method getHeatMapTL (line 1810) | public Point getHeatMapTL() {
    method getHeatMapBR (line 1820) | public Point getHeatMapBR() {
    method getHeatMapC (line 1830) | public Point getHeatMapC() {
    method getHeatMapTR (line 1840) | public Point getHeatMapTR() {
    method getHeatMapBL (line 1850) | public Point getHeatMapBL() {