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

T

T2 - class trans.main.T2.

Runs entire TiMAT2 suite based on a parameter file.

T2(String[]) - Constructor for class trans.main.T2

T2Parameter - class trans.main.T2Parameter.

Container with info related to runing multiple T2 programs.

T2Parameter(File) - Constructor for class trans.main.T2Parameter

TARGET_MEDIAN - Static variable in class trans.bkgrnd.MapControlIntensities

TASSignalChromFileSplitter - class util.apps.TASSignalChromFileSplitter.

TASSignalChromFileSplitter() - Constructor for class util.apps.TASSignalChromFileSplitter

TPMapDensityReducer - class trans.tpmap.TPMapDensityReducer.

Randomly drops a certain fraction of tpmap lines.

TPMapDensityReducer(String[]) - Constructor for class trans.tpmap.TPMapDensityReducer

TPMapDuplicateFilter - class trans.tpmap.TPMapDuplicateFilter.

For extracting duplicate oligo/ features from Affy's bpmap file, can be used as a stand alone but better to use TPMapProcessor.

TPMapDuplicateFilter(String) - Constructor for class trans.tpmap.TPMapDuplicateFilter

For running this alone.

TPMapDuplicateFilter(File, File, String) - Constructor for class trans.tpmap.TPMapDuplicateFilter

For running in combination with TPMapProcessor

TPMapFeature - class trans.tpmap.TPMapFeature.

Container for info about a particular oligo feature from a tpmap file.

TPMapFeature(String[]) - Constructor for class trans.tpmap.TPMapFeature

TPMapLine - class trans.tpmap.TPMapLine.

Minimal tpmap line, chrom, start, nothing else.

TPMapLine(String[]) - Constructor for class trans.tpmap.TPMapLine

For parsing from an Agilent data file.

TPMapLine(String, String, String, String) - Constructor for class trans.tpmap.TPMapLine

For parsing from an Agilent promoter array data file.

TPMapLine(String, int, int, int, String) - Constructor for class trans.tpmap.TPMapLine

Coordinates are zero based!

TPMapLine(String, int, int, int, String, boolean) - Constructor for class trans.tpmap.TPMapLine

Coordinates are zero based!

TPMapLine(String[], boolean) - Constructor for class trans.tpmap.TPMapLine

For parsing from an Nimblegen NDF data file.

TPMapLine(String) - Constructor for class trans.tpmap.TPMapLine

TPMapOligoBlastFilter - class trans.tpmap.TPMapOligoBlastFilter.

Application for remapping and filtering a text version bpmap file with BLAST.

TPMapOligoBlastFilter(String[]) - Constructor for class trans.tpmap.TPMapOligoBlastFilter

TPMapProcessor - class trans.tpmap.TPMapProcessor.

App for processing the tpmap file for use by downstream TiMAT applications.

TPMapProcessor(String[]) - Constructor for class trans.tpmap.TPMapProcessor

TPMapSort - class trans.tpmap.TPMapSort.

This sorts a tpmap first by chromosome, second by base position.

TPMapSort(String[]) - Constructor for class trans.tpmap.TPMapSort

TPMapStripHighLowGC - class trans.tpmap.TPMapStripHighLowGC.

Strips a tpmap file of lines where the %GC is > 0.6 or < 0.4.

TPMapStripHighLowGC() - Constructor for class trans.tpmap.TPMapStripHighLowGC

TableHeading - class bioroot.TableHeading.

TableHeading(String, int) - Constructor for class bioroot.TableHeading

TestScanChip - class trans.main.TestScanChip.

Scores windows of intensity values using several tests.

TestScanChip(String[]) - Constructor for class trans.main.TestScanChip

TextFrame - class util.gen.TextFrame.

Creates a free standing plain editable text window.

TextFrame(int, int, int, int, String) - Constructor for class util.gen.TextFrame

TextPValOrSig2Gr - class trans.misc.TextPValOrSig2Gr.

Converts a bed file to multiple gr files.

TextPValOrSig2Gr() - Constructor for class trans.misc.TextPValOrSig2Gr

TextParser - class util.apps.TextParser.

For parsing a text file into a tab delimited file, working template.

TextParser() - Constructor for class util.apps.TextParser

TextWindow - class gata.main.TextWindow.

TextWindow(String, int, int, String) - Constructor for class gata.main.TextWindow

ToolsFrame - class gata.plotter.ToolsFrame.

