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

M

MD5 - class util.gen.MD5.

This class implements the MD5 algorithm as described in RFC1321.

MD5() - Constructor for class util.gen.MD5

MD5Crypt - class util.gen.MD5Crypt.

This class defines a method, crypt(), which takes a password and a salt string and generates an OpenBSD/FreeBSD/Linux-compatible md5-encoded password entry.

MD5Crypt() - Constructor for class util.gen.MD5Crypt

MakeAllWindows - class trans.main.MakeAllWindows.

Makes all windows given oligo positions.

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

MakeBioTools - class util.apps.MakeBioTools.

Utility app to pull classes into folders and extract menus to html.

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

MakeChromosomeSets - class trans.cel.MakeChromosomeSets.

MakeChromosomeSets(String[]) - Constructor for class trans.cel.MakeChromosomeSets

MapControlIntensities - class trans.bkgrnd.MapControlIntensities.

Loads a bpmap file with oligo intensity measurements from multiple '.cel' files after median scaling to 50.

MapControlIntensities() - Constructor for class trans.bkgrnd.MapControlIntensities

MapFeature - class trans.tpmap.MapFeature.

Tpmap line broken into some components, chromosome, start, pmX, pmY, and optionally, mmX, mmY.

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

Constructor - bpmapLine - seq ori chrom start pmX pmY mmX mmY, (mm coords are optional).

MapSplitter - class trans.tpmap.MapSplitter.

Splits a '.bpmap' text file into different chromosomes, helper script for TPMapProcessor.

MapSplitter(MapFeature[], File) - Constructor for class trans.tpmap.MapSplitter

For running in combination with BPMapProcessor

Marker - class bioroot.Marker.

Marker() - Constructor for class bioroot.Marker

MarkerBean - class bioroot.MarkerBean.

MarkerBean() - Constructor for class bioroot.MarkerBean

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

MemeMotif - class meme.MemeMotif.

This contains info generated from parsing a meme report, each found motif is represented by this class.

MemeMotif() - Constructor for class meme.MemeMotif

MemeParser - class meme.MemeParser.

Parses meme output into MemeMotif objects and stores some generalize info re the meme run.

MemeParser(String) - Constructor for class meme.MemeParser

For single processor meme

MemeParser(String, String, String) - Constructor for class meme.MemeParser

For parallel processor meme on Sapo

MemeR - class meme.MemeR.

Main, wRapper for meme geared toward processing multiple rounds of selex data.

MemeR() - Constructor for class meme.MemeR

MemeResults - class meme.MemeResults.

Holds the results from various parts of MemeR.

MemeResults() - Constructor for class meme.MemeResults

MergeRegions - class trans.anno.MergeRegions.

Takes several tab delimited region files (chrom, start, stop, ...), creates the union and writes to disk.

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

MergeWindowArrays - class trans.main.MergeWindowArrays.

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

MethodTester - class trans.roc.MethodTester.

Application for scoring '.sgr' files for positives and negatives in relation to known (spike in) data.

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

Misc - class util.gen.Misc.

A variety of static methods.

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

MotifHit - class meme.MotifHit.

Holds data related to a particular match of a matrix to a sequence.

MotifHit(int, int, double, String, int) - Constructor for class meme.MotifHit

MotifScanner - class meme.MotifScanner.

MotifScanner objects are used to scan sequences with a particular weight matrix and generate an array of MotifHit objects.

MotifScanner(double[][], MemeResults) - Constructor for class meme.MotifScanner

MotifScanner(double[][]) - Constructor for class meme.MotifScanner

MotifSearchResult - class meme.MotifSearchResult.

Holds the results of searching a multi-fasta seq file with a particular motif.

MotifSearchResult(MemeMotif, String, int) - Constructor for class meme.MotifSearchResult

MultiAlignPanel - class gata.plotter.MultiAlignPanel.

MultiAlignPanel() - Constructor for class gata.plotter.MultiAlignPanel

MultiFastaParser - class util.bio.parsers.MultiFastaParser.

Extracts sequences and headers out of multi fasta files.

MultiFastaParser(File) - Constructor for class util.bio.parsers.MultiFastaParser

MultiFastaParser(String) - Constructor for class util.bio.parsers.MultiFastaParser

MultiFastaParser() - Constructor for class util.bio.parsers.MultiFastaParser

MultiSGRPrinter - class trans.main.MultiSGRPrinter.

Prints a multi sgr file (chr position val1, val2, val3, ....)

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

MultiSetQuantile - class trans.cel.MultiSetQuantile.

Class holding info relating to one quantile value.

MultiSetQuantile(byte, int, float) - Constructor for class trans.cel.MultiSetQuantile

MultiWindowIntervalMaker - class trans.main.MultiWindowIntervalMaker.

