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

P

PWMScoreWindows - class trans.roc.PWMScoreWindows.

Scores windows for hits to a transcription factor PWM, for RocWindow filtering.

PWMScoreWindows(String[]) - Constructor for class trans.roc.PWMScoreWindows

ParseBarsForParticularRegions - class trans.roc.ParseBarsForParticularRegions.

Returns oligo values that overlap particular regions.

ParseBarsForParticularRegions(String[]) - Constructor for class trans.roc.ParseBarsForParticularRegions

ParseMLSHTML - class util.apps.ParseMLSHTML.

ParseMLSHTML(String[]) - Constructor for class util.apps.ParseMLSHTML

ParsePatternedWindows - class trans.roc.ParsePatternedWindows.

Finds RocWindows upstream and withing the neighborhood of the ATG start site of a patterned gene list.

ParsePatternedWindows(String[]) - Constructor for class trans.roc.ParsePatternedWindows

ParseSgrsForParticularRegions - class trans.roc.ParseSgrsForParticularRegions.

Returns oligo values that overlap particular regions.

ParseSgrsForParticularRegions(String[]) - Constructor for class trans.roc.ParseSgrsForParticularRegions

ParseSgrsForParticularScores - class trans.roc.ParseSgrsForParticularScores.

Returns oligo values that overlap particular regions.

ParseSgrsForParticularScores(String[]) - Constructor for class trans.roc.ParseSgrsForParticularScores

ParseXMLFile - class util.xml.ParseXMLFile.

This class represents short example how to parse XML file, get XML nodes values and its values.

It implements method to save XML document to XML file too

ParseXMLFile() - Constructor for class util.xml.ParseXMLFile

Creates a new instance of ParseXMLFile

Parser1lq - class trans.qc.Parser1lq.

Extracts control an pm lines from a text 1lq file.

Parser1lq(String[]) - Constructor for class trans.qc.Parser1lq

Passwords - class util.gen.Passwords.

Methods for generating one time passwords.

Passwords() - Constructor for class util.gen.Passwords

PatternMatch - class bioroot.PatternMatch.

Class to hold information and helper methods relating to pattern matches.

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

PeakPicker - class trans.main.PeakPicker.

Finds peaks in Intervals, both flat topped or peaks with sloping sides.

PeakPicker() - Constructor for class trans.main.PeakPicker

PlasmidBase - class bioroot.plasmid.PlasmidBase.

PlasmidBase() - Constructor for class bioroot.plasmid.PlasmidBase

PlasmidBean - class bioroot.plasmid.PlasmidBean.

PlasmidBean() - Constructor for class bioroot.plasmid.PlasmidBean

PlasmidBean(int, DBUtil) - Constructor for class bioroot.plasmid.PlasmidBean

PlasmidBean(ResultSet) - Constructor for class bioroot.plasmid.PlasmidBean

PlasmidBean(String[], IdNameMatch[], IdNameMatch[], IdNameMatch[], UserBean, DBUtil) - Constructor for class bioroot.plasmid.PlasmidBean

For bulk file upload should be 16 cells 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 Name Alias Source Recipients Reference Gene Organism Markers StrainIds Location Concentration Volume Purification Availability Visibility Notes Sequence

PlasmidModify - class bioroot.plasmid.PlasmidModify.

Servlet to modify plasmids using PlasmidBeans referenced from a Session object.

PlasmidModify() - Constructor for class bioroot.plasmid.PlasmidModify

PlasmidSpreadSheet - class bioroot.plasmid.PlasmidSpreadSheet.

PlasmidSpreadSheet() - Constructor for class bioroot.plasmid.PlasmidSpreadSheet

PlasmidUpload - class bioroot.plasmid.PlasmidUpload.

PlasmidUpload() - Constructor for class bioroot.plasmid.PlasmidUpload

PlasmidUploadBean - class bioroot.plasmid.PlasmidUploadBean.

Plasmid bulk file upload bean.

PlasmidUploadBean() - Constructor for class bioroot.plasmid.PlasmidUploadBean

PlasmidViewPreferences - class bioroot.plasmid.PlasmidViewPreferences.

PlasmidViewPreferences() - Constructor for class bioroot.plasmid.PlasmidViewPreferences

PlotFloatArrays - class trans.graphics.PlotFloatArrays.

PlotFloatArrays() - Constructor for class trans.graphics.PlotFloatArrays

PlotterPreferences - class gata.main.PlotterPreferences.

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

PosRegion - class trans.main.PosRegion.

For holding information about a genomic interval, what genes are up, down, overlap, or contain this genomic inteval.

PosRegion(String, String, int, int) - Constructor for class trans.main.PosRegion

Positive - class trans.roc.Positive.