ToolsFrame(int, int, GATAParams) - Constructor for class gata.plotter.ToolsFrame

TransGroup - class util.bio.annotation.TransGroup.

A TransGroup describes a product derived from a GeneGroup contains one transcript, possibly a translation, and a possibly a set of exons.

TransGroup(Transcript, Translation, ExonIntron[]) - Constructor for class util.bio.annotation.TransGroup

TransGrpGlyph - class gata.geneGlyphs.TransGrpGlyph.

TransGrpGlyph(TransGroup, GATAParams, AnnoSpecParams) - Constructor for class gata.geneGlyphs.TransGrpGlyph

Transcript - class util.bio.annotation.Transcript.

Transcript relevant information, mRNA.

Transcript(int, int, String, int) - Constructor for class util.bio.annotation.Transcript

Transcript(Gff3Feature) - Constructor for class util.bio.annotation.Transcript

TransformRatios - class trans.misc.TransformRatios.

Transforms ratio scores in Intervals based on the BAC GC Corrector.

TransformRatios() - Constructor for class trans.misc.TransformRatios

Translation - class util.bio.annotation.Translation.

Translation specific information, protein but referenced with genomic coordinates thus some bits code for protein, some don't physically exist.

Translation(int, int, int) - Constructor for class util.bio.annotation.Translation

Translation(Gff3Feature) - Constructor for class util.bio.annotation.Translation

tableLastModified(String) - Method in class bioroot.DBUtil

test(float[], float[]) - Method in class trans.main.WilcoxonRankSumTest

Returns a -10LogBase10(pValue) if n1 and n2 >9.

test(float[][], float[][], int, int) - Method in class trans.main.WilcoxonRankSumTest

Returns a -10LogBase10(pValue) if n1 and n2 >9

test() - Method in class trans.main.WilcoxonSignedRankTest

testCelFiles() - Method in class trans.qc.CelFileQualityControl

Main app controler.

testOverlap(Interval[], Interval[], File, File) - Method in class trans.main.OverlapCounter

Returns the average % intersection.

threadedResults - Variable in class util.amazon.S3Manager

thresholdWindows(Window[], double, int) - Method in class trans.main.FDRWindowConverter

throwWarning(JFrame, JTextField, String) - Static method in class gata.main.GATAUtil

throwWarning(JFrame, JTextField, String) - Static method in class util.gen.Swing

toHTMLString() - Method in class gata.aligner.AlignParams

toLowerCase(String[]) - Method in class util.gen.Misc

Lower cases a String[]

toString() - Method in class bioroot.Feature

toString() - Method in class bioroot.LabGroup

toString() - Method in class bioroot.PatternMatch

toString() - Method in class bioroot.SearchHit

toString() - Method in class bioroot.TableHeading

toString() - Method in class com.amazon.s3.Bucket

toString() - Method in class com.amazon.s3.ListEntry

toString() - Method in class expr.CorrelationWindow

Genes NumGenes Chromosome Start Stop CorrelationScore -10Log10(pvalue)

toString() - Method in class expr.ExpressedGene

toString() - Method in class gata.aligner.AlignerPreferences

toString() - Method in class gata.geneGlyphs.GeneRepGlyph

toString() - Method in class gata.geneGlyphs.GenericGlyph

toString() - Method in class meme.MemeMotif

toString() - Method in class meme.MemeParser

toString() - Method in class meme.MemeResults

toString() - Method in class meme.MotifHit

toString() - Method in class trans.anno.BindingRegion

toString() - Method in class trans.anno.Region

toString() - Method in class trans.bkgrnd.BackGroundOligo

toString() - Method in class trans.cel.ControlStats

toString() - Method in class trans.cel.MultiSetQuantile

toString() - Method in class trans.graphics.GenomicRegion

Returns tab delimited rank+1, chrom, st, stp, scr, notes.