Collapses arrays of Windows into an array of Interval based on scores and minimal number of windows that must pass.

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

MummerMapper - class trans.tpmap.MummerMapper.

Application to map 1lq files to fasta files.

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

main(String[]) - Static method in class bioroot.CronArchive

main(String[]) - Static method in class bioroot.DeleteMeNow

main(String[]) - Static method in class bioroot.Spammer

main(String[]) - Static method in class bioroot.parsers.ExtractWords

main(String[]) - Static method in class bioroot.parsers.RenameWords

main(String[]) - Static method in class cgar.CommitFiles

main(String[]) - Static method in class expr.CorrelationMaps

main(String[]) - Static method in class expr.ExpressionScores2CoordinatesViaGFF

main(String[]) - Static method in class gata.aligner.DelmeAligner

main(String[]) - Static method in class gata.aligner.GATAligner

main(String[]) - Static method in class gata.main.GATAPlotter

main(String[]) - Static method in class igb.util.HistogramSgrOrGrFile

main(String[]) - Static method in class igb.util.Windows2HeatMapSgr

main(String[]) - Static method in class meme.MemeR

main(String[]) - Static method in class selex.SelexSeqParser

main(String[]) - Static method in class trans.anno.AnnotateRegions

main(String[]) - Static method in class trans.anno.AnnotateRegionsWithGeneList

main(String[]) - Static method in class trans.anno.BindingRegionsToGff3

main(String[]) - Static method in class trans.anno.BindingRegionsToIntervals

main(String[]) - Static method in class trans.anno.DmelCGNameCoordinatePrinter

main(String[]) - Static method in class trans.anno.Gff2ToBindingRegions

main(String[]) - Static method in class trans.anno.Gff2ToIntervals

main(String[]) - Static method in class trans.anno.IntersectBindingPeaks

main(String[]) - Static method in class trans.anno.IntersectKeyWithRegions

main(String[]) - Static method in class trans.anno.IntersectRegions

main(String[]) - Static method in class trans.anno.MergeRegions

main(String[]) - Static method in class trans.anno.RandomRegions

main(String[]) - Static method in class trans.bkgrnd.CalcBkgrndRatios

main(String[]) - Static method in class trans.bkgrnd.CalculateBackgroundStats

main(String[]) - Static method in class trans.bkgrnd.MapControlIntensities

main(String[]) - Static method in class trans.cel.AverageACels

main(String[]) - Static method in class trans.cel.AveragePCels

main(String[]) - Static method in class trans.cel.CelFileConverter

main(String[]) - Static method in class trans.cel.CelPHistogram

main(String[]) - Static method in class trans.cel.CelProcessor

main(String[]) - Static method in class trans.cel.ConvertTVSToCelps

main(String[]) - Static method in class trans.cel.MakeChromosomeSets

main(String[]) - Static method in class trans.cel.RotateCelFile

main(String[]) - Static method in class trans.cel.SplineScalar

main(String[]) - Static method in class trans.cel.StatIntensityFeatureArray

main(String[]) - Static method in class trans.graphics.AggregatePlots

main(String[]) - Static method in class trans.graphics.CelMasker

main(String[]) - Static method in class trans.graphics.CombineXYSeries

main(String[]) - Static method in class trans.graphics.IntervalPlotter

main(String[]) - Static method in class trans.graphics.PlotFloatArrays

main(String[]) - Static method in class trans.graphics.RankedSetAnalysis

main(String[]) - Static method in class trans.graphics.VirtualCel

main(String[]) - Static method in class trans.main.BindingRegionGraphPrinter

main(String[]) - Static method in class trans.main.ExportIntervalData

main(String[]) - Static method in class trans.main.FDRVsQValues

main(String[]) - Static method in class trans.main.FDRWindowConverter

main(String[]) - Static method in class trans.main.FindSubBindingRegions

main(String[]) - Static method in class trans.main.IntensityPrinter

main(String[]) - Static method in class trans.main.IntervalFilter

main(String[]) - Static method in class trans.main.IntervalGFFPrinter

main(String[]) - Static method in class trans.main.IntervalGraphPrinter

main(String[]) - Static method in class trans.main.IntervalMaker

main(String[]) - Static method in class trans.main.IntervalReportPrinter

main(String[]) - Static method in class trans.main.LoadChipSetIntervalOligoInfo

main(String[]) - Static method in class trans.main.LoadIntervalOligoInfo

main(String[]) - Static method in class trans.main.MakeAllWindows

main(String[]) - Static method in class trans.main.MergeWindowArrays

main(String[]) - Static method in class trans.main.MultiSGRPrinter

main(String[]) - Static method in class trans.main.MultiWindowIntervalMaker

main(String[]) - Static method in class trans.main.OligoIntensityPrinter

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

main(String[]) - Static method in class trans.main.OverlappingWindowScoreExtractor