Container for a positive BAC used by the Sgr scripts.

Positive(String, int, int) - Constructor for class trans.roc.Positive

PositiveComparator - class trans.roc.PositiveComparator.

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

PossumToGFF - class util.bio.converters.PossumToGFF.

Converts a copied Possum output to GFF annotation, prints to screen, sorted by score.

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

Preference - class bioroot.Preference.

Preference() - Constructor for class bioroot.Preference

Preference(String) - Constructor for class bioroot.Preference

databaseConcat = visibility : orderBy: labGroups : features separated by colons, labGroups and feature lines separated by semi-colons

PrependColumn - class trans.misc.PrependColumn.

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

Primer3Pick - class util.bio.wrappers.Primer3Pick.

Container for sequence used in picking primers with Primer3.

Primer3Pick(String) - Constructor for class util.bio.wrappers.Primer3Pick

Primer3Wrapper - class util.bio.wrappers.Primer3Wrapper.

This app wraps the command line primer3 app to make it useful for picking qPCR primers.

Primer3Wrapper(String[]) - Constructor for class util.bio.wrappers.Primer3Wrapper

Uses a shell script file to execute the primer3 app due to a problem feeding to STDIN from java.

PrintSelectColumns - class util.apps.PrintSelectColumns.

Prints out select columns from a tab delimited file, skips lines, appends words, etc.

PrintSelectColumns(String[]) - Constructor for class util.apps.PrintSelectColumns

pValue() - Method in class trans.anno.IntersectRegions

pValue(double) - Method in class util.gen.Histogram

Returns a two tailed, p value given a threshold.

pValueLeftSide(double) - Method in class util.gen.Histogram

Returns a one tailed, left side, p value given a threshold.

pValueRightSide(double) - Method in class util.gen.Histogram

Returns a one tailed, right side, p value given a threshold.

paintComponent(Graphics) - Method in class gata.geneGlyphs.GlyphPanel

Watch order of drawing, optimize to avoid changing stroke

paintComponent(Graphics) - Method in class gata.plotter.AlignPanel

paintComponent(Graphics) - Method in class trans.graphics.IntervalDrawPanel

paintComponent(Graphics) - Method in class trans.graphics.RankedSetDrawPanel

paintComponent(Graphics) - Method in class trans.graphics.VirtualCelPanel

paintComponent(Graphics) - Method in class util.apps.ScatterDrawPanel

paintComponent(Graphics) - Method in class util.bio.cluster.ClusterDrawPanel

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

Given two float[replica][values] for treat and cont, for each replica makes matched pairwise log ratios between treat and control.

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

Given two float[replica][values] for treat and cont, for each replica makes matched pairwise ratios between treat and control.

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

Given two float[replica][values] for treat and cont, for each replica makes matched pairwise relative differences between treat and control.

pairwiseCorrelationScore(ExpressedGene[]) - Method in class expr.CorrelationMaps

Average coorelation coefficient * square root of number of genes.

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

Returns all pairwise averages.

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

Returns all pairwise averages.

paramsPresent() - Method in class bioroot.LoginBean

parseAgilentFile() - Method in class trans.misc.ConvertAgilentData

parseBl2SeqResults(String[]) - Method in class util.bio.wrappers.BL2Seq

This takes an array of BLAST bl2seq results and parses the info into an array

parseBlast(String[]) - Method in class gata.aligner.Blast

parseBlast(String[]) - Static method in class util.bio.wrappers.SimpleBlast

parseBlastGeneral(String[]) - Static method in class util.bio.wrappers.SimpleBlast

Parses blast output from blastall for dna into BlastResult objects.

parseChromosomeName(String) - Static method in class trans.misc.Util

Attempts to parse a chromosome name.

parseControlGeneFile(File) - Static method in class trans.roc.ControlGene

parses a control gene file ex: #name chrom strand exonStarts exonEnds notes ex: NM_001035267 chr12 + 54796640,54797239,54797532, 54796850,54797262,54797882, Z12962_Homologue to yeast ribosomal protein L41_H

parseCyberT(File) - Method in class trans.main.ReplaceWindowScores

Parses a file for a tab delimited list of at minimum, chrom, start, stop, (optional) notes into a GenomicRegion[].

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

parseDoubles(String[]) - Static method in class util.gen.Num

Parses doubles from a String[] of doubles.

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

parseFile(File) - Method in class util.apps.Flash

Strips out " that stupid excel adds in.

