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

G

GATAFrame - class gata.menu.GATAFrame.

GATAFrame(GATAParams) - Constructor for class gata.menu.GATAFrame

GATAParams - class gata.main.GATAParams.

GATAParams() - Constructor for class gata.main.GATAParams

GATAPlotter - class gata.main.GATAPlotter.

GATAPlotter() - Constructor for class gata.main.GATAPlotter

GATAUtil - class gata.main.GATAUtil.

GATAUtil() - Constructor for class gata.main.GATAUtil

GATAligner - class gata.aligner.GATAligner.

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

GCRatio - class trans.misc.GCRatio.

Container for a ratio and associated %GC content for a particular oligo.

GCRatio(double, int) - Constructor for class trans.misc.GCRatio

GZIP - Static variable in class com.amazon.thirdparty.Base64

Specify that data should be gzip-compressed.

GadFlyGffExtractor - class util.bio.parsers.gff.GadFlyGffExtractor.

Class for building annotation objects from GffFeatures, basically a converter, specific to the old dmel GadFly annotation.

GadFlyGffExtractor(File, int, int) - Constructor for class util.bio.parsers.gff.GadFlyGffExtractor

Gene - class bioroot.Gene.

Gene() - Constructor for class bioroot.Gene

GeneBean - class bioroot.GeneBean.

GeneBean() - Constructor for class bioroot.GeneBean

GeneBean(int, DBUtil) - Constructor for class bioroot.GeneBean

GeneGroup - class util.bio.annotation.GeneGroup.

A GeneGroup is the top organizing level of a "Gene".

GeneGroup(String, String, int, int, String, TransGroup[], int, String) - Constructor for class util.bio.annotation.GeneGroup

GeneNameCounter - class util.apps.GeneNameCounter.

Counts the frequency of words in the master list, then assigns these frequencies to words in the test list.

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

GeneRep - class util.bio.annotation.GeneRep.

A GeneRep resentation contains a genomic sequence designating a gene broken into various segments.

GeneRep(TransGroup[], GeneGroup) - Constructor for class util.bio.annotation.GeneRep

GeneRepGlyph - class gata.geneGlyphs.GeneRepGlyph.

GeneRepGlyph(GeneRep, GATAParams, AnnoSpecParams) - Constructor for class gata.geneGlyphs.GeneRepGlyph

GenericFeature - class util.bio.annotation.GenericFeature.

Class to hold user defined gff items like CRMs, enhancers, unpublished single track notation.

GenericFeature(GffFeature) - Constructor for class util.bio.annotation.GenericFeature

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

GenericGlyph - class gata.geneGlyphs.GenericGlyph.

GenericGlyph(GenericFeature) - Constructor for class gata.geneGlyphs.GenericGlyph

GenomeFASTASplitter - class util.bio.converters.GenomeFASTASplitter.

Splits a whole genome fasta into different files, also rewrites the fasta header to just the first word following the >

GenomeFASTASplitter() - Constructor for class util.bio.converters.GenomeFASTASplitter

GenomicRegion - class trans.graphics.GenomicRegion.

GenomicRegion(String, int) - Constructor for class trans.graphics.GenomicRegion

GenomicRegionGlyph - class trans.graphics.GenomicRegionGlyph.

GenomicRegionGlyph(String, int) - Constructor for class trans.graphics.GenomicRegionGlyph

GetResponse - class com.amazon.s3.GetResponse.

A Response object returned from AWSAuthConnection.get().

GetResponse(HttpURLConnection) - Constructor for class com.amazon.s3.GetResponse

Pulls a representation of an S3Object out of the HttpURLConnection response.

Gff2ToBindingRegions - class trans.anno.Gff2ToBindingRegions.

Converts a gff2 file to a binding region file (chr start end mockSequence).

Gff2ToBindingRegions() - Constructor for class trans.anno.Gff2ToBindingRegions

Gff2ToIntervals - class trans.anno.Gff2ToIntervals.

Converts a gff2 file to an interval object file.

Gff2ToIntervals() - Constructor for class trans.anno.Gff2ToIntervals

Gff3Feature - class util.bio.parsers.gff.Gff3Feature.

A container for each of the values in a GFF3 line.

Gff3Feature() - Constructor for class util.bio.parsers.gff.Gff3Feature

Gff3Feature(String) - Constructor for class util.bio.parsers.gff.Gff3Feature

Always check if the GFF3Feature is valid after instantiating with this constructor.

Gff3Parser - class util.bio.parsers.gff.Gff3Parser.

For parsing a GFF3 text file into GFF3Feature objects, be sure to set the regExTypes String filter to match which types you want to save!

Gff3Parser(File) - Constructor for class util.bio.parsers.gff.Gff3Parser

Gff3Parser() - Constructor for class util.bio.parsers.gff.Gff3Parser

GffFeature - class util.bio.parsers.gff.GffFeature.

A container for each of the values in a GFF 2 line.

GffFeature(String) - Constructor for class util.bio.parsers.gff.GffFeature

GffParser - class util.bio.parsers.gff.GffParser.

Parses GFF files extracting the annotation according to GFF(2).

GffParser(File, int, int) - Constructor for class util.bio.parsers.gff.GffParser

GlyphPanel - class gata.geneGlyphs.GlyphPanel.

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

Gr - class trans.roc.Gr.

Gr line container.

Gr(String) - Constructor for class trans.roc.Gr

Gr(int, float) - Constructor for class trans.roc.Gr

Gr2Bar - class trans.misc.Gr2Bar.

Gr2Bar(String[]) - Constructor for class trans.misc.Gr2Bar

GrComparator - class trans.roc.GrComparator.

GrComparator() - Constructor for class trans.roc.GrComparator

GrGraph - class trans.misc.GrGraph.

Container for holding info related to a xxx.gr file.

GrGraph(String, String, int[], float[]) - Constructor for class trans.misc.GrGraph

Graph - class trans.graphics.Graph.

Graph for IntervalPlotter.

Graph(double[], double[], double, double, Color) - Constructor for class trans.graphics.Graph

gata.aligner - package gata.aligner

For aligning and post processing DNA sequences using BLAST for subsequent import into GATAPlotter.

gata.geneGlyphs - package gata.geneGlyphs

For representing annotation, scale bars, and generic tracks.

gata.main - package gata.main

Main app, utility, and params for GATAPlotter.

gata.menu - package gata.menu

GATAPlotter menus, panels, and frames.

gata.plotter - package gata.plotter

GATAPlotter primary panel, sliders, tools, and conservation panels.

gatherInfo() - Method in class trans.tpmap.MapSplitter

genDashes(String, String) - Static method in class gata.main.GATAUtil

genDashes(String, String) - Static method in class util.bio.seq.Seq

Generates identitiy dashes (ie"||| | |||") between two aligned sequences

generateConservedSeqs() - Method in class gata.plotter.ConservedSeqs

generateIntervalStats(Interval) - Method in class trans.main.IntervalReportPrinter

Calculate stats on oligos from best window.

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

Takes the geometric mean of float[][] values to double[], [numChips][OligoValues], returns the values in log base 2.

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

Geometric mean.

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

Takes a geometric average of float[][] values [numChips][OligoValues].

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

Returns the log2 ratio of each pair, takes a geometric mean of replicas.

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

Takes a geometric average of float[][] values to double[], averages repeats [numChips][OligoValues].

get(String, String, Map) - Method in class com.amazon.s3.AWSAuthConnection

Reads an object from S3.

get(String, String, Map) - Method in class com.amazon.s3.QueryStringAuthGenerator

getA() - Method in class gata.main.GATAParams

getAAlignPanel() - Method in class gata.main.GATAParams

getACL(String, String, Map) - Method in class com.amazon.s3.AWSAuthConnection

Get the ACL for a given object (or bucket, if key is null).

getACL(String, String, Map) - Method in class com.amazon.s3.QueryStringAuthGenerator

getAP() - Method in class gata.aligner.LocalAlignment

getARFA() - Method in class util.gen.SpearmanCorrelation

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

getAdd1PSPM() - Method in class meme.MemeMotif

getAddOneLLPSPMCutOffScore() - Method in class meme.MotifSearchResult

getAlias() - Method in class bioroot.ReagentBean

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

Reserved Attribute.

getAlignFrameHeight() - Method in class gata.plotter.AlignPanel

getAlignFrameWidth() - Method in class gata.plotter.AlignPanel

getAlignPanel() - Method in class gata.main.GATAParams

getAlignParams() - Method in class gata.main.GATAParams

getAlignScrollPane() - Method in class gata.main.GATAPlotter

getAlignerPrefReference() - Method in class gata.aligner.AlignerInputPanel

getAlignerPreferences() - Method in class gata.aligner.AlignerInputPanel

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

getAlignmentString() - Method in class gata.aligner.Alignment

getAlignments() - Method in class gata.plotter.AlignPanel

getAnnoPanelHeight() - Method in class gata.main.AnnoSpecParams

getAnnotation() - Method in class gata.main.AnnoSpecParams

getAntibodyForm(AntibodyBean, DBUtil, UserBean) - Static method in class bioroot.antibody.AntibodyBase

Returns an antibody form filled with the values in the bean.