main(String[]) - Static method in class trans.main.RandomizeLabels

main(String[]) - Static method in class trans.main.ReplaceWindowScores

main(String[]) - Static method in class trans.main.ScanChip

main(String[]) - Static method in class trans.main.ScanChromosomes

main(String[]) - Static method in class trans.main.ScanGenes

main(String[]) - Static method in class trans.main.ScoreIntervals

main(String[]) - Static method in class trans.main.SetNumberIntervalMaker

main(String[]) - Static method in class trans.main.SplitWindowArraysByChromosome

main(String[]) - Static method in class trans.main.T2

main(String[]) - Static method in class trans.main.TestScanChip

main(String[]) - Static method in class trans.main.WilcoxonRankSumTest

main(String[]) - Static method in class trans.main.WilcoxonSignedRankTest

main(String[]) - Static method in class trans.main.WindowBlockMaker

main(String[]) - Static method in class trans.main.WindowBlockMakerTwoColor

main(String[]) - Static method in class trans.misc.AverageDoubles

main(String[]) - Static method in class trans.misc.Bar2Gr

main(String[]) - Static method in class trans.misc.Bed2Gr

main(String[]) - Static method in class trans.misc.CalcGCAndTransform

main(String[]) - Static method in class trans.misc.CalcGCRatiosFromIntervals

main(String[]) - Static method in class trans.misc.ConvertAgilentData

main(String[]) - Static method in class trans.misc.ConvertGeoData

main(String[]) - Static method in class trans.misc.ConvertNimblegenNDF2TPMap

main(String[]) - Static method in class trans.misc.ConvertNimblegenPAIR2Cela

main(String[]) - Static method in class trans.misc.CorrelateGrFiles

main(String[]) - Static method in class trans.misc.Gr2Bar

main(String[]) - Static method in class trans.misc.InefficientPseudoMedian

main(String[]) - Static method in class trans.misc.PrependColumn

Prepends a column on columns of data.