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

Parses a tab delimited file where the sequence to pick primers from is in column 0.

parseFile(String) - Method in class util.xml.ParseXMLFile

Parses XML file and returns XML document.

parseGeneFile(File) - Static method in class expr.CorrelationMaps

Converts a tab delimited file of (name chr start stop val1 val2 ...) into an ExpressedGene[]

parseGeneTableFile(File, int) - Method in class util.bio.parsers.UCSCGeneModelTableReader

parseGenomicRegionsFile(File) - Static method in class trans.graphics.RankedSetAnalysis

Parses a regions file.

parseGrGraph(GrGraph) - Static method in class trans.roc.Gr

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

Attemps to parse an int, returns failNumber if it fails.

parseIntervalFile(File, int) - Static method in class trans.anno.AnnotateRegions

Attempts to fetch a serialized array of Interval[], then sorts/ ranks the intervals by the median ratio of the sub window.

parseIntervalFile(File, int) - Static method in class trans.anno.AnnotateRegionsWithGeneList

Attempts to fetch a serialized array of Interval[], then sorts/ ranks the intervals by the median ratio of the sub window.

parseIntervalFile(File) - Static method in class trans.anno.IntersectRegions

parseInts(String[]) - Static method in class util.gen.Num

Parses ints from a String[] of ints.

parseIt(File) - Method in class trans.misc.ConvertGeoData

parseIt(File) - Method in class util.bio.parsers.MultiFastaParser

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

parseJobId(String[]) - Static method in class util.gen.Job

Attempts to parse 'Job Id:', returns null if not found.

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

Given a String of 'treat1=/file1,/file2*treat2=/file3,/file4*treat3=/file5,file6' Will return an ArrayList contining first a String[] of the keys {treat1,treat2,treat3} and second a String[][] of the parsed values matching the keys.

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

Given a String of 'treat1=/file1,treat2=/file3, etc', no spaces, returns a LinkedHashMap of keys=values.

parseLine(String, Pattern) - Static method in class gata.aligner.Blast

parseLine(String, Pattern) - Static method in class util.bio.wrappers.BL2Seq

parseLine(String, Pattern) - Static method in class util.bio.wrappers.SimpleBlast

parseListingsFile() - Method in class util.apps.ParseMLSHTML

Parses listing lines on 'List Price'

parseMemeText(String[]) - Method in class meme.MemeParser

parseMultiPartRequest(HttpServletRequest) - Static method in class util.gen.HTML

Parses a multipart request returning a HashMap of fieldName: String, if the same fieldName is found more than once, a String[] is created.

parseNDF() - Method in class trans.misc.ConvertNimblegenNDF2TPMap

parsePAIR() - Method in class trans.misc.ConvertNimblegenPAIR2Cela

parsePicksFile(File, int) - Static method in class trans.anno.AnnotateRegions

parsePicksFile(File, int) - Static method in class trans.anno.AnnotateRegionsWithGeneList

parsePrimer3Results(String[]) - Method in class util.bio.wrappers.Primer3Wrapper

Takes the output of the primer3 app and breaks by record loading appriopriate Primer3Pick.

parseRegionFile(File) - Static method in class trans.roc.ParseSgrsForParticularRegions

parseRegionFiles() - Method in class trans.anno.IntersectKeyWithRegions

parseRegions(File) - Static method in class trans.anno.Region

Parses a file for a tab delimited list of at minimum, chrom, start, stop, (optional) notes into a GenomicRegion[].

parseRegionsFile(File) - Static method in class trans.anno.IntersectRegions

parseSgrFile(File, boolean) - Static method in class trans.roc.MethodTester

Reads in an Sgr file.

parseStringArray(Object) - Static method in class util.gen.HTML

For extracting either a String[] or making a new String[] by casting the object as a String.

parseStringToDouble(String) - Static method in class util.bio.parsers.gff.GffFeature

parseView(HttpServletRequest) - Static method in class bioroot.Util

Parses a 12-49 type parameter named view to just the ints

parseWindowFile(File) - Method in class igb.util.Windows2HeatMapSgr

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

Returns all pairwise averages between a and b but not self pairwise.

pentamerGenerator() - Static method in class util.bio.xamer.XamerCounter

percent(int, int) - Static method in class trans.main.OverlapCounter

percentile(Quantile[], double) - Static method in class trans.cel.QuantileNormalization

Returns the value of a given percentile from a SORTED Quantile array.