getAntibodyId() - Method in class bioroot.antibody.AntibodyPrep

getAntibodyPreference() - Method in class bioroot.UserBean

getAntibodyPrefs() - Method in class bioroot.UserBean

getAntibodyPrepForm(AntibodyPrep, DBUtil, StringBuffer, int) - Static method in class bioroot.antibody.AntibodyBase

getAntibodyPrepForms(AntibodyBean, DBUtil, StringBuffer) - Static method in class bioroot.antibody.AntibodyBase

getAntibodyPrepReport(AntibodyPrep, DBUtil, StringBuffer, int, boolean) - Static method in class bioroot.antibody.AntibodyBase

getAntibodyPrepReports(AntibodyBean, DBUtil, StringBuffer, boolean) - Static method in class bioroot.antibody.AntibodyBase

getAntibodyPreps(DBUtil) - Method in class bioroot.antibody.AntibodyBean

getAntibodyReport(AntibodyBean, DBUtil, UserBean, boolean) - Static method in class bioroot.antibody.AntibodyBase

Returns an antibody report filled with the values in the bean.

getAntibodyUse() - Method in class bioroot.antibody.UseDilution

getAntigen() - Method in class bioroot.antibody.AntibodyBean

getAnyGenericGlyphs() - Method in class gata.main.AnnoSpecParams

getAppsDirectory() - Method in class trans.main.T2Parameter

getArrayType() - Method in class bioroot.strain.StrainBean

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

getAttributes() - Method in class util.bio.annotation.GenericFeature

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

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

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

getAvail() - Method in class util.bio.digest.Enzyme

getAvailability() - Method in class bioroot.ReagentBean

getAveExpSeqLength() - Method in class selex.SelexParams

getAveNumExpSubSeqs() - Method in class selex.SelexParams

getAveNumObsSubSeqs() - Method in class selex.SelexParams

getAveObsExpRatio() - Method in class selex.SelexParams

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

getAverageInts(int, int) - Static method in class util.gen.Num

Gets the average of the integers bracketed and including the start and end.

getAwsCredentials() - Method in class util.amazon.S3Manager

getB() - Method in class gata.main.GATAParams

getBRFA() - Method in class util.gen.SpearmanCorrelation

getBackgroundColor() - Method in class gata.main.GATAParams

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

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

getBaseNumArray(String, int) - Static method in class gata.main.GATAUtil

getBasePositions() - Method in class trans.misc.GrGraph

getBaseScore() - Method in class trans.main.WindowBlockMaker

getBaseScores() - Method in class meme.MotifScanner

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

getBasicTm(String) - Method in class bioroot.oligo.OligoBean

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

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

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

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

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

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

getBiggestAlignPanelY() - Method in class gata.main.GATAParams

getBiggestGlyphPanelY() - Method in class gata.main.AnnoSpecParams

getBinCounts() - Method in class util.gen.Histogram

getBinLabels() - Method in class util.gen.Histogram

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

getBioroot() - Method in class bioroot.UserRegistrationBean

getBitScore() - Method in class gata.aligner.Alignment

getBl2F() - Method in class gata.aligner.AlignerInputPanel

getBl2SeqHits() - Method in class bioroot.BlastMatcher

getBl2SeqProg() - Method in class gata.aligner.AlignerPreferences

getBl2seq() - Method in class gata.aligner.AlignParams

getBlastResults() - Method in class bioroot.SearchBean

getBottomCluster() - Method in class util.bio.cluster.Cluster

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

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

getBpMatches() - Method in class bioroot.plasmid.OligoMatch

getBucket() - Method in class util.amazon.S3Manager

getBucketACL(String, Map) - Method in class com.amazon.s3.AWSAuthConnection

Get the ACL for a given bucket

getBucketACL(String, Map) - Method in class com.amazon.s3.QueryStringAuthGenerator

getBucketLogging(String, Map) - Method in class com.amazon.s3.AWSAuthConnection

Get the logging xml document for a given bucket

getBucketLogging(String, Map) - Method in class com.amazon.s3.QueryStringAuthGenerator

getBucketName() - Method in class util.amazon.S3Manager

getC() - Method in class gata.main.GATAParams

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

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

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

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

getCelMasker() - Method in class trans.graphics.VirtualCelFrame

getCell(String) - Method in class bioroot.DBUtil

Returns the first cell from an sql statement.

getCell(String) - Method in class util.gen.SQL

Returns the first cell from an sql statement.

getCellTypeId(String, int) - Method in class bioroot.DBUtil

Fetches an tissueId given a tissue name and labGroupId (they aren't unique except within a labGroup)

getCellTypeId() - Method in class bioroot.strain.StrainBean

getCellTypeName(DBUtil) - Method in class bioroot.strain.StrainBean

Will look one time for a name, all other times will just return "".

getCelpFiles() - Method in class trans.cel.QuantileNormalization

getChallenge() - Method in class bioroot.LoginBean

getChallengeConcatinate() - Method in class util.gen.Passwords

getChallengeDate() - Method in class bioroot.LoginBean

getChart() - Method in class trans.graphics.RankedSetAnalysis

getChartPanel() - Method in class trans.graphics.RankedSetAnalysis

getCheckBoxNumber() - Method in class bioroot.Feature

Makes a checkbox and textfield where the box is checked if Feature is visible and a rounded double orderNumber is put in text field if it's not 1000

getCheckBoxNumber(String) - Method in class bioroot.TableHeading

Makes a checkbox and textfield where the box is checked if TableHeading is visible and a rounded double orderNumber is put in text field if it's not 1000

getChipSetDirectories() - Method in class trans.main.ChromSet

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

getChromSpecificGeneLines() - Method in class util.bio.parsers.UCSCGeneModelTableReader

getChromSplitFeatures() - Method in class util.bio.parsers.gff.Gff3Parser

Returns the features split by chromosome.

getChromosome() - Method in class expr.CorrelationWindow

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

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

getChromosome() - Method in class trans.bkgrnd.LoadedOligo

getChromosome() - Method in class trans.cel.ChromosomeIndex

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

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

getChromosome() - Method in class trans.main.PosRegion

getChromosome() - Method in class trans.main.Window

getChromosome() - Method in class trans.misc.GrGraph

getChromosome() - Method in class trans.roc.ControlGene

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

getChromosome() - Method in class trans.roc.RocWindow

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

getChromosome() - Method in class trans.tpmap.BlastFilterResult

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

getChromosome() - Method in class trans.tpmap.TPMapLine

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

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

getChromosome() - Method in class util.bio.seq.IndexedSequence

getChromosomeNumber() - Static method in class trans.misc.Util

Creates a HashMap of "chr1"=Byte(1) through "chr22"=Byte(22) plus chrX=23, chrY=24, and chrMT=25.

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

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

getClosestInterval() - Method in class trans.main.PosRegion

getClosestNonOverlappingInterval() - Method in class trans.main.PosRegion

getClusters() - Method in class util.bio.cluster.HierarchicalClustering

getCmdLn() - Method in class meme.MemeParser

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

Conservative estimate of coding segments.

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

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

getCollapsed() - Method in class bioroot.IdNameMatch

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

getColumnName() - Method in class bioroot.Feature

getColumnName() - Method in class bioroot.SearchHit

getColumnText() - Method in class bioroot.SearchHit

getCommandArray() - Method in class util.bio.wrappers.BL2Seq

getComments() - Method in class bioroot.ReagentBean

getCompAnnoSpecParams() - Method in class gata.main.GATAParams

getCompScrollPane() - Method in class gata.main.GATAPlotter

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

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

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

getCompTexF() - Method in class gata.aligner.AlignerInputPanel

getConcatStart() - Method in class bioroot.BlastMatcher

getConcatStop() - Method in class bioroot.BlastMatcher

getConcentration() - Method in class bioroot.oligo.OligoBean

getConcentration() - Method in class bioroot.plasmid.PlasmidBean

getConcentrationUnits() - Method in class bioroot.oligo.OligoBean

getConnection() - Method in class bioroot.DBUtil

getConnection() - Method in class util.gen.SQL

getConsole() - Method in class gata.main.GATAParams

getConsole() - Method in class gata.plotter.ConservedSeqs

getContactEmail() - Method in class bioroot.ContactBean

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

getControlCelFiles() - Method in class trans.main.T2Parameter

getControlIntensities(int) - Method in class trans.main.Oligo

getControlIntensities() - Method in class trans.main.ScanChromosomes

getControlStats() - Method in class trans.cel.QuantileNormalization

getControlValues() - Method in class trans.main.ScoredGene

getCoordinates() - Method in class expr.ExpressedGene

getCoordinates() - Method in class gata.aligner.Alignment

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

getCorrelationCoefficient() - Method in class util.bio.cluster.Cluster

getCovertedScore() - Method in class expr.CorrelationWindow

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

getCredentialsFile() - Method in class util.amazon.S3Manager

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

Any Attribute that is not a reserve attribute is grouped here.

getCutBottom() - Method in class util.bio.digest.Enzyme

getCutTop() - Method in class util.bio.digest.Enzyme

getD() - Method in class gata.main.GATAParams

getDNAColor() - Method in class gata.main.GATAParams

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

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

getDashStroke() - Method in class gata.main.GATAParams

getDate() - Method in class bioroot.antibody.AntibodyPrep

getDate() - Static method in class util.gen.Misc

Returns a nicely formated time (15 May 2004).

getDate() - Method in class util.gen.Passwords

getDateNoSpaces() - Static method in class util.gen.Misc

Returns a nicely formated time (15May2004).