toString(Oligo[], int) - Method in class trans.main.BindingPeak

Score, Left, Peak, Right

toString() - Method in class trans.main.Interval

toString() - Method in class trans.main.Oligo

toString(int, int, String) - Method in class trans.main.Oligo

toString() - Method in class trans.main.WilcoxonSamplePair

toString() - Method in class trans.main.WilcoxonSignedRankTest

toString() - Method in class trans.qc.CelFileStats

toString() - Method in class trans.qc.StatFlag

toString() - Method in class trans.roc.Bin

toString() - Method in class trans.roc.Gr

toString() - Method in class trans.roc.Positive

toString() - Method in class trans.roc.Sgr

toString() - Method in class trans.tpmap.TPMapFeature

toString() - Method in class util.apps.HouseBean

toString() - Method in class util.bio.annotation.Coordinates

toString() - Method in class util.bio.annotation.ExonIntron

toString() - Method in class util.bio.annotation.GeneGroup

toString() - Method in class util.bio.annotation.GeneRep

toString() - Method in class util.bio.annotation.TransGroup

toString() - Method in class util.bio.annotation.Transcript

toString() - Method in class util.bio.annotation.Translation

toString() - Method in class util.bio.parsers.UCSCGeneLine

toString() - Method in class util.bio.parsers.gff.GadFlyGffExtractor

toString() - Method in class util.bio.parsers.gff.Gff3Feature

Generates a GFF3 line.

toString() - Method in class util.bio.parsers.gff.GffFeature

toString() - Method in class util.bio.wrappers.BlastResult

toStringALInts(ArrayList) - Static method in class util.bio.annotation.Translation

toStringBarGraph(int[]) - Method in class util.bio.xamer.Xamer

Run pairwise comparisons between percentHitsPerRound if any round is less than the others return true public boolean isEnriched(){ int tester =0; int len = percentHitsPerRound.length; for (int i=0; itoStringNoAttributes() - Method in class util.bio.parsers.gff.Gff3Feature

Generates a GFF3 line.

toStringPercent(int[]) - Method in class util.bio.xamer.Xamer

toStringSimple() - Method in class trans.roc.Positive

totalLength(Object[][]) - Static method in class util.gen.Misc

Counts the total length of an Object[][]

totalNumberRatiosByWindowSize(int, int) - Static method in class trans.misc.InefficientPseudoMedian

Precaluculates the total number of pairwise ratios for a range of window sizes.

trans.anno - package trans.anno

For associating intervals, binding regions, and binding peaks with GFF annotation.

trans.bkgrnd - package trans.bkgrnd

For examining background GC content and ratio bias.

trans.cel - package trans.cel

Apps and methods for manipulating cel files.

trans.graphics - package trans.graphics

For graphically representing '.cel' files and intervals.

trans.main - package trans.main

Principle classes and scripts used in TiMAT2 analysis.

trans.misc - package trans.misc

Rough working scripts.

trans.qc - package trans.qc

Quality control apps for cel files.

trans.roc - package trans.roc

For manipulating the BAC dmel spike in data and generating ROC curves.

trans.tpmap - package trans.tpmap

For maping, filtering, and calculating statistics about text version bpmap files.

transform10Log10(double) - Static method in class util.bio.calc.Alignment

Calculates a -10Log10(number) transformation

transformPMMM(float[]) - Static method in class trans.cel.QuantileNormalization

Performs a max(PM-MM,1) on the float array where MM is just after each PM.

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

Trims the comon chars from the front and back of each line, won't entirely delete line.

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

Trims characters common to all from start of lines.

trimOutliers(float[], float, float) - Static method in class util.gen.Num

Sets values exceeding the cutoff to the default.

trimOutliers(float[][], float, float) - Static method in class util.gen.Num

For each f[replica][]Sets values exceeding the cutoff to the default.

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

Trims "" from the beginning and end of String if both are found.

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

Removes .txt from end of String if present

trimmedMean(double[], double) - Static method in class util.gen.Num

Trims the fraction off the top and bottom, returns the mean of the remainder, rounds trimming # up.

trimmedMean(float[], double) - Static method in class util.gen.Num

Trims the fraction off the top and bottom, returns the mean of the remainder, rounds trimming # up.

trimmedMean(double[], int) - Static method in class util.gen.Num

Makes a trimmed mean, note the trim number is not a % but the number of values to drop from the beginning and end of the ordered set.

trimmedMean(float[], int) - Static method in class util.gen.Num

Makes a trimmed mean, note the trim number is not a % but the number of values to drop from the beginning and end of the ordered set.

truncate(String, int) - Static method in class util.gen.Misc

Truncates a String adding three periods if too long.

tukeyBiWeight(double[]) - Static method in class util.gen.Num

Calculates a one-step tukey biweight estimator using 5 as the tuning constant and adding 0.0001 to the denominator to avoid dividing by zero, Affy's params.