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

Returns the value of a given percentile from a SORTED array.

permutate() - Method in class trans.main.RandomizeLabels

Randomly permutates the ArrayName[].

pickPeaks(Interval[]) - Method in class trans.main.PeakPicker

plot() - Method in class trans.graphics.AggregatePlots

plotHistogram() - Method in class selex.SelexParams

pmX - Variable in class trans.tpmap.MapFeature

pmY - Variable in class trans.tpmap.MapFeature

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

Builds a pooled from part of a float[replica][intensities] for treat and control.

populateBean(Object, HttpServletRequest) - Static method in class util.gen.HTML

Fills in all the params of a bean.

position - Variable in class trans.cel.Quantile

positive(Positive[], Sgr) - Static method in class trans.roc.MethodTester

Checks to see if an sgr object is one of the positives, if not returns -1, otherwise returns index number.

positive(Positive[], Sgr) - Static method in class trans.roc.SgrBacCounter

Checks to see if an sgr object is one of the positives, if not returns -1, otherwise returns index number.

postMail(String[], String, String, String) - Method in class util.gen.Email

postMailNoAuthentication(String[], String, String, String, String, String) - Static method in class util.gen.Email

Simple static method for sending email, no authentication, modified from http://www.javacommerce.com/articles/sendingmail.htm Sudhir Ancha.

postWithAttachment(String[], String, String, String, String, String) - Method in class util.gen.Email

prefix - Variable in class com.amazon.s3.CommonPrefixEntry

The prefix common to the delimited keys it represents

prefix - Variable in class com.amazon.s3.ListBucketResponse

The prefix echoed back from the request.

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

Returns a new array with the newValue appended on the beginning.

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

Returns a new array with the newValue appended on the beginning.

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

print(String, boolean[], PrintWriter) - Static method in class trans.anno.MergeRegions

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

printArray(float[][]) - Static method in class trans.graphics.AggregatePlots

Prints x as row, y as column with row index, float[y][x]

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

Prints a Object[] to System.out

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

Prints a Object[][] to System.out

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

Prints a String[] to System.out

printArray(ArrayList) - Static method in class util.gen.Misc

Prints ArrayList to System.out

printArray(int[]) - Static method in class util.gen.Misc

Prints a int[] to System.out

printArray(float[]) - Static method in class util.gen.Misc

Prints a int[] to System.out

printArray(double[]) - Static method in class util.gen.Misc

Prints a double[] to System.out on a single line.

printArray(double[][]) - Static method in class util.gen.Misc

Print to System.out a double[][]

printArray(float[][]) - Static method in class util.gen.Misc

Print to System.out a float[][]

printArray(int[][]) - Static method in class util.gen.Misc

Print to System.out a int[][]

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

Prints a String[] to System.out

printBarFiles() - Method in class expr.CorrelationMaps

printBarFiles(Sgr[][], String) - Method in class trans.misc.Sgr2Bar

printBlocks(int[][], String, File) - Method in class util.bio.annotation.ExportIntergenicRegions

Prints a file containing the block regions.

printCalculations(ArrayList, int) - Static method in class trans.misc.CalcGCAndTransform

Prints %GC, Mean, 3xStdErr

printCalculations(ArrayList, int) - Static method in class trans.misc.CalcGCRatiosFromIntervals

Prints %GC, Mean, 3xStdErr

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

Runs through groups of cel files, calling statSingleCelFile() on each and prints the results.

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

Prints two columns, forward counts and reversed counts centered on max value with zeros as filler.

printChroms(RocWindow[]) - Static method in class trans.roc.ParsePatternedWindows

printClusters(LinkedHashMap) - Method in class util.bio.parsers.gff.ExtractGffFeatures

Prints all the gff lines.

printCorrelationWindows() - Method in class expr.CorrelationMaps

Prints a spread sheet summary and a xxx.bed file for all of the windows.

printDistToClosestATGAndTranscript(BindingRegion[]) - Method in class trans.anno.AnnotateRegions

Prints rank, chrom, start, stop, distance to closest ATG, to closest transcript start.

printDistToClosestATGAndTranscript(BindingRegion[]) - Method in class trans.anno.AnnotateRegionsWithGeneList

Prints rank, chrom, start, stop, distance to closest ATG, to closest transcript start.