main(String[]) - Static method in class trans.misc.Regions2Intervals

main(String[]) - Static method in class trans.misc.ScoredRegionsFormatFixer

main(String[]) - Static method in class trans.misc.Sgr2Bar

main(String[]) - Static method in class trans.misc.TextPValOrSig2Gr

main(String[]) - Static method in class trans.misc.TransformRatios

main(String[]) - Static method in class trans.misc.Util

main(String[]) - Static method in class trans.misc.WindowHistogram

main(String[]) - Static method in class trans.qc.CelFileQualityControl

main(String[]) - Static method in class trans.qc.CoordinateExtractor1lq

main(String[]) - Static method in class trans.qc.DestypeIntensityCalculator

main(String[]) - Static method in class trans.qc.Parser1lq

main(String[]) - Static method in class trans.roc.ExonScoreExtractor

main(String[]) - Static method in class trans.roc.ExtractNonOverlappingWindows

main(String[]) - Static method in class trans.roc.ExtractSaveSgrScores

main(String[]) - Static method in class trans.roc.ExtractScoresForRoc

main(String[]) - Static method in class trans.roc.MethodTester

main(String[]) - Static method in class trans.roc.PWMScoreWindows

main(String[]) - Static method in class trans.roc.ParseBarsForParticularRegions

main(String[]) - Static method in class trans.roc.ParsePatternedWindows

main(String[]) - Static method in class trans.roc.ParseSgrsForParticularRegions

main(String[]) - Static method in class trans.roc.ParseSgrsForParticularScores

main(String[]) - Static method in class trans.roc.RocWindowScanner

main(String[]) - Static method in class trans.roc.SgrBacCounter

main(String[]) - Static method in class trans.tpmap.CollapseTPMap

main(String[]) - Static method in class trans.tpmap.ConvertTPMapsToFeatures

main(String[]) - Static method in class trans.tpmap.FilterTPMapByRegions

main(String[]) - Static method in class trans.tpmap.MummerMapper

main(String[]) - Static method in class trans.tpmap.OligoFlipper

main(String[]) - Static method in class trans.tpmap.Stat1lq

main(String[]) - Static method in class trans.tpmap.StatTPMap

main(String[]) - Static method in class trans.tpmap.StatTPMapControlSeqs

main(String[]) - Static method in class trans.tpmap.TPMapDensityReducer

main(String[]) - Static method in class trans.tpmap.TPMapDuplicateFilter

main(String[]) - Static method in class trans.tpmap.TPMapOligoBlastFilter

main(String[]) - Static method in class trans.tpmap.TPMapProcessor

main(String[]) - Static method in class trans.tpmap.TPMapSort

main(String[]) - Static method in class trans.tpmap.TPMapStripHighLowGC

main(String[]) - Static method in class trans.tpmap.WindowMaker

main(String[]) - Static method in class util.amazon.S3CodeSamples

main(String[]) - Static method in class util.amazon.S3Manager

main(String[]) - Static method in class util.apps.ArrayPrinter

main(String[]) - Static method in class util.apps.ConvertFasta2GCBoolean

main(String[]) - Static method in class util.apps.Correlate

main(String[]) - Static method in class util.apps.Delme2

main(String[]) - Static method in class util.apps.FileJoiner

main(String[]) - Static method in class util.apps.FileSplitter

main(String[]) - Static method in class util.apps.FileTrimmer

main(String[]) - Static method in class util.apps.Flash

main(String[]) - Static method in class util.apps.GeneNameCounter

main(String[]) - Static method in class util.apps.HouseBean

main(String[]) - Static method in class util.apps.IntersectLists

main(String[]) - Static method in class util.apps.JQSub

main(String[]) - Static method in class util.apps.MakeBioTools

main(String[]) - Static method in class util.apps.ParseMLSHTML

main(String[]) - Static method in class util.apps.PrintSelectColumns

main(String[]) - Static method in class util.apps.RenameRWSResults

main(String[]) - Static method in class util.apps.ScatterPlot

main(String[]) - Static method in class util.apps.ScoreChromosomes

main(String[]) - Static method in class util.apps.ScoreSequences

main(String[]) - Static method in class util.apps.SubtractOneFromLastColumn

main(String[]) - Static method in class util.apps.TASSignalChromFileSplitter

main(String[]) - Static method in class util.apps.TextParser

main(String[]) - Static method in class util.apps.WindowScoreSmoother

main(String[]) - Static method in class util.bio.annotation.ExportIntergenicRegions

main(String[]) - Static method in class util.bio.annotation.ExportIntronicRegions

main(String[]) - Static method in class util.bio.cluster.HierarchicalClustering

main(String[]) - Static method in class util.bio.converters.AlignedBaseCounter

main(String[]) - Static method in class util.bio.converters.GenomeFASTASplitter

main(String[]) - Static method in class util.bio.converters.PossumToGFF

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

main(String[]) - Static method in class util.bio.digest.REDigest

main(String[]) - Static method in class util.bio.parsers.ADFDataBaseSplitter

main(String[]) - Static method in class util.bio.parsers.DrosGeneCollFileParser

main(String[]) - Static method in class util.bio.parsers.FetchGenomicSequences

main(String[]) - Static method in class util.bio.parsers.SynonymTables

main(String[]) - Static method in class util.bio.parsers.UCSCGeneModelTableReader

main(String[]) - Static method in class util.bio.parsers.gff.DmelRel4Extractor

main(String[]) - Static method in class util.bio.parsers.gff.ExtractGffFeatures

main(String[]) - Static method in class util.bio.parsers.gff.Gff3Parser

main(String[]) - Static method in class util.bio.seq.FetchIndexedSequence

main(String[]) - Static method in class util.bio.seq.IndexFastas

main(String[]) - Static method in class util.bio.seq.LowerCase2Xs

main(String[]) - Static method in class util.bio.wrappers.Primer3Wrapper

main(String[]) - Static method in class util.bio.xamer.XamerCounter

main(String[]) - Static method in class util.gen.CubicSpline

main(String[]) - Static method in class util.gen.LinearRegression

An example.

main(String[]) - Static method in class util.gen.MD5Crypt

main(String[]) - Static method in class util.gen.ReadZip

main(String[]) - Static method in class util.gen.SpearmanCorrelation

main(String[]) - Static method in class util.xml.ParseXMLFile

Starts XML parsing example

makeAddOnePSPM(String[]) - Static method in class meme.MemeMotif

This method returns a position specific probability weight matrix given an array of Strings, each of the same size, containing GATC, no gaps, no N's.

makeAlignmentObjects(ArrayList) - Method in class gata.aligner.LocalAlignment

makeAllShapes(int, int) - Method in class gata.plotter.AlignPanel

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

File management for intervals.

makeAndSetAntibodyBeans(HttpSession, DBUtil, UserBean) - Static method in class bioroot.antibody.AntibodySpreadSheet

Makes an array of AntibodyBeans based on Users AntibodyPreferences and sets them in the session.

makeAndSetOligoBeans(HttpSession, DBUtil, UserBean) - Static method in class bioroot.oligo.OligoSpreadSheet

Makes an array of OligoBeans based on Users OligoPreferences and sets them in the session.

makeAndSetPlasmidBeans(HttpSession, DBUtil, UserBean) - Static method in class bioroot.plasmid.PlasmidSpreadSheet

Makes an array of PlasmidBeans based on Users PlasmidPreferences and sets them in the session.