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

Reserved Attribute.

getDefaultTrackThickness() - Method in class gata.main.GATAParams

getDemoResponse() - Method in class bioroot.LoginBean

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

getDifferentUserConcat() - Method in class bioroot.UserRegistrationBean

getDilution() - Method in class bioroot.antibody.UseDilution

getDistanceTo3PrimeGeneGrp() - Method in class trans.anno.BindingRegion

getDistanceTo5PrimeGeneGrp() - Method in class trans.anno.BindingRegion

getDocs() - Static method in class meme.UtilMeme

getDottedProteinLines() - Method in class gata.main.AnnoSpecParams

getE() - Method in class gata.main.GATAParams

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

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

getEditHistory() - Method in class bioroot.CellTypeBean

getEditHistory() - Method in class bioroot.GeneBean

getEditHistory() - Method in class bioroot.MarkerBean

getEditHistory() - Method in class bioroot.OrganismBean

getEditHistory() - Method in class bioroot.ReagentBean

getEditHistory() - Method in class bioroot.UserBean

getElementValue(Node) - Static method in class util.xml.ParseXMLFile

Returns element value

getEmail() - Method in class bioroot.UserBean

getEmail() - Method in class bioroot.UserRegistrationBean

getEmailAddresses() - Method in class bioroot.LabGroup

getEmailObject() - Static method in class bioroot.Contact

Returns an Email object for posting email.

getEmailObject() - Static method in class bioroot.Login

Returns an Email object for posting email.

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

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

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

getEnd() - Method in class trans.main.PosRegion

getEnd() - Method in class trans.roc.RocWindow

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

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

getEnd() - Method in class util.bio.annotation.GenericFeature

getEnd() - Method in class util.bio.annotation.StartEnd

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

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

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

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

getEnzymes() - Method in class util.bio.digest.NEBParser

getExactMatches() - Method in class trans.tpmap.BlastFilterResult

getExonEnds() - Method in class trans.roc.ControlGene

getExonStarts() - Method in class trans.roc.ControlGene

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

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

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

getExpectation() - Method in class util.bio.wrappers.BL2Seq

getExpectedSize() - Method in class selex.SelexParams

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

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

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

getF() - Method in class gata.main.GATAParams

getFailedLogins() - Method in class bioroot.UserBean

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

getFatLineThicknes() - Method in class gata.main.GATAParams

getFatRNALines() - Method in class gata.main.AnnoSpecParams

getFatStroke() - Method in class gata.main.GATAParams

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

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

getFeatureNames(Feature[]) - Static method in class bioroot.Feature

getFeatureType() - Method in class util.bio.annotation.GenericFeature

getFeatures() - Method in class bioroot.Preference

getFeatures() - Method in class util.bio.parsers.gff.Gff3Parser

getFieldGroup() - Method in class bioroot.SearchBean

getFields() - Method in class bioroot.SearchBean

getFileName() - Method in class bioroot.antibody.AntibodyBean

getFileName() - Method in class bioroot.antibody.AntibodyPrep

getFileName() - Method in class bioroot.oligo.OligoUploadBean

getFileName() - Method in class bioroot.plasmid.PlasmidBean

getFileName() - Method in class bioroot.plasmid.PlasmidUploadBean

getFileName() - Method in class bioroot.strain.StrainBean

getFileName() - Method in class bioroot.strain.StrainUploadBean

getFileName() - Method in class util.bio.parsers.MultiFastaParser

getFileName() - Method in class util.bio.parsers.QualityFileParser

getFileNumber() - Method in class meme.MotifSearchResult

getFirstName() - Method in class bioroot.UserBean

getFirstName() - Method in class bioroot.UserRegistrationBean

getFirstPeakIndex() - Method in class trans.main.BindingPeak

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

Conservative estimate returning smallest non coding region.

getFloatArrayFile() - Method in class util.bio.cluster.Cluster

getFont() - Method in class gata.main.GATAParams

getFormattedTimeFromFraction(double) - Static method in class util.gen.Misc

Returns a formatted time 2:15:00 given 2.25

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

getFreqMatrix() - Method in class meme.MemeMotif

getFullName() - Method in class bioroot.TableHeading

getFullPathName(File) - Static method in class util.gen.IO

Gets full path name using getCanonicalPath() on a File

getFullPathToBL2seq() - Method in class util.bio.wrappers.BL2Seq

getFurthestDown() - Method in class gata.aligner.AlignerInputPanel

getFurthestRight() - Method in class gata.aligner.AlignerInputPanel

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

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

getGC(String) - Method in class bioroot.oligo.OligoBean

getGFFFile() - Method in class util.bio.parsers.gff.Gff3Parser

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

Reserved Attribute.

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

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

getGataFrame() - Method in class gata.main.GATAParams

getGataPlotter() - Method in class gata.main.GATAParams

getGc() - Method in class trans.bkgrnd.LoadedOligo

getGc() - Method in class trans.misc.GCRatio

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

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

getGene() - Method in class trans.main.ScoredGene

getGeneGlyphs() - Method in class gata.main.AnnoSpecParams

getGeneGroupArrayList() - Method in class util.bio.parsers.gff.DmelRel4Extractor

getGeneGroups() - Method in class util.bio.parsers.gff.DmelRel4Extractor

Final product from the extractor.

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

getGeneGrp3Prime() - Method in class trans.anno.BindingRegion

getGeneGrp5Prime() - Method in class trans.anno.BindingRegion

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

getGeneId(String, int) - Method in class bioroot.DBUtil

Fetches an geneId given a geneName and labGroupId (they aren't unique except within a labGroup), assumes connection to BioRoot+Database.

getGeneId(DBUtil) - Method in class bioroot.antibody.AntibodyBean

getGeneId() - Method in class bioroot.oligo.OligoBean

getGeneId() - Method in class bioroot.plasmid.PlasmidBean

getGeneLines() - Method in class util.bio.parsers.UCSCGeneModelTableReader

getGeneName(int) - Method in class bioroot.DBUtil

Fetches an geneName given an geneId, assumes connection to BioRoot+Database.

getGeneName(DBUtil) - Method in class bioroot.antibody.AntibodyBean

getGeneName(DBUtil) - Method in class bioroot.oligo.OligoBean

getGeneName(DBUtil) - Method in class bioroot.plasmid.PlasmidBean

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

getGeneSequence() - Method in class bioroot.oligo.OligoBean

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

getGenericFeatureHash() - Method in class util.bio.parsers.gff.DmelRel4Extractor

Contains all the feature types that were not recognized by the Extractor.

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

Contains all the feature types that were not recognized by the GadFlyGFFExtractor.

getGenericFeatures() - Method in class util.bio.parsers.gff.DmelRel4Extractor

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

getGenericFeaturesAL() - Method in class util.bio.parsers.gff.DmelRel4Extractor

getGenericFeaturesHash() - Method in class util.bio.parsers.gff.DmelRel4Extractor

getGenericVisibility() - Method in class bioroot.ReagentBean

Returns one of the standard visibility settings (WWW, Lab mates, Private) or the generic 'Organization'

getGenomeFastaDirectory() - Method in class trans.main.T2Parameter

getGenomeVersion() - Method in class trans.main.T2Parameter

getGenomeVersion() - Method in class trans.misc.GrGraph

getGenotype() - Method in class bioroot.strain.StrainBean

getGffFeatures() - Method in class util.bio.parsers.gff.GffParser

getGffFile() - Method in class gata.main.AnnoSpecParams

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

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

getGlyphPanel() - Method in class gata.geneGlyphs.Annotation

getGlyphPanel() - Method in class gata.main.AnnoSpecParams

getGraphics2DN() - Method in class gata.main.AnnoSpecParams

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

getGrowthConditions() - Method in class bioroot.strain.StrainBean

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

getHandlingInstructions() - Method in class bioroot.oligo.OligoBean

getHeader(int, int) - Static method in class trans.main.ExportIntervalData

getHeader() - Method in class util.bio.digest.NEBParser

getHeader() - Static method in class util.bio.wrappers.Primer3Pick

getHeight() - Method in class gata.main.GATAParams

getHeightBuffImage() - Method in class gata.plotter.AlignPanel

getHeightLabels() - Method in class gata.main.GATAParams

getHits() - Method in class meme.MemeMotif

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

getHits() - Method in class util.bio.wrappers.BL2Seq

getHits() - Method in class util.gen.Bin

getHitsAddOneLLPSPM() - Method in class meme.MotifSearchResult

getHitsMemeLLPSPM() - Method in class meme.MotifSearchResult

getHitsPerRound() - Method in class util.bio.xamer.Xamer

getHotLinkedOligos() - Method in class bioroot.plasmid.PlasmidBean

Returns HTML for of oligoMatches for display.