printDoc() - Static method in class selex.UtilSelex

printDocs() - Static method in class expr.CorrelationMaps

printDocs() - Static method in class igb.util.Windows2HeatMapSgr

printDocs() - Static method in class meme.UtilMeme

printDocs() - Static method in class trans.anno.AnnotateRegions

printDocs() - Static method in class trans.anno.AnnotateRegionsWithGeneList

printDocs() - Static method in class trans.anno.IntersectKeyWithRegions

printDocs() - Static method in class trans.anno.IntersectRegions

printDocs() - Static method in class trans.cel.CelFileConverter

printDocs() - Static method in class trans.cel.CelProcessor

printDocs() - Static method in class trans.cel.MakeChromosomeSets

printDocs() - Static method in class trans.graphics.AggregatePlots

printDocs() - Static method in class trans.graphics.CelMasker

printDocs() - Static method in class trans.graphics.IntervalPlotter

printDocs() - Static method in class trans.graphics.RankedSetAnalysis

printDocs() - Static method in class trans.graphics.VirtualCel

printDocs() - Static method in class trans.main.BindingRegionGraphPrinter

printDocs() - Static method in class trans.main.ExportIntervalData

printDocs() - Static method in class trans.main.FDRWindowConverter

printDocs() - Static method in class trans.main.FindSubBindingRegions

printDocs() - Static method in class trans.main.IntensityPrinter

printDocs() - Static method in class trans.main.IntervalFilter

printDocs() - Static method in class trans.main.IntervalGFFPrinter

printDocs() - Static method in class trans.main.IntervalGraphPrinter

printDocs() - Static method in class trans.main.IntervalMaker

printDocs() - Static method in class trans.main.IntervalReportPrinter

printDocs() - Static method in class trans.main.LoadChipSetIntervalOligoInfo

printDocs() - Static method in class trans.main.LoadIntervalOligoInfo

printDocs() - Static method in class trans.main.MakeAllWindows

printDocs() - Static method in class trans.main.MergeWindowArrays

printDocs() - Static method in class trans.main.MultiSGRPrinter

printDocs() - Static method in class trans.main.MultiWindowIntervalMaker

printDocs() - Static method in class trans.main.OligoIntensityPrinter

printDocs() - Static method in class trans.main.OverlapCounter

printDocs() - Static method in class trans.main.OverlappingWindowScoreExtractor

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

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

printDocs() - Static method in class trans.main.ScanGenes

printDocs() - Static method in class trans.main.ScoreIntervals

printDocs() - Static method in class trans.main.SetNumberIntervalMaker

printDocs() - Static method in class trans.main.SplitWindowArraysByChromosome

printDocs() - Static method in class trans.main.T2

printDocs() - Static method in class trans.main.TestScanChip

printDocs() - Static method in class trans.main.WindowBlockMaker

printDocs() - Static method in class trans.main.WindowBlockMakerTwoColor

printDocs() - Static method in class trans.misc.Bar2Gr

printDocs() - Static method in class trans.misc.ConvertAgilentData

printDocs() - Static method in class trans.misc.ConvertGeoData

printDocs() - Static method in class trans.misc.ConvertNimblegenNDF2TPMap

printDocs() - Static method in class trans.misc.ConvertNimblegenPAIR2Cela

printDocs() - Static method in class trans.misc.Gr2Bar

printDocs() - Static method in class trans.misc.Sgr2Bar

printDocs() - Static method in class trans.qc.CelFileQualityControl

printDocs() - Static method in class trans.qc.CoordinateExtractor1lq

printDocs() - Static method in class trans.qc.Parser1lq

printDocs() - Static method in class trans.roc.PWMScoreWindows

printDocs() - Static method in class trans.roc.ParseBarsForParticularRegions

printDocs() - Static method in class trans.roc.ParsePatternedWindows

printDocs() - Static method in class trans.roc.RocWindowScanner

printDocs() - Static method in class trans.tpmap.ConvertTPMapsToFeatures

printDocs() - Static method in class trans.tpmap.FilterTPMapByRegions

printDocs() - Static method in class trans.tpmap.MummerMapper

printDocs() - Static method in class trans.tpmap.OligoFlipper

printDocs() - Static method in class trans.tpmap.TPMapDensityReducer

printDocs() - Static method in class trans.tpmap.TPMapOligoBlastFilter

printDocs() - Static method in class trans.tpmap.TPMapProcessor

printDocs() - Static method in class trans.tpmap.TPMapSort

printDocs() - Static method in class util.apps.ConvertFasta2GCBoolean

printDocs() - Static method in class util.apps.FileJoiner

printDocs() - Static method in class util.apps.FileSplitter

printDocs() - Static method in class util.apps.FileTrimmer

printDocs() - Static method in class util.apps.JQSub

printDocs() - Static method in class util.apps.PrintSelectColumns

printDocs() - Static method in class util.apps.ScatterPlot

printDocs() - Static method in class util.apps.ScoreChromosomes

printDocs() - Static method in class util.apps.ScoreSequences

printDocs() - Static method in class util.bio.annotation.ExportIntergenicRegions

printDocs() - Static method in class util.bio.annotation.ExportIntronicRegions

printDocs() - Static method in class util.bio.cluster.HierarchicalClustering

printDocs() - Static method in class util.bio.parsers.FetchGenomicSequences

printDocs() - Static method in class util.bio.parsers.gff.ExtractGffFeatures

printDocs() - Static method in class util.bio.seq.IndexFastas

printDocs() - Static method in class util.bio.wrappers.Primer3Wrapper

printEachArray(float[][]) - Static method in class trans.graphics.AggregatePlots

Prints x as row, y as column with row index, float[y][x]