makeAndSetStrainBeans(HttpSession, DBUtil, UserBean) - Static method in class bioroot.strain.StrainSpreadSheet

Makes an array of StrainBeans based on Users StrainPreferences and sets them in the session.

makeAnnotation(AnnoSpecParams) - Method in class gata.main.GATAPlotter

makeAntibodyBeans(DBUtil, UserBean) - Static method in class bioroot.Archive

Makes an array of all visibile AntibodyBeans

makeArchive(DBUtil, UserBean) - Static method in class bioroot.CronArchive

Returns null or a zip file containing a labGroup's full archive.

makeArrayNames(float[][], float[][]) - Method in class trans.main.RandomizeLabels

Convert intensity arrays into an ArrayName[].

makeArrowAndButt(int, int, int, double, int, double, double, double) - Static method in class gata.main.GATAUtil

Makes an arrow and butt but no base line.

makeArrowLine(int, int, int, double, int, double, double, double) - Static method in class gata.main.GATAUtil

Makes an arrow line with half arrow up for -1 or down for 1.

makeArrowLine(int, int, int, float, int, float, float, float, float) - Static method in class gata.main.GATAUtil

Makes an arrow line with half arrow up for -1 or down for 1.

makeArrowedTableRow(String[], String[]) - Static method in class util.gen.HTML

Example table row with arrow buttons.

makeBarFiles(Window[], File, int) - Method in class trans.main.ScanChromosomes

Makes xxx.bar.zip files from a Window[], one per chromosome.

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

makeBindingRegions(int[][], String) - Static method in class trans.anno.IntersectRegions

Given an array of start stops and a chromosome, makes BindingRegions.

makeBins() - Method in class trans.roc.MethodTester

makeBins() - Method in class trans.roc.SgrBacCounter

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

makeBlastSummaryTable(BlastResult[]) - Static method in class bioroot.Search

Returns a summary HTML table, hotlinked id, name, score, expect

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

Takes an array of Window

makeBufferedImage(double, boolean) - Method in class gata.geneGlyphs.GlyphPanel

makeBufferedImage(double, boolean) - Method in class gata.plotter.AlignPanel

Generates a BufferedImage from the panel.

makeBufferedImage() - Method in class trans.graphics.VirtualCelPanel

makeButton(String, int, ActionListener, JPanel) - Static method in class gata.main.GATAUtil

makeButton(String) - Method in class gata.plotter.ToolsFrame

makeButton(String, int, ActionListener, JPanel) - Static method in class util.gen.Swing

makeByte4BaseMap() - Static method in class util.bio.seq.Seq

Makes a hash map of each 4bp combination in the all4BaseCombinations String[] and a unique Byte.

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

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

Writes charts to the save directory and if so indicated displays them.

makeChromSet(File[][], boolean) - Method in class trans.main.T2

makeChromosomeNameFileHash(File[]) - Static method in class util.bio.seq.Seq

Uses Seq.extractChromosomeName() to extract a chromosome name from each file.

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

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

Makes chromosome wide scores.

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

Makes chromosome wide scores.

makeColors() - Static method in class trans.graphics.VirtualCelPanel

Generates 768 diff colors along a black red yellow white gradient.

makeConcatination() - Method in class bioroot.Preference

Makes a visibility: orderBy: labGroups: features concat.

makeConcatination() - Method in class bioroot.strain.StrainPreference

Makes a visibility | orderBy | labGroups | features | strain types concat.

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

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

Builds tree and associated corr coeff JLabels.

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

Instantiates a ControlStats object for each Quantile[] object.

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

makeDirectories() - Method in class trans.main.MakeAllWindows

Makes directories and files to hold point gr files and tempRatios

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

Makes directories and files to hold point gr files and tempRatios

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

makeDoubleInputDialog(String, String, double) - Static method in class util.gen.Swing

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

makeDoublePercentInputDialog(String, String, double) - Static method in class util.gen.Swing

makeEditHistory(String, String, String) - Static method in class bioroot.Util

Makes an edit history entry.

makeEnzymeArray(String, int) - Method in class util.bio.digest.NEBParser

makeExonMask(UCSCGeneLine[]) - Method in class util.bio.annotation.ExportIntronicRegions

makeExons(int) - Method in class trans.roc.ControlGene

Subtracts the endOffSet from the end and only creates an exon if 1+ end-start > 0

makeExons(ControlGene[], int) - Static method in class trans.roc.ControlGene

Fires makeExons on each CG within the ControlGene[].

makeFastaAndFilter() - Method in class trans.tpmap.MummerMapper

Makes a fasta file from a 1lq file, reverses the sequence of each oligo, drops control probes

makeFeatures(String) - Static method in class bioroot.Feature

Makes a Feature[] from a String concatinate, the thing that is actually stored in the database.