getHotLinkedParents(DBUtil) - Method in class bioroot.strain.StrainBean

Returns HTML parent/ strain names for display.

getHotLinkedPlasmids(DBUtil) - Method in class bioroot.antibody.AntibodyBean

Returns HTML plasmid names for display.

getHotLinkedPlasmids(DBUtil) - Method in class bioroot.strain.StrainBean

Returns HTML plasmid names for display.

getHotLinkedStrains(DBUtil) - Method in class bioroot.antibody.AntibodyBean

Returns HTML strain names for display.

getHotLinkedStrains(DBUtil) - Method in class bioroot.plasmid.PlasmidBean

Returns HTML strain names for display.

getHtmlChallengeTable() - Method in class util.gen.Passwords

getId() - Method in class bioroot.BlastMatcher

getId() - Method in class bioroot.CellTypeBean

getId() - Method in class bioroot.ContactBean

getId() - Method in class bioroot.GeneBean

getId() - Method in class bioroot.IdNameMatch

getId() - Method in class bioroot.LabGroup

getId() - Method in class bioroot.MarkerBean

getId() - Method in class bioroot.OrganismBean

getId() - Method in class bioroot.Organization

getId() - Method in class bioroot.ReagentBean

getId() - Method in class bioroot.SearchHit

getId() - Method in class bioroot.UserBean

getId() - Method in class bioroot.antibody.AntibodyPrep

getId() - Method in class bioroot.antibody.UseDilution

getId() - Method in class bioroot.plasmid.OligoMatch

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

Reserved Attribute.

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

getIncrement() - Method in class util.gen.Histogram

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

getIndex() - Method in class trans.main.SubWindow

getInnerSplitPane() - Method in class gata.main.GATAPlotter

getIntensities() - Method in class trans.cel.QuantileNormalization

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

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

getIntensities() - Method in class trans.roc.ControlGene

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

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

getIntensityMM() - Method in class trans.bkgrnd.LoadedOligo

getIntensityPM() - Method in class trans.bkgrnd.LoadedOligo

getIntercept() - Method in class util.gen.LinearRegression

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

getInterval() - Method in class trans.main.PeakPicker

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

getIso() - Method in class util.bio.digest.Enzyme

getJava() - Method in class trans.main.T2Parameter

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

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

getLAScore() - Method in class gata.aligner.LocalAlignment

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

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

getLLAdd1PSPM(double, double, double, double) - Method in class meme.MemeMotif

getLLMemePSPM(double, double, double, double) - Method in class meme.MemeMotif

getLabGroup() - Method in class bioroot.LoginBean

getLabGroup() - Method in class bioroot.UserBean

getLabGroup() - Method in class bioroot.UserRegistrationBean

getLabGroupId() - Method in class bioroot.CellTypeBean

getLabGroupId() - Method in class bioroot.GeneBean

getLabGroupId() - Method in class bioroot.LoginBean

getLabGroupId() - Method in class bioroot.ReagentBean

getLabGroupId() - Method in class bioroot.UserBean

getLabGroupName() - Method in class bioroot.ContactBean

getLabGroupName(DBUtil) - Method in class bioroot.ReagentBean

getLabGroupSchedule(DBUtil) - Method in class bioroot.UserBean

getLabGroups() - Method in class bioroot.Preference

getLabGroupsToArchive(DBUtil) - Static method in class bioroot.CronArchive

Identifies lab groups that should be archived based on their last archive date and schedule.

getLabel() - Method in class trans.graphics.GenomicRegionGlyph

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

getLabel() - Method in class util.gen.Bin

getLabelColor() - Method in class gata.main.GATAParams

getLabels() - Method in class gata.main.AnnoSpecParams

getLabels() - Method in class util.bio.cluster.ClusterDrawPanel

getLastInsertId(String) - Method in class bioroot.DBUtil

Returns the last inserted row auto increment number.

getLastInsertId(String) - Method in class util.gen.SQL

Returns the last inserted row auto increment number.

getLastLogin() - Method in class bioroot.UserBean

getLastName() - Method in class bioroot.UserBean

getLastName() - Method in class bioroot.UserRegistrationBean

getLastUser() - Method in class bioroot.ReagentBean

getLastUser() - Method in class bioroot.antibody.AntibodyPrep

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

getLeftFlankingIndex() - Method in class trans.main.BindingPeak

getLeftIndex() - Method in class trans.main.PeakPicker

getLeftLR() - Method in class trans.cel.SplineScalar

getLeftSideMatch() - Method in class selex.SelexParams

getLeftSideReplace() - Method in class selex.SelexParams

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

getLenMax() - Method in class selex.SelexParams

getLenMin() - Method in class selex.SelexParams

getLength() - Method in class bioroot.oligo.OligoBean

getLength() - Method in class bioroot.plasmid.PlasmidBean

getLength() - Method in class selex.SubSeq

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

End-Start+1

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

Returns end - start +1, thus last base is included, not interbase numbering!

getLength() - Method in class util.bio.digest.Enzyme

getLine() - Method in class trans.cel.CelLine

getLine() - Method in class trans.tpmap.TPMapLine

getLine() - Method in class util.bio.cluster.Cluster

getLine() - Method in class util.bio.wrappers.Primer3Pick

getLineNumber() - Method in class trans.tpmap.TPMapDuplicateFilter

getLocalAlignString(int, int) - Method in class gata.aligner.LocalAlignment

getLocation() - Method in class bioroot.ReagentBean

getLocation() - Method in class bioroot.antibody.AntibodyPrep

getLogFile() - Method in class trans.main.T2Parameter

getLogTPvalue() - Method in class trans.main.WilcoxonRankSumTest

getLoginName() - Method in class bioroot.LoginBean

getLoginName() - Method in class bioroot.UserBean

getLoginName() - Method in class bioroot.UserRegistrationBean

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

getLooseMatches() - Method in class bioroot.SearchHit

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

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

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

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

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

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

getMW(String) - Method in class bioroot.oligo.OligoBean

getMarkers(DBUtil) - Method in class bioroot.plasmid.PlasmidBean

getMarkers(DBUtil) - Method in class bioroot.strain.StrainBean

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

getMaskValue() - Method in class trans.graphics.CelMasker

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

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

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

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

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

getMatches() - Method in class trans.tpmap.BlastFilterResult

getMatching() - Method in class bioroot.SearchBean

getMatingType() - Method in class bioroot.strain.StrainBean

getMaxBit() - Method in class gata.plotter.ToolsFrame

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

getMaxE() - Method in class gata.plotter.ToolsFrame

getMaxGap() - Method in class trans.main.T2Parameter

getMaxHeight() - Method in class gata.menu.FileInputPanel

getMaxHeight() - Method in class gata.menu.SaveImagePanel

getMaxIntensityValueToPlot() - Method in class trans.graphics.CelMasker

getMaxMemory() - Method in class trans.main.T2Parameter

getMaxNumFeatures() - Method in class trans.tpmap.WindowMaker

getMaxNumPeaks() - Method in class trans.main.PeakPicker

getMaxNumberPeaks() - Method in class trans.main.T2Parameter

getMaxWidth() - Method in class gata.menu.FileInputPanel

getMaxWidth() - Method in class gata.menu.SaveImagePanel

getMaxWindowFilter() - Method in class trans.main.WindowBlockMakerTwoColor

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

getMaximum() - Method in class util.gen.Histogram

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

getMedian() - Method in class trans.main.ScoredGene

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

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

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

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

getMedianRatio() - Method in class trans.main.SubWindow

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

getMegaCluster() - Method in class util.bio.cluster.HierarchicalClustering

getMemeLLPSPMCutOffScore() - Method in class meme.MotifSearchResult

getMemeMotif() - Method in class meme.MotifSearchResult

getMemeMotifs() - Method in class meme.MemeParser

getMemePSPM() - Method in class meme.MemeMotif

getMemeParser() - Method in class meme.MemeMotif

getMemeReports() - Method in class meme.MemeResults

getMessage() - Method in class bioroot.ContactBean

getMessage(LabGroup, boolean) - Static method in class bioroot.CronArchive

getMessage(String) - Static method in class bioroot.Spammer

getMessages() - Method in class bioroot.CellTypeBean

getMessages() - Method in class bioroot.ContactBean

getMessages() - Method in class bioroot.GeneBean

getMessages() - Method in class bioroot.LoginBean

getMessages() - Method in class bioroot.MarkerBean

getMessages() - Method in class bioroot.OrganismBean

getMessages() - Method in class bioroot.ReagentBean

getMessages() - Method in class bioroot.SearchBean

getMessages() - Method in class bioroot.UserRegistrationBean

getMethSens() - Method in class util.bio.digest.Enzyme

getMiddle() - Method in class trans.roc.RocWindow

getMiddle() - Method in class util.gen.Bin

getMinBit() - Method in class gata.plotter.ToolsFrame

getMinBpSides() - Method in class trans.main.PeakPicker

getMinE() - Method in class gata.plotter.ToolsFrame

getMinNumberOligosInSubWin() - Method in class trans.main.T2Parameter

getMinPercent() - Method in class trans.main.PeakPicker

getMinRun() - Method in class trans.main.PeakPicker

getMinWindowFilter() - Method in class trans.main.WindowBlockMakerTwoColor

getMinimalCorrelationCoefficient() - Method in class util.bio.cluster.HierarchicalClustering