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

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

Prints message to screen, then exits.

printForGeoCode() - Method in class util.apps.ParseMLSHTML

printGFF() - Method in class trans.main.IntervalGFFPrinter

printHashSetToFile(HashSet, String) - Static method in class util.gen.Misc

Prints a HashSet to a file.

printHistogram(int[], int[], String[]) - Static method in class util.gen.Histogram

Prints a simple histogram scaled using stars but real counts shown.

printHistogram(int[], PrintWriter) - Static method in class util.gen.Histogram

Prints a simple histogram to a PrintWriter.

printHistogram(int[]) - Static method in class util.gen.Histogram

Prints a simple histogram.

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

Prints statistics about the current intensity float[][] arrays

printIntervalGraphs() - Method in class trans.main.T2

Prints interval bed and sgr files via IntervalGraphPrinter.

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

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

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

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

printOligoRatios() - Method in class trans.main.ScanChip

Prints log2 oligo ratios.

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

Prints log2 oligo ratios as a chromosome specific xxx.bar file.

printRankedIntersection(int[]) - Method in class trans.graphics.RankedSetAnalysis

Prints to screen the results of rankedIntersection(GenomicRegion[] r).

printRankedIntersectionAll(GenomicRegion[]) - Method in class trans.graphics.RankedSetAnalysis

Rank analysis where each regions is check against the entire other list.

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

Used when making mock Intervals from which you want to calculate various oligo based measurements.

printReport() - Method in class trans.main.IntervalReportPrinter

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

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

printSGRWindows(RocWindow[]) - Static method in class trans.roc.RocWindow

printSave(String) - Method in class meme.MemeResults

printSave(String) - Method in class selex.SelexParams

printSaveIntervalScoreGraphFiles() - Method in class trans.main.IntervalGraphPrinter

Prints and saves a Affy .sgr file

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

Prints scaled histogram.

printScores(Interval[], File, boolean) - Static method in class trans.main.IntervalGraphPrinter

Prints to a File a line for every Oligo in each Interval.

printSeqFiles() - Method in class selex.SeqFiles

printSeqRead() - Method in class selex.SeqRead

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

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

printSpreadSheets() - Method in class trans.main.T2

Prints interval reports in a spread sheet via IntervalReportPrinter.

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

Prints name, median min max for each stat flag

printStringArray(String[], String) - Static method in class util.bio.converters.RepeatMaskerToGFF

Prints out the string array on a line divided by the separator, good for debugging

printSubSeq() - Method in class selex.SubSeq

printTable(Object[][], String[]) - Static method in class trans.main.OverlapCounter

printToTextArea(String) - Method in class gata.plotter.Console

printTruncatedSeqsToConsole(int, int, int, int) - Method in class gata.plotter.ConservedSeqs

printUCSCFormat(LinkedHashMap) - Method in class util.bio.parsers.gff.ExtractGffFeatures

Print each cluster in ucsc table format refGene.name refGene.chrom refGene.strand refGene.txStart refGene.txEnd refGene.cdsStart refGene.cdsEnd refGene.exonCount refGene.exonStarts refGene.exonEnds refLink.product geneName.name refSeqSummary.summary NM_198576 chr1 + 995569 1031415 995619 1030284 36 995569,997647,1010723,1016111,1016522,1016827,1017258,1018541,1018840,1019125,1019411,1019636,1020463,1020661,1021035,1021266,1021462,1021699,1022122,1022629,1022875,1023078,1023314,1024169,1024538,1024868,1025205,1025535,1025729,1026028,1026555,1026755,1027030,1029055,1029750,1030126, 995820,997909,1010771,1016327,1016747,1017052,1017465,1018760,1019035,1019326,1019560,1019742,1020580,1020826,1021179,1021391,1021568,1022038,1022260,1022757,1022990,1023198,1023668,1024362,1024754,1025098,1025340,1025632,1025894,1026140,1026672,1026948,1027118,1029280,1029854,1031415, agrin AGRIN Agrin is a neuronal aggregating factor that induces the aggregation of ...

