A B C D E F G H I J L M N O P Q R S T U V W X Z

A

ALToLine2DArray(ArrayList) - Static method in class nix.gata.main.GATAUtil

ALToString(ArrayList) - Static method in class nix.gata.main.GATAUtil

ALToString(ArrayList) - Static method in class nix.util.bio.annotation.GeneGroup

AlignPanel - class nix.gata.plotter.AlignPanel.

AlignPanel(GATAParams) - Constructor for class nix.gata.plotter.AlignPanel

AlignParams - class nix.gata.aligner.AlignParams.

AlignParams() - Constructor for class nix.gata.aligner.AlignParams

AlignParams(AlignerPreferences) - Constructor for class nix.gata.aligner.AlignParams

AlignedBaseCounter - class nix.util.bio.converters.AlignedBaseCounter.

Counts and parses the bases in a multiple alignment where each string is broken into three sections like gatcc GGCCAATT cgatcca, ccat GGCCAATT cctttt, like the output from meme the central portion is aligned, the left and right flanks are not.

AlignedBaseCounter() - Constructor for class nix.util.bio.converters.AlignedBaseCounter

AlignerInputForm - class nix.gata.aligner.AlignerInputForm.

AlignerInputForm(GATAligner) - Constructor for class nix.gata.aligner.AlignerInputForm

AlignerInputPanel - class nix.gata.aligner.AlignerInputPanel.

AlignerInputPanel(JFrame, GATAligner) - Constructor for class nix.gata.aligner.AlignerInputPanel

AlignerPreferences - class nix.gata.aligner.AlignerPreferences.

AlignerPreferences() - Constructor for class nix.gata.aligner.AlignerPreferences

AlignerThread - class nix.gata.aligner.AlignerThread.

AlignerThread(ProgressMonitor, AlignerInputForm) - Constructor for class nix.gata.aligner.AlignerThread

Alignment - class nix.gata.aligner.Alignment.

Alignment(String, int, int, String, int, int, int, int, AlignParams, LocalAlignment) - Constructor for class nix.gata.aligner.Alignment

Alignment - class nix.util.bio.calc.Alignment.

Methods associated with alignments, pvalues, blast.

Alignment() - Constructor for class nix.util.bio.calc.Alignment

AnnoSpecParams - class nix.gata.main.AnnoSpecParams.

AnnoSpecParams() - Constructor for class nix.gata.main.AnnoSpecParams

AnnotateRegions - class nix.affy.anno.AnnotateRegions.

For annotating Intervals or binding regions with gene information, proximity, neighbors, and bias based on random trials.

AnnotateRegions(String[]) - Constructor for class nix.affy.anno.AnnotateRegions

AnnotateRegionsWithGeneList - class nix.affy.anno.AnnotateRegionsWithGeneList.

For annotating a picks file (chr, start, stop) with gene information for a particular list of CG names.

AnnotateRegionsWithGeneList(String[]) - Constructor for class nix.affy.anno.AnnotateRegionsWithGeneList

Annotation - class nix.gata.geneGlyphs.Annotation.

Annotation(AnnoSpecParams, GATAParams) - Constructor for class nix.gata.geneGlyphs.Annotation

ArrayPrinter - class nix.util.apps.ArrayPrinter.

Prints serialized arrays to screen.

ArrayPrinter() - Constructor for class nix.util.apps.ArrayPrinter

AverageDoubles - class nix.affy.misc.AverageDoubles.

Slides a 50 index window along an array averaging the contents.

AverageDoubles() - Constructor for class nix.affy.misc.AverageDoubles

actionPerformed(ActionEvent) - Method in class nix.gata.aligner.BrowseButtonAction

actionPerformed(ActionEvent) - Method in class nix.gata.menu.SaveImagePanel

addAction(JButton, int) - Method in class nix.gata.plotter.ToolsFrame

addExpectedSubSeq(int) - Method in class nix.selex.SelexParams

addIt() - Method in class nix.affy.main.IntervalMaker

addIt() - Method in class nix.affy.main.WindowScanner

addLabel(ArrayList) - Method in class nix.gata.main.AnnoSpecParams

addNormalDNALines(ArrayList) - Method in class nix.gata.main.AnnoSpecParams

addObsExpRatio(double) - Method in class nix.selex.SelexParams

addObservedSubSeq(int) - Method in class nix.selex.SelexParams

addProteinLines(ArrayList, ArrayList) - Method in class nix.gata.main.AnnoSpecParams