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

getMinimum() - Method in class util.gen.Histogram

getMinimumNumberOfOligos() - Method in class trans.main.T2Parameter

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

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

getModel() - Method in class util.gen.LinearRegression

Returns Y=mX+b with full precision, no rounding of numbers.

getModelPoints() - Method in class trans.cel.SplineScalar

getModifications() - Method in class bioroot.oligo.OligoBean

getMotifDesc() - Method in class meme.MemeMotif

getMotifHitPlot() - Method in class meme.MemeResults

Rude and crude method to plot the percent hits of each motif to each file using data from motifHitSummary

getMotifHitPlotText() - Method in class meme.MemeResults

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

Sums the logged motif hit values using the best AID window or the entire interval.

getMotifHits() - Method in class meme.MotifScanner

getMotifHitsSummary() - Method in class meme.MemeResults

Method to return a summary of all the motif hits to each file, modify this to build an HTML table

getMotifHitsSummaryText() - Method in class meme.MemeResults

getMotifSig() - Method in class meme.MotifSearchResult

getMotifSites() - Method in class meme.MemeMotif

getMotifSumLn() - Method in class meme.MemeMotif

getMotifSummary() - Method in class meme.MemeResults

Method to return a summary of all the motifs generated by MemeR, modify this to build an HTML table

getMotifSummaryText() - Method in class meme.MemeResults

getMutagen() - Method in class bioroot.strain.StrainBean

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

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

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

getName() - Method in class bioroot.BlastMatcher

getName() - Method in class bioroot.CellTypeBean

getName() - Method in class bioroot.Feature

getName() - Method in class bioroot.GeneBean

getName() - Method in class bioroot.IdNameMatch

getName() - Method in class bioroot.LabGroup

getName() - Method in class bioroot.MarkerBean

getName() - Method in class bioroot.OrganismBean

getName() - Method in class bioroot.Organization

getName() - Method in class bioroot.ReagentBean

getName() - Method in class bioroot.TableHeading

getName() - Method in class bioroot.antibody.AntibodyPrep

getName() - Method in class bioroot.plasmid.OligoMatch

getName() - Method in class expr.ExpressedGene

getName() - Method in class trans.main.PosRegion

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

getName() - Method in class trans.roc.ControlGene

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

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

getName() - Method in class util.bio.annotation.GenericFeature

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

getName() - Method in class util.bio.cluster.Cluster

getName() - Method in class util.bio.digest.Enzyme

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

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

Reserved Attribute.

getName() - Method in class util.gen.FileSize

getNameLabel() - Method in class util.bio.cluster.Cluster

getNameLabelCenterYCoordinate() - Method in class util.bio.cluster.Cluster

getNameLowerCase() - Method in class bioroot.IdNameMatch

getNames() - Method in class expr.CorrelationWindow

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

getNames() - Method in class util.bio.parsers.MultiFastaParser

getNames() - Method in class util.bio.parsers.QualityFileParser

getNearestNbrTm(String) - Method in class bioroot.oligo.OligoBean

Returns -1 if non GATC's are found.

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

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

getNgUl() - Method in class bioroot.oligo.OligoBean

getNonAmbiguousLetters() - Static method in class util.gen.Passwords

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

Conservative estimate of non coding segments between coding exons.

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

getNormalDNALines() - Method in class gata.main.AnnoSpecParams

getNormalStroke() - Method in class gata.main.GATAParams

getNormalizedControlReplicas() - Method in class trans.main.T2Parameter

getNormalizedTreatmentReplicas() - Method in class trans.main.T2Parameter

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

Reserved Attribute.

getNotes() - Method in class bioroot.CellTypeBean

getNotes() - Method in class bioroot.GeneBean

getNotes() - Method in class bioroot.MarkerBean

getNotes() - Method in class bioroot.OrganismBean

getNotes() - Method in class bioroot.ReagentBean

getNotes() - Method in class bioroot.antibody.AntibodyPrep

getNotes() - Method in class bioroot.antibody.UseDilution

getNotes() - Method in class bioroot.oligo.OligoUploadBean

getNotes() - Method in class bioroot.plasmid.PlasmidUploadBean

getNotes() - Method in class bioroot.strain.StrainUploadBean

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

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

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

getNotes() - Method in class trans.roc.ControlGene

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

getNtAtXZero() - Method in class gata.main.AnnoSpecParams

getNtPerPixel() - Method in class gata.main.GATAParams

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

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

getNumHitsAddOneLLPSPM() - Method in class meme.MotifSearchResult

getNumHitsMemeLLPSPM() - Method in class meme.MotifSearchResult

getNumLessThanMin() - Method in class util.gen.Histogram

getNumMoreThanMax() - Method in class util.gen.Histogram

getNumMotifs() - Method in class meme.MemeParser

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

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

getNumOligos() - Method in class trans.main.PeakPicker

getNumPermutations() - Method in class trans.main.ScanChromosomes

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

getNumReads() - Method in class selex.SeqFiles

getNumReads() - Method in class util.bio.parsers.MultiFastaParser

getNumStretchesGoodQuality(int[], int, int) - Static method in class selex.SeqRead

Counts the number of stretches of scores above a cut off in an int[].

getNumberChromosome() - Static method in class trans.misc.Util

Creates a String[] containing [1]"chr1", [2]"chr2" ...

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

getNumberLetters() - Static method in class util.gen.Passwords

getNumberMisMatches() - Method in class trans.bkgrnd.LoadedOligo

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

getNumberName() - Method in class meme.MemeMotif

getNumberOfBins() - Method in class util.gen.Histogram

getNumberOfCuts() - Method in class util.bio.digest.Enzyme

getNumberOfIntervals() - Method in class trans.main.T2Parameter

getNumberOfRandomPermutations() - Method in class trans.main.T2Parameter

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

getNumberOligos() - Method in class trans.main.ChromSet

getNumberOligos() - Method in class trans.main.Window

getNumberPrepUseLines() - Method in class bioroot.antibody.AntibodyBean

getNumberToDisplay() - Method in class bioroot.Preference

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

getNumberTreatmentsControls() - Method in class trans.main.WilcoxonRankSumTest

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

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

getObjectsFile() - Method in class gata.main.GATAParams

getObjectsFile() - Method in class gata.main.GATAPlotter

getOldFileName() - Method in class bioroot.antibody.AntibodyBean

getOldFileName() - Method in class bioroot.antibody.AntibodyPrep

getOligoBeans() - Method in class bioroot.oligo.OligoUploadBean

getOligoForm(OligoBean, DBUtil, UserBean) - Static method in class bioroot.oligo.OligoBase

Returns an oligo form filled it with the values in the oligo bean.

getOligoMatches() - Method in class bioroot.plasmid.PlasmidBean

getOligoPreference() - Method in class bioroot.UserBean

getOligoPrefs() - Method in class bioroot.UserBean

getOligoReport(OligoBean, DBUtil, UserBean, boolean) - Static method in class bioroot.oligo.OligoBase

Returns an oligo report.

getOligoReports() - Method in class bioroot.oligo.OligoUploadBean

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

getOligos() - Method in class trans.main.PeakPicker

getOligos() - Method in class trans.main.SubWindow

getOneBPMisMatches() - Method in class trans.tpmap.BlastFilterResult

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

Reserved Attribute.

getOrder() - Method in class bioroot.Feature

getOrderBy() - Method in class bioroot.Preference

getOrderBy() - Method in class bioroot.ReagentBean

getOrderNumber() - Method in class bioroot.TableHeading

getOrganismId(String) - Method in class bioroot.DBUtil

Fetches an organismId given a organismName, assumes connection to BioRoot.

getOrganismId() - Method in class bioroot.ReagentBean

getOrganismId() - Method in class bioroot.antibody.AntibodyPrep

getOrganismName(int) - Method in class bioroot.DBUtil

Fetches an organismName given an organismId, assumes connection to BioRoot.

getOrganismName(DBUtil) - Method in class bioroot.ReagentBean

getOrganismName(DBUtil) - Method in class bioroot.antibody.AntibodyPrep

getOrganization(DBUtil) - Method in class bioroot.ReagentBean

getOrganization() - Method in class bioroot.UserBean

getOri() - Method in class gata.aligner.LocalAlignment

getOrientation() - Method in class bioroot.oligo.OligoBean

getOrientation() - Method in class gata.aligner.Alignment

getOrientation() - Method in class meme.MotifHit

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

getOrientation() - Method in class util.bio.annotation.GenericFeature

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

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

getOrientation() - Method in class util.bio.wrappers.BL2SeqHit

getOriginalOrderNumber() - Method in class bioroot.TableHeading

getOverHangs() - Method in class util.bio.digest.Enzyme

getOverlap3PrimeGeneGrps() - Method in class trans.anno.BindingRegion

getOverlap5PrimeGeneGrps() - Method in class trans.anno.BindingRegion

getOverlapping() - Method in class trans.main.PosRegion

getOwnerId() - Method in class bioroot.MarkerBean

getOwnerId() - Method in class bioroot.OrganismBean

getOwnerId() - Method in class bioroot.ReagentBean

getOwnerName() - Method in class bioroot.ContactBean

getOwnerName(DBUtil) - Method in class bioroot.ReagentBean

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

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

getPanel() - Method in class gata.aligner.AlignerInputForm

getPanel() - Method in class trans.graphics.IntervalDrawFrame

getPanelHeight() - Method in class trans.graphics.RankedSetDrawPanel

getPanelHeight() - Method in class util.bio.cluster.ClusterDrawPanel

getPanelWidth() - Method in class trans.graphics.RankedSetDrawPanel

getPanelWidth() - Method in class util.bio.cluster.ClusterDrawPanel

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

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

Reserved Attribute.