processArgs(String[]) - Method in class expr.CorrelationMaps

This method will process each argument and assign new varibles

processArgs(String[]) - Method in class igb.util.Windows2HeatMapSgr

This method will process each argument and assign any new varibles

processArgs(String[]) - Method in class selex.SelexParams

processArgs(String[]) - Method in class trans.anno.AnnotateRegions

This method will process each argument and assign new varibles

processArgs(String[]) - Method in class trans.anno.AnnotateRegionsWithGeneList

This method will process each argument and assign new varibles

processArgs(String[]) - Method in class trans.anno.IntersectKeyWithRegions

This method will process each argument and assign new varibles

processArgs(String[]) - Method in class trans.anno.IntersectRegions

This method will process each argument and assign new varibles

processArgs(String[]) - Method in class trans.cel.CelFileConverter

This method will process each argument and assign any new varibles

processArgs(String[]) - Method in class trans.cel.CelProcessor

This method will process each argument and assign any new varibles

processArgs(String[]) - Method in class trans.cel.MakeChromosomeSets

This method will process each argument and assign any new varibles

processArgs(String[]) - Method in class trans.graphics.AggregatePlots

This method will process each argument and assign new varibles

processArgs(String[]) - Method in class trans.graphics.CelMasker

This method will process each argument and assign any new varibles

processArgs(String[]) - Method in class trans.graphics.IntervalPlotter

This method will process each argument and assign any new varibles

processArgs(String[]) - Method in class trans.graphics.RankedSetAnalysis

This method will process each argument and assign any new varibles

processArgs(String[]) - Method in class trans.graphics.VirtualCel

This method will process each argument and assign any new varibles

processArgs(String[]) - Method in class trans.main.BindingRegionGraphPrinter

This method will process each argument and assign any new varibles

processArgs(String[]) - Method in class trans.main.ExportIntervalData

This method will process each argument and assign new varibles

processArgs(String[]) - Method in class trans.main.FDRWindowConverter

This method will process each argument and assign new varibles

processArgs(String[]) - Method in class trans.main.FindSubBindingRegions

This method will process each argument and assign new varibles

processArgs(String[]) - Method in class trans.main.IntensityPrinter

This method will process each argument and assign any new varibles

processArgs(String[]) - Method in class trans.main.IntervalFilter

This method will process each argument and assign any new varibles

processArgs(String[]) - Method in class trans.main.IntervalGFFPrinter

This method will process each argument and assign any new varibles

processArgs(String[]) - Method in class trans.main.IntervalGraphPrinter

This method will process each argument and assign any new varibles

processArgs(String[]) - Method in class trans.main.IntervalMaker

This method will process each argument and assign new varibles

processArgs(String[]) - Method in class trans.main.IntervalReportPrinter

This method will process each argument and assign any new varibles

processArgs(String[]) - Method in class trans.main.LoadChipSetIntervalOligoInfo

This method will process each argument and assign new varibles

processArgs(String[]) - Method in class trans.main.LoadIntervalOligoInfo

This method will process each argument and assign new fields

processArgs(String[]) - Method in class trans.main.MakeAllWindows

This method will process each argument and assign new varibles

processArgs(String[]) - Method in class trans.main.MergeWindowArrays

This method will process each argument and assign new varibles

processArgs(String[]) - Method in class trans.main.MultiSGRPrinter

This method will process each argument and assign new varibles

processArgs(String[]) - Method in class trans.main.MultiWindowIntervalMaker

This method will process each argument and assign new varibles

processArgs(String[]) - Method in class trans.main.OligoIntensityPrinter

This method will process each argument and assign any new varibles

processArgs(String[]) - Method in class trans.main.OverlapCounter

This method will process each argument and assign any new varibles

processArgs(String[]) - Method in class trans.main.OverlappingWindowScoreExtractor