addRNALines(Line2D.Double, ArrayList) - Method in class nix.gata.main.AnnoSpecParams

addScaleRuler(JMenu, String) - Method in class nix.gata.menu.GATAFrame

addScaleTrackColors(JMenu) - Method in class nix.gata.menu.GATAFrame

addShowHide(JMenu, String, boolean) - Method in class nix.gata.menu.GATAFrame

addShowHideLabel(JMenu, String) - Method in class nix.gata.menu.GATAFrame

addShowHideWithPath(JMenu, String, String) - Method in class nix.gata.menu.GATAFrame

addStainId(String) - Method in class nix.bdtnp.bid.HybridizationBean

addThinDNALines(ArrayList) - Method in class nix.gata.main.AnnoSpecParams

addTrack(JMenu, String, boolean) - Method in class nix.gata.menu.GATAFrame

addZeros(String) - Static method in class nix.util.gen.Misc

Prepends zeros to a string such that its total length = 10.

addZeros(String[]) - Static method in class nix.util.gen.Misc

Prepends zeros to each String such that its total length = 10.

ap - Variable in class nix.gata.aligner.Blast

append(String) - Method in class nix.util.gen.TextFrame

appendLength(int) - Method in class nix.selex.SelexParams

appendMemeParserReport(String) - Method in class nix.meme.MemeResults

appendMemeReports(String) - Method in class nix.meme.MemeResults

appendMotifSearchResults(String) - Method in class nix.meme.MemeResults

appendMummerHits() - Method in class nix.affy.bpmap.MummerFilter

Runs through mummer results and appends any hits to probeExporterFile.

appendSelexOligoFiles(String) - Method in class nix.meme.MemeResults

appendSub(String) - Method in class nix.selex.SelexParams

areGenericLabelsVis() - Method in class nix.gata.main.GATAParams

areLabelsVis() - Method in class nix.gata.main.GATAParams

arrayListOfDoubleToArray(ArrayList) - Static method in class nix.util.gen.Num

ArrayList of Double to double[]

arrayListOfFloatToArray(ArrayList) - Static method in class nix.util.gen.Num

ArrayList of Float to float[]

arrayListToArray(ArrayList) - Static method in class nix.bdtnp.bid.PatternMatch

Convert an ArrayList of PatternMatch to PatternMatch[]

arrayListToDoubles(ArrayList) - Static method in class nix.util.gen.Num

ArrayList of Double to double[]

arrayListToInts(ArrayList) - Static method in class nix.util.gen.Num

ArrayList of Integer to int[]

assignGenericFeatureTracks() - Method in class nix.gata.geneGlyphs.Annotation

aveFoldDiffCombine(int[], int[]) - Static method in class nix.util.gen.Num

Calculates the average fold difference between two int[]s of the same length.

aveFoldDiffIndividual(int[], int[]) - Static method in class nix.util.gen.Num

Calculates the average fold difference between two int[]s of the same length.

aveMedianAbsDiffSubWinControl(Interval) - Static method in class nix.affy.main.IntervalReportPrinter

Calculate maximum median absolute diff of SubWindow control values

averageDoubleArrayList(ArrayList) - Static method in class nix.selex.UtilSelex

Averages an ArrayList of Double objects.

averageDuplicates(BPMapFeature[][], float[][]) - Static method in class nix.affy.main.CelMapper

Averages the intesities of duplicates, will not include 0 values in average.

averageFloatArray(float[]) - Static method in class nix.util.gen.Num

Averages a float[]

averageFloatArrays(float[][]) - Static method in class nix.affy.main.QuantileNormalization

Takes arrays of float[][], averages their values returning a single float[].

averageFloatArrays(float[][]) - Static method in class nix.util.gen.Num

Average float[][] values to double[], averages repeats [values][numRepeats]

averageFloatArraysFlipped(float[][]) - Static method in class nix.util.gen.Num

Average float[][] values to double[], averages repeats [numChips][OligoValues].

averageIntArray(int[]) - Static method in class nix.util.gen.Num

Averages a int[]

averageIntIntArray(int[][]) - Static method in class nix.util.gen.Num

Average int[][] values to double[], averages repeats [numRepeats][values]

averageIntIntArray2(int[][]) - Static method in class nix.util.gen.Num

Average int[][] values to double[], averages values [numRepeats][values]

averageIntegerArrayList(ArrayList) - Static method in class nix.selex.UtilSelex

Averages an ArrayList of Integer objects.