getParentCluster() - Method in class util.bio.cluster.Cluster

getParentConcats(DBUtil) - Method in class bioroot.strain.StrainBean

Returns an array of id: strainName, or empty String[]{""} if there are none.

getParentLocAlignString() - Method in class gata.aligner.Alignment

getParentPoint() - Method in class util.bio.cluster.Cluster

getParsedFileName() - Method in class meme.MemeParser

getPassageNumber() - Method in class bioroot.strain.StrainBean

getPassword() - Method in class bioroot.LoginBean

getPassword() - Method in class bioroot.UserBean

getPassword1() - Method in class bioroot.UserRegistrationBean

getPassword2() - Method in class bioroot.UserRegistrationBean

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

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

getPeakBP() - Method in class trans.main.BindingPeak

getPeakBp() - Method in class trans.main.PeakPicker

getPeakIndex() - Method in class trans.main.PeakPicker

getPeakPickerWindowSize() - Method in class trans.main.T2Parameter

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

getPermMeanDiff() - Method in class trans.main.SamChromosomeData

getPermTStats() - Method in class trans.main.SamChromosomeData

getPermVariance() - Method in class trans.main.SamChromosomeData

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

getPhenotype() - Method in class bioroot.strain.StrainBean

getPhone() - Method in class bioroot.UserBean

getPhone() - Method in class bioroot.UserRegistrationBean

getPixBtwDNATracks() - Method in class gata.main.GATAParams

getPixBtwLabelTrack() - Method in class gata.main.GATAParams

getPixBtwProtRNA() - Method in class gata.main.GATAParams

getPixBtwTracks() - Method in class gata.main.GATAParams

getPixBtwTransGrpLabel() - Method in class gata.main.GATAParams

getPixBtwTransGrps() - Method in class gata.main.GATAParams

getPixBtwTransGrpsGene() - Method in class gata.main.GATAParams

getPixFatLineThickness() - Method in class gata.main.GATAParams

getPixHeightArrows() - Method in class gata.main.GATAParams

getPixNormalLineThickness() - Method in class gata.main.GATAParams

getPixPerNt() - Method in class gata.main.GATAParams

getPixThinLineThickness() - Method in class gata.main.GATAParams

getPixelsPerBase() - Method in class trans.graphics.Graph

getPlainTextOligos() - Method in class bioroot.plasmid.PlasmidBean

Returns plain text of oligoMatches for archive.

getPlainTextParent() - Method in class bioroot.strain.StrainBean

Returns plain text of parent ids for archive.

getPlainTextPlasmid() - Method in class bioroot.antibody.AntibodyBean

Returns plain text of plasmid ids for archive.

getPlainTextPlasmid() - Method in class bioroot.strain.StrainBean

Returns plain text of plasmid ids for archive.

getPlainTextStrain() - Method in class bioroot.antibody.AntibodyBean

Returns plain text of strain ids for archive.

getPlainTextStrain() - Method in class bioroot.plasmid.PlasmidBean

Returns plain text of strain ids for archive.

getPlasmidBeans() - Method in class bioroot.plasmid.PlasmidUploadBean

getPlasmidConcats(DBUtil) - Method in class bioroot.antibody.AntibodyBean

Returns an array of id: plasmidName, or empty String[]{""} if there are none.

getPlasmidConcats(DBUtil) - Method in class bioroot.strain.StrainBean

Returns an array of id: plasmidName, or empty String[]{""} if there are none.

getPlasmidForm(PlasmidBean, DBUtil, UserBean) - Static method in class bioroot.plasmid.PlasmidBase

Returns a plasmid form filled with the values in the bean.

getPlasmidPreference() - Method in class bioroot.UserBean

getPlasmidPrefs() - Method in class bioroot.UserBean

getPlasmidReport(PlasmidBean, DBUtil, UserBean, boolean) - Static method in class bioroot.plasmid.PlasmidBase

Returns an plasmid report.

getPlasmidReports() - Method in class bioroot.plasmid.PlasmidUploadBean

getPlotterPreferences() - Method in class gata.main.GATAParams

getPmX() - Method in class trans.tpmap.TPMapLine

getPmY() - Method in class trans.tpmap.TPMapLine

getPngResultFile() - Method in class util.bio.cluster.HierarchicalClustering

getPoint() - Method in class trans.graphics.GenomicRegionGlyph

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

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

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

getPositions() - Method in class trans.graphics.Graph

getPositions() - Method in class trans.main.ScanChromosomes

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

getPrintWriter() - Method in class util.apps.FileSplitter

getProteinColor() - Method in class gata.main.GATAParams

getPurification() - Method in class bioroot.antibody.AntibodyPrep

getPurification() - Method in class bioroot.oligo.OligoBean

getPurification() - Method in class bioroot.plasmid.PlasmidBean

getPvalue() - Method in class expr.CorrelationWindow

getQualFile(int) - Method in class selex.SelexParams

getQualFile() - Method in class selex.SeqFiles

getQualFiles() - Method in class selex.SelexParams

getQualScores() - Method in class selex.SubSeq

getQuals() - Method in class util.bio.parsers.QualityFileParser

getQuantiles() - Method in class trans.cel.QuantileNormalization

Fetches an array of sorted normalized Quantiles

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

getRApp() - Method in class trans.main.T2Parameter

getRNAColor() - Method in class gata.main.GATAParams

getRSquared() - Method in class util.gen.LinearRegression

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

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

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

getRanks() - Method in class util.gen.RankedFloatArray

getRatio() - Method in class trans.misc.GCRatio

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

getRawScore() - Method in class util.bio.wrappers.BL2SeqHit

getRawScoreCutOff() - Method in class util.bio.wrappers.BL2Seq

getRawUnparsedResults() - Method in class util.bio.wrappers.BL2Seq

getReagentNames() - Method in class bioroot.ContactBean

getRealMeanDiff() - Method in class trans.main.SamChromosomeData

getRealTStats() - Method in class trans.main.SamChromosomeData

getRealVariance() - Method in class trans.main.SamChromosomeData

getRecipients() - Method in class bioroot.antibody.AntibodyPrep

getRecipients() - Method in class bioroot.plasmid.PlasmidBean

getRecipients() - Method in class bioroot.strain.StrainBean

getRecogSeq() - Method in class util.bio.digest.Enzyme

getRectangle() - Method in class trans.graphics.GenomicRegionGlyph

getRefAnnoSpecParams() - Method in class gata.main.GATAParams

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

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

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

getRefTexF() - Method in class gata.aligner.AlignerInputPanel

getReference() - Method in class bioroot.ReagentBean

getReferenceY() - Method in class gata.main.AnnoSpecParams

getRegEx() - Method in class util.bio.digest.Enzyme

getRegExGeneTypes() - Method in class util.bio.parsers.gff.DmelRel4Extractor

getRegExTypes() - Method in class util.bio.parsers.gff.Gff3Parser

getRegion() - Method in class trans.main.PosRegion

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

getRegionsOne() - Method in class trans.graphics.RankedSetAnalysis

getRegionsTwo() - Method in class trans.graphics.RankedSetAnalysis

getRelativeCoordinates() - Method in class gata.aligner.Alignment

getRemainingAliquots() - Method in class bioroot.antibody.AntibodyPrep

getRemainingAliquots() - Method in class bioroot.strain.StrainBean

getRemoteHost() - Method in class bioroot.UserBean

getRepeatRegionFiles() - Method in class trans.main.T2Parameter

getRequesterEmail() - Method in class bioroot.ContactBean

getResponse() - Method in class bioroot.LoginBean

getRestSite() - Method in class selex.SelexParams

getRestock() - Method in class bioroot.strain.StrainBean

getRestrictionCutSites(Enzyme[]) - Method in class bioroot.oligo.OligoBean

getRestrictionCutSites(Enzyme[]) - Method in class bioroot.plasmid.PlasmidBean

getRestrictionMapString(String, Enzyme[]) - Static method in class util.bio.digest.REDigest

getResult(ResultSet) - Static method in class bioroot.DBUtil

getResultSetInt(String) - Method in class bioroot.DBUtil

Use to avoid a null return when attempting to fetch a ResultSet.getInt().

getResultSetInt(String) - Method in class util.gen.SQL

Use to avoid a null return when attempting to fetch a ResultSet.getInt().

getResultSetString(String) - Method in class bioroot.DBUtil

Use to avoid a null return when attempting to fetch a ResultSet.getString().

