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

W

WilcoxonRankSumTest - class trans.main.WilcoxonRankSumTest.

Implementation of a Wilcoxon Rank Sum Test.

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

WilcoxonSample - class trans.main.WilcoxonSample.

Used by the WilcoxonRankSumTest.

WilcoxonSample(float, boolean) - Constructor for class trans.main.WilcoxonSample

WilcoxonSamplePair - class trans.main.WilcoxonSamplePair.

Used by the WilcoxonSignedRankTest.

WilcoxonSamplePair(float, float) - Constructor for class trans.main.WilcoxonSamplePair

WilcoxonSamplePair(float) - Constructor for class trans.main.WilcoxonSamplePair

WilcoxonSignedRankTest - class trans.main.WilcoxonSignedRankTest.

Implementation of a Wilcoxon Signed Rank Test.

WilcoxonSignedRankTest(float[], float[]) - Constructor for class trans.main.WilcoxonSignedRankTest

Minimal constructor, fastest way to calculate a transformedPValueFloat

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

Window - class trans.main.Window.

Class to hold information about a window, a defined portion of the genome typically < 1kb.

Window(String, int, int, int, double[]) - Constructor for class trans.main.Window

WindowBlockMaker - class trans.main.WindowBlockMaker.

Converts a Window[] into a heat map specific sgr file for import into IGB.

WindowBlockMaker(int) - Constructor for class trans.main.WindowBlockMaker

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

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

WindowBlockMakerTwoColor - class trans.main.WindowBlockMakerTwoColor.

Converts a Window[] into a heat map specific bar file for import into IGB.

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

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

WindowComparator - class trans.main.WindowComparator.

Class to help sort an array of Window[] by chromosome, start position, length shortest first.

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

WindowHistogram - class trans.misc.WindowHistogram.

Makes a histogram of scores from a Window[].

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

WindowMaker - class trans.tpmap.WindowMaker.

Creates Windows (start position, end position) of a given length, containing a given number of oligo start positions and maximum number of features.

WindowMaker(int, int) - Constructor for class trans.tpmap.WindowMaker

WindowMaker(int, int, int) - Constructor for class trans.tpmap.WindowMaker

WindowScoreSmoother - class util.apps.WindowScoreSmoother.

Slides a window across an array of numbers averaging the scores.

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

Windows2HeatMapSgr - class igb.util.Windows2HeatMapSgr.

Converts a text file (columns: chrom, start, stop, score) into a heat/block map specific sgr file for import into IGB.

Windows2HeatMapSgr(String[]) - Constructor for class igb.util.Windows2HeatMapSgr

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

Checks to see if the browser sending the request is from a windows machine.

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

Splits a chromosome of ExpressedGenes into windows based on the windowSize and minNumberGenes

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

Slides a window along an array, one index at a time, averaging the contents.

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

Slides a window along an array, one index at a time, averaging the contents.

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

Slides a window along an array, one index at a time, averaging the contents, ignores zero values.

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

Slides a window along an array, one index at a time, averaging the contents.

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

Slides a window along an array, one index at a time, averaging the contents, ignores zero values.

windowMidPoint(Window) - Static method in class trans.main.OverlappingWindowScoreExtractor

write(int) - Method in class com.amazon.thirdparty.Base64.OutputStream

Writes the byte to the output stream after converting to/from Base64 notation.

write(byte[], int, int) - Method in class com.amazon.thirdparty.Base64.OutputStream

Calls Base64.OutputStream.write(int) repeatedly until len bytes are written.

writeBinary(Coordinates[], File) - Static method in class util.bio.annotation.Coordinates

Writes a binary Coordinate[].

writeBinaryCoordinates(File, Region[]) - Static method in class trans.anno.Region

Writes the chrom start stop of a Region[] as a binary file.

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

Writes a binary sequence, gatc, anything else is assumed to be n.

writeBindingRegions(BindingRegion[], File) - Static method in class trans.anno.IntersectRegions

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

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

writeDocumentToOutput(Node, int) - Method in class util.xml.ParseXMLFile

Writes node and all child nodes into System.out

writeEncryptedCredentialsFile(File, String, String, String) - Static method in class util.amazon.S3Manager

Write a password protected encripted credentials file.

writeGrFile(File) - Method in class trans.misc.GrGraph

Writes to the file base tab value.

writePNGs(boolean) - Method in class trans.qc.CelFileQualityControl

Writes PNG files for CelFileStats.

writeReport() - Method in class selex.SelexParams

writeSGRFile(RocWindow[], File) - Static method in class trans.roc.ParsePatternedWindows

Writes an sgr file.

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

writeSimpleBarFile(GrGraph, File) - Static method in class trans.misc.Util

Writes a simple bar format graph for a xxx.gr type graph.

writeSimpleBarFile(String, String, int[], float[], File) - Static method in class trans.misc.Util

Writes a simple bar format graph for a xxx.gr type graph.

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

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

Writes a String to disk.

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

Writes a String to disk.

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

Writes a String onto the end of a file.

writeSubSeqFasta() - Method in class selex.SelexParams

writeTempFile(Object, HttpServletRequest, String) - Static method in class bioroot.antibody.AntibodyBase

Looks for an uploaded file, writes it to the directory with a tempRNDMWord_FileName, will return the name, or null, or 'Too big'

writeTxtRocFile(RocWindow[], File) - Static method in class trans.roc.ParsePatternedWindows

Writes a chrom, start, stop, score file.