makeFeatures(String[]) - Static method in class bioroot.Util

Use to make a default Feature[].

makeField(String, AlignerInputPanel.NumberFocusListener) - Method in class gata.aligner.AlignerInputPanel

makeField(JPanel, String, JFrame, JFileChooser, FileFocusListener) - Static method in class gata.main.GATAUtil

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

makeFieldSimple(JPanel, String) - Static method in class util.gen.Swing

makeFileNameHash() - Method in class meme.MemeResults

makeFinalReport() - Method in class selex.SelexParams

makeFrequencyMatrix(String[]) - Static method in class meme.MemeMotif

Generates a matrix of the number of As Cc Gg Ts (top) by 1,2,3,4...positions in the motif (side) observed in all the Strings of the String[].

makeFrequencyMatrix(String[]) - Static method in class util.bio.seq.Seq

Generates a matrix of the number of As Cc Gg Ts (top) by 1,2,3,4...positions in the motif (side) observed in all the Strings of the String[].

makeFullPathName(String, String) - Static method in class meme.UtilMeme

makeFullPathName(String, String) - Static method in class util.gen.IO

Attempts to make a file and return it's canonical path name (full path name).

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

This makes a sorted array of GenericGlyphs broken down by track

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

Call once to make the glyphs used in rendering the gene annotation.

makeGlyphs(Graph, double) - Method in class trans.graphics.Box

makeGlyphs(double, double, double, double) - Method in class trans.graphics.Graph

Returns bottom y coordinate of graph.

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

Makes and places a GenomicRegionGlyph in each region using the rank number as the label.

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

makeHashSelectStatement(String, HashMap, UserBean) - Static method in class bioroot.Search

Makes an SQL SELECT statement using a HashMap.

makeHeatMapBarFiles(Window[], File) - Method in class trans.main.WindowBlockMaker

Be sure to set the scoreIndex, defaults to 0.

makeHeatMapBarFiles(Window[], File, int) - Method in class trans.main.WindowBlockMakerTwoColor

makeHeatMapBarFiles(Window[]) - Method in class trans.main.WindowBlockMakerTwoColor

Makes a stair step heat map from an array of windows in bar format.

makeHeatMapGrFiles(Window[], File) - Method in class trans.main.WindowBlockMaker

Be sure to set the scoreIndex, defaults to 0.

makeHeatMapSgrFile(Window[], File, boolean) - Method in class trans.main.WindowBlockMaker

Be sure to set the scoreIndex, defaults to 0.

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

Uses a hash to toss duplicate records, same mls#

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

An example in how to make a huge random word table.

makeIndexedSequences() - Method in class util.bio.seq.FetchIndexedSequence

makeInitialBGOs(File) - Static method in class trans.bkgrnd.MapControlIntensities

makeInputDialog(String, String, String) - Static method in class meme.MemeR

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

makeIntInputDialog(String, String, int) - Static method in class util.gen.Swing

makeIntervals(File) - Method in class trans.main.IntervalMaker

makeLLPSPM(double[][], double, double, double, double) - Static method in class meme.MemeMotif

takes a double[][] where array[0] refers to the first position in a motif array[0][0 to 3] = probability of A, C, G, or T nucleotide at that position.

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

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

makeLabel(String) - Method in class gata.plotter.ToolsFrame

makeLabel(String) - Method in class util.bio.cluster.ClusterDrawPanel

makeLabel(JPanel, String, int, int) - Static method in class util.gen.Swing

makeLibrary() - Method in class util.apps.MakeBioTools

Makes the code library jar from the directoriesForLibJar array.

makeLine(int, int, double, double, double) - Static method in class gata.main.GATAUtil

Converts an int[2] (startStop) in nucleotides to a Line2D.Double

makeLocalAlignments(ArrayList) - Method in class gata.aligner.Seqs

makeMenuHTMLDoc() - Method in class util.apps.MakeBioTools

Generates the cmdLnMenus.html doc.

makeMockIntervals(double) - Method in class trans.main.SetNumberIntervalMaker

Returns the number of intervals that can be made at a given cutoff

makeMockJars() - Method in class util.apps.MakeBioTools

Makes mock Jar files.

makeMultiFASTA(String, DBUtil) - Static method in class bioroot.Search

makeOligoBeans(DBUtil, UserBean) - Static method in class bioroot.Archive

Makes an array of all visibile OligoBeans

makeOligoConcat(BlastMatcher[]) - Static method in class bioroot.plasmid.PlasmidBase

Converts a BlastMatcher[] to a concat of oligo sequences and NNNNNNNNNN spacers.

makePNG(File, double) - Method in class gata.menu.SaveImagePanel

makePNGPanel(float[][], int, File) - Method in class trans.graphics.VirtualCelFrame

makePSPM(String[]) - Static method in class meme.MemeMotif

This method returns a position specific probability weight matrix given an array of Strings, each of the same size, containing GATC, no gaps, no N's.