getResultSetString(String) - Method in class util.gen.SQL

Use to avoid a null return when attempting to fetch a ResultSet.getString().

getResultString() - Method in class bioroot.DBUtil

returns the first column values from a result, for testing

getResultSummaryLine() - Method in class util.bio.wrappers.Primer3Pick

getResults() - Method in class meme.MemeResults

getResults() - Method in class util.gen.SQL

getResultsDirectory() - Method in class trans.main.ScanChromosomes

getResultsDirectory() - Method in class trans.main.T2Parameter

getResultsName() - Method in class trans.main.T2Parameter

getRevCompRef() - Method in class util.bio.xamer.Xamer

getReversedBinCounts() - Method in class util.gen.Histogram

getRfa() - Method in class expr.ExpressedGene

getRightFlankingIndex() - Method in class trans.main.BindingPeak

getRightIndex() - Method in class trans.main.PeakPicker

getRightLR() - Method in class trans.cel.SplineScalar

getRightSideMatch() - Method in class selex.SelexParams

getRightSideReplace() - Method in class selex.SelexParams

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

getRoundedModel() - Method in class util.gen.LinearRegression

Returns Y=mX+b

getRowsEffected() - Method in class bioroot.DBUtil

getRunning() - Method in class selex.SelexParams

getRunningX() - Method in class trans.graphics.IntervalDrawPanel

getRunningY() - Method in class trans.graphics.IntervalDrawPanel

getS3Service() - Method in class util.amazon.S3Manager

getSCORE_DESCRIPTION() - Static method in class trans.main.ScanChip

getSCORE_DESCRIPTION() - Static method in class trans.main.ScanChromosomes

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

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

getSaveDirectory() - Method in class trans.main.ChromSet

getScaleBar() - Method in class gata.main.AnnoSpecParams

getScaleBarLabel() - Method in class gata.geneGlyphs.ScaleBar

getScaleBarLines() - Method in class gata.geneGlyphs.ScaleBar

getScaleBarWidth() - Method in class gata.geneGlyphs.ScaleBar

getScaleBarX() - Method in class gata.main.AnnoSpecParams

getScaleBarY() - Method in class gata.main.AnnoSpecParams

getScaleLineColor() - Method in class gata.main.AnnoSpecParams

getScaleLines() - Method in class gata.geneGlyphs.ScaleBar

getScaleRulerLines() - Method in class gata.geneGlyphs.ScaleBar

getScaleRulerY() - Method in class gata.main.AnnoSpecParams

getSchedule() - Method in class bioroot.LabGroup

getScore() - Method in class bioroot.SearchHit

getScore() - Method in class expr.CorrelationWindow

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

getScore() - Method in class gata.aligner.Alignment

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

getScore() - Method in class meme.MotifHit

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

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

getScore() - Method in class trans.main.BindingPeak

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

getScore() - Method in class trans.roc.RocWindow

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

getScore() - Method in class util.bio.annotation.GenericFeature

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

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

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

getScoreCutOff() - Method in class selex.SelexParams

getScoreCutOff() - Method in class trans.main.PeakPicker

getScoreIndex() - Method in class trans.main.WindowBlockMaker

getScores() - Method in class trans.main.Window

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

getScrollPane() - Method in class trans.graphics.VirtualCelFrame

getSearchColumnNames() - Static method in class bioroot.antibody.AntibodyBase

Returns a list of the search column names used in an SQL statment , ie Oligo.name, 1/2 the searchHash.

getSearchColumnNames() - Static method in class bioroot.oligo.OligoBase

Returns a list of the search column names used in an SQL statment , ie Oligo.name, 1/2 the searchHash.

getSearchColumnNames() - Static method in class bioroot.plasmid.PlasmidBase

Returns a list of the search column names used in an SQL statment , ie Oligo.name, 1/2 the searchHash.

getSearchColumnNames() - Static method in class bioroot.strain.StrainBase

Returns a list of the search column names used in an SQL statment , ie name, 1/2 the searchHash.

getSearchFor() - Method in class bioroot.SearchBean

getSearchHash() - Static method in class bioroot.antibody.AntibodyBase

getSearchHash() - Static method in class bioroot.oligo.OligoBase

getSearchHash() - Static method in class bioroot.plasmid.PlasmidBase

getSearchHash() - Static method in class bioroot.strain.StrainBase

getSearchNames() - Static method in class bioroot.antibody.AntibodyBase

getSearchNames() - Static method in class bioroot.oligo.OligoBase

getSearchNames() - Static method in class bioroot.plasmid.PlasmidBase

getSearchNames() - Static method in class bioroot.strain.StrainBase

getSearchedSeqFile() - Method in class meme.MotifSearchResult

getSeedType() - Method in class bioroot.strain.StrainBean

getSelexOligos() - Method in class util.bio.xamer.Xamer

getSeq() - Method in class meme.MotifHit

getSeq() - Method in class selex.SubSeq

getSeq1() - Method in class gata.aligner.Alignment

getSeq1() - Method in class util.bio.wrappers.BL2SeqHit

getSeq2() - Method in class gata.aligner.Alignment

getSeq2() - Method in class util.bio.wrappers.BL2SeqHit

getSeqFile(int) - Method in class selex.SelexParams

getSeqFile() - Method in class selex.SeqFiles

getSeqFiles() - Method in class selex.SelexParams

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

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

getSeqRead() - Method in class selex.SubSeq

getSeqReads() - Method in class selex.SeqFiles

getSeqs() - Method in class util.bio.parsers.MultiFastaParser

getSequence() - Method in class bioroot.BlastMatcher

getSequence() - Method in class bioroot.oligo.OligoBean

getSequence() - Method in class bioroot.plasmid.PlasmidBean

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

getSequence() - Method in class trans.bkgrnd.LoadedOligo

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

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

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

getSequence() - Method in class util.bio.seq.IndexedSequence

getSequence() - Method in class util.bio.wrappers.Primer3Pick

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

getSetOneFile() - Method in class trans.graphics.RankedSetAnalysis

getSetTwoFile() - Method in class trans.graphics.RankedSetAnalysis

getShapes() - Method in class gata.aligner.Alignment

getSimpleMulti() - Method in class util.amazon.S3Manager

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

getSize() - Method in class util.gen.FileSize

getSizeMappedFeatures() - Method in class trans.cel.CelMapper

getSizeOfOligo() - Method in class trans.main.T2Parameter

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

getSliders() - Method in class gata.plotter.Sliders

getSlope() - Method in class util.gen.LinearRegression

getSmallestAlignPanelY() - Method in class gata.main.GATAParams

getSmallestGlyphPanelY() - Method in class gata.main.AnnoSpecParams

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

getSortBy() - Method in class bioroot.BlastMatcher

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

getSortBy() - Method in class trans.main.Window

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

getSource() - Method in class bioroot.antibody.AntibodyBean

getSource() - Method in class bioroot.plasmid.PlasmidBean

getSource() - Method in class bioroot.strain.StrainBean

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

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

getSpline() - Method in class trans.cel.SplineScalar

getStart() - Method in class expr.CorrelationWindow

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

getStart() - Method in class meme.MotifHit

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

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

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

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

getStart() - Method in class trans.main.PosRegion

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

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

getStart() - Method in class trans.roc.RocWindow

getStart() - Method in class trans.tpmap.TPMapLine

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

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

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

getStart() - Method in class util.bio.annotation.GenericFeature

getStart() - Method in class util.bio.annotation.StartEnd

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

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

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

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

getStart() - Method in class util.bio.seq.IndexedSequence

getStart() - Method in class util.gen.Bin

getStart1stOligo() - Method in class trans.main.Interval

getStart1stOligo() - Method in class trans.main.Window

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

Conservative estimate of the start ATG position, from the longest transcript

getStartEnd() - Method in class util.bio.annotation.StartEnd

getStartExactMatch() - Method in class trans.tpmap.BlastFilterResult

getStartIndex() - Method in class trans.cel.ChromosomeIndex

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

getStartLastOligo() - Method in class trans.main.Window

getStartPosition() - Method in class trans.bkgrnd.LoadedOligo

getStartSeq1() - Method in class util.bio.wrappers.BL2SeqHit

getStartSeq2() - Method in class util.bio.wrappers.BL2SeqHit

getStartStop() - Method in class gata.plotter.StartStop

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

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

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

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

getStop() - Method in class expr.CorrelationWindow

getStop() - Method in class meme.MotifHit

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

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

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

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

getStop() - Method in class util.bio.seq.IndexedSequence

getStop() - Method in class util.gen.Bin

getStopIndex() - Method in class trans.cel.ChromosomeIndex

getStopSeq1() - Method in class util.bio.wrappers.BL2SeqHit

getStopSeq2() - Method in class util.bio.wrappers.BL2SeqHit

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

getStrainBeans() - Method in class bioroot.strain.StrainUploadBean

getStrainConcats(DBUtil) - Method in class bioroot.antibody.AntibodyBean

Returns an array of id: strainName, or empty String[]{""} if there are none.

getStrainConcats(DBUtil) - Method in class bioroot.plasmid.PlasmidBean

Returns an array of id: strainName, or empty String[]{""} if there are none.