This method will process each argument and assign any new varibles

processArgs(String[]) - Method in class trans.main.ScanChip

This method will process each argument and assign new varibles

processArgs(String[]) - Method in class trans.main.ScanChromosomes

This method will process each argument and assign new varibles

processArgs(String[]) - Method in class trans.main.ScanGenes

This method will process each argument and assign new varibles

processArgs(String[]) - Method in class trans.main.ScoreIntervals

This method will process each argument and assign any new varibles

processArgs(String[]) - Method in class trans.main.SetNumberIntervalMaker

This method will process each argument and assign new varibles

processArgs(String[]) - Method in class trans.main.SplitWindowArraysByChromosome

This method will process each argument and assign new varibles

processArgs(String[]) - Method in class trans.main.T2

This method will process each argument and assign new varibles

processArgs(String[]) - Method in class trans.main.TestScanChip

This method will process each argument and assign new varibles

processArgs(String[]) - Method in class trans.main.WindowBlockMaker

This method will process each argument and assign new varibles

processArgs(String[]) - Method in class trans.main.WindowBlockMakerTwoColor

This method will process each argument and assign new varibles

processArgs(String[]) - Method in class trans.misc.Bar2Gr

This method will process each argument and assign new varibles

processArgs(String[]) - Method in class trans.misc.ConvertAgilentData

This method will process each argument and assign new varibles

processArgs(String[]) - Method in class trans.misc.ConvertGeoData

This method will process each argument and assign new varibles

processArgs(String[]) - Method in class trans.misc.ConvertNimblegenNDF2TPMap

This method will process each argument and assign new varibles

processArgs(String[]) - Method in class trans.misc.ConvertNimblegenPAIR2Cela

This method will process each argument and assign new varibles

processArgs(String[]) - Method in class trans.misc.Gr2Bar

This method will process each argument and assign new varibles

processArgs(String[]) - Method in class trans.misc.Sgr2Bar

This method will process each argument and assign new varibles

processArgs(String[]) - Method in class trans.qc.CelFileQualityControl

This method will process each argument and assign any new varibles

processArgs(String[]) - Method in class trans.qc.CoordinateExtractor1lq

This method will process each argument and assign any new varibles

processArgs(String[]) - Method in class trans.qc.Parser1lq

This method will process each argument and assign any new varibles

processArgs(String[]) - Method in class trans.roc.PWMScoreWindows

This method will process each argument and assign new varibles

processArgs(String[]) - Method in class trans.roc.ParseBarsForParticularRegions

This method will process each argument and assign new varibles

processArgs(String[]) - Method in class trans.roc.ParsePatternedWindows

This method will process each argument and assign new varibles

processArgs(String[]) - Method in class trans.roc.RocWindowScanner

This method will process each argument and assign new varibles

processArgs(String[]) - Method in class trans.tpmap.ConvertTPMapsToFeatures

This method will process each argument and assign any new varibles

processArgs(String[]) - Method in class trans.tpmap.FilterTPMapByRegions

This method will process each argument and assign any new varibles

processArgs(String[]) - Method in class trans.tpmap.MummerMapper

This method will process each argument and assign any new varibles

processArgs(String[]) - Method in class trans.tpmap.OligoFlipper

This method will process each argument and assign any new varibles

processArgs(String[]) - Method in class trans.tpmap.TPMapDensityReducer

This method will process each argument and assign any new varibles

processArgs(String[]) - Method in class trans.tpmap.TPMapOligoBlastFilter

This method will process each argument and assign any new varibles

processArgs(String[]) - Method in class trans.tpmap.TPMapProcessor

This method will process each argument and assign any new varibles

processArgs(String[]) - Method in class trans.tpmap.TPMapSort

This method will process each argument and assign any new varibles

processArgs(String[]) - Method in class util.apps.ConvertFasta2GCBoolean

This method will process each argument and assign any new varibles

processArgs(String[]) - Method in class util.apps.FileJoiner

This method will process each argument and assign any new varibles

processArgs(String[]) - Method in class util.apps.FileSplitter

This method will process each argument and assign any new varibles

processArgs(String[]) - Method in class util.apps.FileTrimmer

This method will process each argument and assign any new varibles

processArgs(String[]) - Method in class util.apps.PrintSelectColumns

This method will process each argument and assign any new varibles

processArgs(String[]) - Method in class util.apps.ScoreChromosomes

This method will process each argument and assign any new varibles

processArgs(String[]) - Method in class util.apps.ScoreSequences

This method will process each argument and assign any new varibles

processArgs(String[]) - Method in class util.bio.annotation.ExportIntergenicRegions

This method will process each argument and assign new varibles

processArgs(String[]) - Method in class util.bio.annotation.ExportIntronicRegions

This method will process each argument and assign new varibles

processArgs(String[]) - Method in class util.bio.cluster.HierarchicalClustering

This method will process each argument and assign new varibles

processArgs(String[]) - Method in class util.bio.parsers.FetchGenomicSequences

This method will process each argument and assign new varibles

processArgs(String[]) - Method in class util.bio.parsers.gff.ExtractGffFeatures

This method will process each argument and assign new varibles

processArgs(String[]) - Method in class util.bio.seq.IndexFastas

This method will process each argument and assign new varibles

processArgs(String[]) - Method in class util.bio.wrappers.Primer3Wrapper

This method will process each argument and assign any new varibles

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

processSearchForField() - Method in class bioroot.SearchBean

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

Returns a Hodges-Lehmann estimator, the median of all pairwise means.

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

Calculates the pseudoMedian on each replica of intensities.

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

Returns a Hodges-Lehmann estimator, the median of all pairwise means.

put(String, String, S3Object, Map) - Method in class com.amazon.s3.AWSAuthConnection

Writes an object to S3.

put(String, String, S3Object, Map) - Method in class com.amazon.s3.QueryStringAuthGenerator

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

Write a new ACL for a given object

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

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

Write a new ACL for a given bucket

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

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

Write a new logging xml document for a given bucket

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

putLargestWindowArrayFirst() - Method in class trans.main.MultiWindowIntervalMaker

Puts longest window array first and it's associated minScore.