makePanel(Interval, int, TextFrame, boolean) - Method in class trans.graphics.IntervalDrawFrame

makePanel(float[][], int, float) - Method in class trans.graphics.VirtualCelFrame

makePlasmidBeans(DBUtil, UserBean) - Static method in class bioroot.Archive

Makes an array of all visibile PlasmidBeans

makePositives() - Method in class trans.roc.MethodTester

makePositives(File) - Method in class trans.roc.MethodTester

makePositives() - Method in class trans.roc.SgrBacCounter

makeQPCRWindows(Window[]) - Method in class trans.main.OverlappingWindowScoreExtractor

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

Makes a Quantile[][] given float[][] where the quantile.position is assigned its array index position and the quantile.value is assigned the float value.

makeRandom(Positive, double) - Method in class trans.roc.ParseBarsForParticularRegions

Takes a Positive and finds 1000 chrom, length, gc, and number scores matched random regions.

makeRandomBindingRegions(BindingRegion[], HashMap, int) - Static method in class trans.anno.AnnotateRegions

For each binding region this will make another binding region from the same chromosome with the same length, yet at a random location.

makeRandomBindingRegions(BindingRegion[], HashMap, int) - Static method in class trans.anno.AnnotateRegionsWithGeneList

For each binding region this will make another binding region from the same chromosome with the same length, yet at a random location.

makeRandomRegions(String) - Method in class trans.anno.IntersectRegions

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

Makes and places RankedFloatArrays in each ExpressedGene, also nulls the ExpressedGene.values.

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

makeRectangle(int, int, double, double, double, double) - Static method in class gata.main.GATAUtil

Returns a rectangle given start stop in nucleotides and y coords in pixels

makeRectangleAndPoint(boolean, double, double, double, double, Color) - Method in class trans.graphics.GenomicRegionGlyph

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

makeRegions(File) - Method in class trans.anno.RandomRegions

Parses the regions file but then adds a pointer per base pair length/ divider to the Region[] for every region.

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

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

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

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

Makes a scale bar between 10 and 100 pixels in length at 1, 10, 100 bp or kb or mb sizes, change the scaleBarX and scaleBarY coordinates to relocate the bar

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

Makes a scale ruler with intervals between 10 and 100 pixels in length at 1, 10, 100 bp or kb or mb sizes, change the scaleRulerStartStopX and scaleRulerY coordinates to relocate the bar

makeSegments(ArrayList, double, double, double) - Static method in class gata.main.GATAUtil

Converts an ArrayList of int[2]'s (startStop) in nucleotides to an ArrayList of Line2D.Double's

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

makeSegmentsInt(int[][], double, double, double) - Static method in class gata.main.GATAUtil

Converts an int[x][2]'s (startStop) in nucleotides to an ArrayList of Line2D.Double's

makeSets(File[], File) - Method in class trans.cel.MakeChromosomeSets

Merges chromosome info together and saves as whole chromosomes, will also save the oligoPositions if oligoPositionsDirectory isn't null.

makeSgrFile(Window[], File, int) - Method in class trans.main.ScanChip

Makes a xxx.sgr.zip file from a sorted Window[].

makeShapes(double, double, double, double, double, double, double) - Method in class gata.aligner.Alignment

makeSlider(JSlider, int, int) - Method in class gata.plotter.Sliders

makeSource() - Method in class util.apps.MakeBioTools

Makes the code library jar from the directoriesForLibJar array.

makeStrainBeans(DBUtil, UserBean) - Static method in class bioroot.Archive

Makes an array of all visibile StrainBeans

makeSubAligns(LocalAlignment[]) - Static method in class gata.main.GATAUtil

makeSubSeqs() - Method in class selex.SeqRead

makeTransformer() - Static method in class trans.misc.TransformRatios

makeVirtualCel(int[][], int) - Static method in class trans.qc.CoordinateExtractor1lq

Make a virtual cel file loading xyCoors with an intensity of 100.

makeVirtualCel(int[][], int) - Static method in class trans.qc.Parser1lq

Make a virtual cel file loading xyCoors with an intensity of 100.

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

Resets an array of visable alignments

makeWindows(File) - Static method in class trans.main.OverlappingWindowScoreExtractor

Converts a tab delimited txt file of chr, start, stop, scores (multiple permitted or none) into an array of Windows.

makeWindows(int[]) - Method in class trans.tpmap.WindowMaker

Takes an int[] of sorted bp start positions and finds unique windows of a maximized width with a minimal # of oligos.