getStrainForm(StrainBean, DBUtil, UserBean) - Static method in class bioroot.strain.StrainBase

Returns a strain form filled with the values in the bean.

getStrainPreference() - Method in class bioroot.UserBean

getStrainPrefs() - Method in class bioroot.UserBean

getStrainReport(StrainBean, DBUtil, UserBean, boolean) - Static method in class bioroot.strain.StrainBase

Returns an strain report.

getStrainReports() - Method in class bioroot.strain.StrainUploadBean

getStrainTypes() - Method in class bioroot.strain.StrainPreference

getStrand() - Method in class trans.roc.ControlGene

getStrand() - Method in class util.bio.annotation.GenericFeature

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

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

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

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

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

getStrippedRecogSeq() - Method in class util.bio.digest.Enzyme

getSubSeq() - Method in class selex.SubSeq

getSubWindowSize() - Method in class trans.main.T2Parameter

getSubmitterUserBean() - Method in class bioroot.UserRegistrationBean

getSymmetricNullApp() - Method in class trans.main.T2Parameter

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

getTableName() - Method in class bioroot.SearchBean

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

Reserved Attribute.

getTargetMedian() - Method in class trans.cel.QuantileNormalization

getTargetMedian() - Method in class trans.main.T2Parameter

getTextArea() - Method in class gata.plotter.Console

getTextArea() - Method in class util.gen.TextFrame

getTextFrame() - Method in class trans.graphics.RankedSetAnalysis

getThinDNALines() - Method in class gata.main.AnnoSpecParams

getThinProteinLines() - Method in class gata.main.AnnoSpecParams

getThinRNALines() - Method in class gata.main.AnnoSpecParams

getThinStroke() - Method in class gata.main.GATAParams

getThreadedResults() - Method in class util.amazon.S3Manager

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

Conservative estimate returning smallest non coding region.

getTitle() - Method in class trans.graphics.IntervalDrawPanel

getTitle() - Method in class util.bio.cluster.HierarchicalClustering

getTm() - Method in class trans.bkgrnd.LoadedOligo

getToolsFrameRef() - Method in class gata.main.GATAParams

getTopCluster() - Method in class util.bio.cluster.Cluster

getTopCuts() - Method in class util.bio.digest.Enzyme

getTotalBinCounts() - Method in class util.gen.Histogram

Including num less than and num more than.

getTotalClusters() - Method in class util.bio.cluster.Cluster

getTotalDelta(double[][], String) - Static method in class util.bio.calc.NucleicAcid

Returns the total delta given a lower case DNA sequence.

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

getTpmapFiles() - Method in class trans.main.T2Parameter

getTrackConverter() - Method in class gata.geneGlyphs.Annotation

getTrackLabelVis() - Method in class gata.main.AnnoSpecParams

getTrackLabels() - Method in class gata.main.AnnoSpecParams

getTrackNumber() - Method in class gata.main.AnnoSpecParams

getTrackNumber() - Method in class util.bio.annotation.GenericFeature

getTrackStrokes() - Method in class gata.main.AnnoSpecParams

getTrackThickness() - Method in class gata.main.AnnoSpecParams

getTrackVis() - Method in class gata.main.AnnoSpecParams

getTrackedGenericGlyphs() - Method in class gata.main.AnnoSpecParams

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

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

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

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

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

getTreatmentCelFiles() - Method in class trans.main.T2Parameter

getTreatmentIntensities(int) - Method in class trans.main.Oligo

getTreatmentIntensities() - Method in class trans.main.ScanChromosomes

getTreatmentValues() - Method in class trans.main.ScoredGene

getTruncatedNames(File[]) - Static method in class util.gen.IO

Fetches and truncates common chars, from file names, front and back, uses getName() so no path info is involved.

getTruncatedNames(File[][]) - Static method in class util.gen.IO

Fetches and truncates common chars, from file names, front and back, uses getName() so no path info is involved.

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

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

getType() - Method in class bioroot.ContactBean

getType() - Method in class bioroot.LoginBean

getType() - Method in class bioroot.UserBean

getType() - Method in class bioroot.UserRegistrationBean

getType() - Method in class bioroot.antibody.AntibodyBean

getType() - Method in class bioroot.oligo.OligoBean

getType() - Method in class bioroot.strain.StrainBean

getType() - Method in class trans.roc.RocWindow

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

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

getUM() - Method in class bioroot.oligo.OligoBean

getUMNgUl() - Method in class bioroot.oligo.OligoBean

getUseDilutionForm(UseDilution, StringBuffer, int, int, boolean) - Static method in class bioroot.antibody.AntibodyBase

Returns a UseDilutionNotes where the names are apended with apbIndex.index ie 0.0, 0.1, 0.2,,1.0,1.1...

getUseDilutionForms(AntibodyPrep, DBUtil, StringBuffer, int) - Static method in class bioroot.antibody.AntibodyBase

Pumps out useDilution forms, should always have one with each Prep

getUseDilutionReport(UseDilution, StringBuffer, int, int) - Static method in class bioroot.antibody.AntibodyBase

getUseDilutionReports(AntibodyPrep, DBUtil, StringBuffer, int, boolean) - Static method in class bioroot.antibody.AntibodyBase

Pumps out useDilution reports

getUseDilutions(DBUtil) - Method in class bioroot.antibody.AntibodyPrep

getUser(DBUtil, String) - Static method in class bioroot.AccountManagement

fetch all items from a specific user

getUserBean() - Method in class bioroot.LoginBean

getUserComments() - Method in class bioroot.antibody.AntibodyPrep

getUserId() - Method in class bioroot.LoginBean

getUserId() - Method in class bioroot.UserRegistrationBean

getUserInputs() - Method in class meme.MemeR

Uses JOptionPane dialog input boxes to get user inputs

getUsers(DBUtil, int) - Static method in class bioroot.AccountManagement

Returns a String[] of Users belonging to a particular labgroup.

getValues() - Method in class expr.ExpressedGene

getValues() - Method in class trans.misc.GrGraph

getValues() - Method in class util.bio.cluster.Cluster

getViewLine(ReagentBean[], int[], Preference, String) - Static method in class bioroot.Util

Returns hot linked html for 1-30 31-60 ...

getViewPort() - Method in class gata.geneGlyphs.GlyphPanel

getViewPort() - Method in class gata.plotter.AlignPanel

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

getVisableAlignments() - Method in class gata.plotter.AlignPanel

getVisibilities(DBUtil, UserBean) - Method in class bioroot.Preference

getVisibilities(UserBean, DBUtil) - Static method in class bioroot.Util

If user is part of an organization, it returns WWW, orgName, Lab Mates, Private.

getVisibility() - Method in class bioroot.Preference

getVisibility(DBUtil) - Method in class bioroot.ReagentBean

getVolume() - Method in class bioroot.oligo.OligoBean

getVolume() - Method in class bioroot.plasmid.PlasmidBean

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

getW() - Method in class util.bio.wrappers.BL2Seq

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

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

getWOffSet() - Method in class trans.graphics.Graph

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

getWidth() - Method in class gata.main.GATAParams

getWidthBuffImage() - Method in class gata.plotter.AlignPanel

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

getWindowSize() - Method in class trans.main.T2Parameter

getWindows() - Method in class trans.main.ScanChromosomes

getWord() - Method in class bioroot.SearchHit

getWordBoundaryMatches() - Method in class bioroot.SearchHit

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

getX() - Method in class trans.graphics.Graph

getX() - Method in class util.gen.LinearRegression

getXamer() - Method in class util.bio.xamer.Xamer

getYTop() - Method in class gata.geneGlyphs.TransGrpGlyph

Top most y coordinate for this transGroup, including transGrp spacer, start next Shape here for no overlap

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

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

getZoomedWidth() - Method in class gata.main.GATAParams

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

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

getnumSeqsSearched() - Method in class meme.MotifSearchResult

gff(Oligo, Interval, String, int, StringBuffer) - Static method in class trans.main.IntervalGFFPrinter

Appends a GFF3 line for an Oligo.

gff(BindingPeak, Interval, String, int, StringBuffer) - Static method in class trans.main.IntervalGFFPrinter

Appends a GFF3 line for a BindingPeak

gff(SubWindow, Interval, String, StringBuffer) - Static method in class trans.main.IntervalGFFPrinter

Appends a GFF3 line for a SubWindow.

gff(Interval, int, String, StringBuffer) - Method in class trans.main.IntervalGFFPrinter

Appends a GFF3 line for an Interval.

gff(Interval, String, StringBuffer) - Method in class trans.main.IntervalGFFPrinter

Appends a GFF3 line for a Window.

groupName(RandomizeLabels.ArrayName[]) - Method in class trans.main.RandomizeLabels

Returns a sorted groupName where the sort is on the treatments and controls, not both.

growIntArrays(int[][]) - Static method in class gata.plotter.ConservedSeqs

growLeft(int) - Method in class trans.main.PeakPicker

Uses the idea of a local window, counts the number of pos slopes within the window, if > minPercent, keeps advancing.

growRight(int) - Method in class trans.main.PeakPicker

Uses the idea of a local window, counts the number of neg slopes within the window, if > minPercent, keeps advancing.