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

makeWindowsFromFiles(String[]) - Method in class trans.tpmap.WindowMaker

Takes int[] files containing bp start positions for each oligo, ordered.

makeXMLReader() - Static method in class util.gen.XML

create a new XML reader, returns null if a problem is encountered.

mapCelFiles(File[]) - Method in class trans.cel.CelMapper

mapCelFiles(File[], File[]) - Method in class trans.cel.CelMapper

Maps float[][] to MapFeature[][] saving under the index matched File in matchedSaveAsFiles as a MultiSetQuantile[].

mapIt(Matcher) - Static method in class bioroot.PatternMatch

Returns an array of hits (PatternMatch[]) given a Matcher.

mapItArrayList(Matcher) - Static method in class bioroot.PatternMatch

Returns an ArrayList of PatternMatch given a Matcher.

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

The marker echoed back from the request.

mask(int, int) - Method in class trans.main.PeakPicker

maskBoolean(Gff3Feature[]) - Method in class util.bio.annotation.ExportIntergenicRegions

Uses a boolean[] to score whether a base is part of an annotation (true) or not (false).

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

Runs through float[][] setting any values that exceed the outlierThreshold to zero.

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

Takes unlogged MAT normalized t-values, sorts, logs and takes a variant of a number stabilized trimmed mean ratio.

matchIt(boolean) - Method in class bioroot.SearchHit

matchIt(Pattern) - Method in class util.apps.HouseBean

matches(BL2SeqHit[]) - Method in class bioroot.BlastMatcher

matches(Sgr) - Method in class trans.roc.Positive

matches - Variable in class trans.tpmap.MapFeature

matches(TPMapFeature, TPMapFeature) - Static method in class trans.tpmap.TPMapDuplicateFilter

Only checks coordinates!

maxFileSize - Static variable in class bioroot.Util

Maximum allowable file size for upload

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

The maxKeys echoed back from the request if specified.

maxLength(Positive[]) - Static method in class trans.graphics.AggregatePlots

Finds max length of the Region[], stop-start+1

maxMedianAbsDiffSubWinTreatment(Interval) - Static method in class trans.main.IntervalReportPrinter

Calculate maximum median absolute diff of SubWindow treatment values

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

Averages a float array.

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

Averages two float[]s .

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

Averages two float[][]s, assumes a square.

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

Averages a int array.

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

Averages a double array.

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

Averages an ArrayList of Double objects.

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

Calculates a mean on the non zero floats, return zero if no non zero values were found.

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

Averages an ArrayList of Integer objects.

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

Calculates Median of a sorted double[].

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

Calculates Median of a sorted int[].

median(short[]) - Static method in class util.gen.Num

Calculates Median of a sorted short[].

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

Calculates Median of a sorted float[].

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

Calculates the median absolute difference.

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

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

Calculates the median value of a sorted float[] ignoring leading zero values!

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

Median normalize unsorted array to a given number.

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

Median normalizes an unsorted float[][] array to a given target.

medianRatioSubWindow(Interval) - Static method in class trans.main.IntervalReportPrinter

Calculate Median ratio of SubWindow where the treatments are averaged, and the controls are averaged

medianScale(LoadedOligo[]) - Static method in class trans.bkgrnd.CalcBkgrndRatios

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

Median scale current intensity values.

meme - package meme

Wrapper for meme tweaked for processing multiple rounds of SELEX oligos.

menuHeader - Static variable in class util.apps.MakeBioTools

mergeClusters(double[]) - Method in class util.bio.cluster.HierarchicalClustering

Merges Clusters from best pair notes whether they have a bad cc.

mergeLAArrays(LocalAlignment[], LocalAlignment[]) - Static method in class gata.main.GATAUtil

mergeSubAligns(ArrayList) - Method in class gata.aligner.LocalAlignment

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

Creats one or two window merged window arrays containing all of the chromosomes.

metadata - Variable in class com.amazon.s3.S3Object

A Map from String to List of Strings representing the object's metadata

millisecToDays(long) - Static method in class util.gen.Num

Converts milliseconds to days.

minMaxWindowArray(Window[], int) - Static method in class trans.misc.Util

Returns the min and max values of a given score index in a Window[].

minMaxWindowScores() - Method in class trans.main.SetNumberIntervalMaker

Finds min max

minMaxWindowScores(Window[], int) - Static method in class trans.misc.Util

Finds min max score

minus10log10(double) - Static method in class util.gen.Num

Returns the -10 * LOG base 10 of the number.

mmX - Variable in class trans.tpmap.MapFeature

mmY - Variable in class trans.tpmap.MapFeature

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

Finds mode of a int[] histogram array, assumes one peak, returns the index position, value/frequency.

modifyEnds() - Method in class selex.SelexParams

modifySequenceEnds(String[], String[], String, String, String, String) - Static method in class selex.SeqFiles

Modifies the left side and right side of Sequences also adds (100's) or subtracts quanilty scores to match.