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

B

BL2Seq - class util.bio.wrappers.BL2Seq.

This is a bit of a hack from the SimpleBlast, expand as needed.

BL2Seq(String) - Constructor for class util.bio.wrappers.BL2Seq

BL2SeqHit - class util.bio.wrappers.BL2SeqHit.

BL2Seq result container.

BL2SeqHit() - Constructor for class util.bio.wrappers.BL2SeqHit

BackGroundOligo - class trans.bkgrnd.BackGroundOligo.

A control oligo spotted multiple times on the array.

BackGroundOligo(String, int[][]) - Constructor for class trans.bkgrnd.BackGroundOligo

Bar2Gr - class trans.misc.Bar2Gr.

Utility to convert simple one graph xxx.bar files to xxx.gr files.

Bar2Gr(String[]) - Constructor for class trans.misc.Bar2Gr

Base64 - class com.amazon.thirdparty.Base64.

Encodes and decodes to and from Base64 notation.

Base64.InputStream - class com.amazon.thirdparty.Base64.InputStream.

A Base64.InputStream will read data from another java.io.InputStream, given in the constructor, and encode/decode to/from Base64 notation on the fly.

Base64.InputStream(InputStream) - Constructor for class com.amazon.thirdparty.Base64.InputStream

Constructs a Base64.InputStream in DECODE mode.

Base64.InputStream(InputStream, int) - Constructor for class com.amazon.thirdparty.Base64.InputStream

Constructs a Base64.InputStream in either ENCODE or DECODE mode.

Base64.OutputStream - class com.amazon.thirdparty.Base64.OutputStream.

A Base64.OutputStream will write data to another java.io.OutputStream, given in the constructor, and encode/decode to/from Base64 notation on the fly.

Base64.OutputStream(OutputStream) - Constructor for class com.amazon.thirdparty.Base64.OutputStream

Constructs a Base64.OutputStream in ENCODE mode.

Base64.OutputStream(OutputStream, int) - Constructor for class com.amazon.thirdparty.Base64.OutputStream

Constructs a Base64.OutputStream in either ENCODE or DECODE mode.

Bed2Gr - class trans.misc.Bed2Gr.

Converts a bed file to multiple gr files.

Bed2Gr() - Constructor for class trans.misc.Bed2Gr

Bin - class trans.roc.Bin.

Score collector for Sgr apps.

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

Bin(double, double) - Constructor for class trans.roc.Bin

Bin - class util.gen.Bin.

Info and methods about a particular bin, used by the Histogram class.

Bin(double, double) - Constructor for class util.gen.Bin

BindingPeak - class trans.main.BindingPeak.

Holds information about a binding peak within an interval.

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

BindingRegion - class trans.anno.BindingRegion.

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

BindingRegion(int, double, String, int, int, int) - Constructor for class trans.anno.BindingRegion

BindingRegion(int, String, int, int) - Constructor for class trans.anno.BindingRegion

BindingRegion(Interval, int) - Constructor for class trans.anno.BindingRegion

BindingRegionComparator - class trans.anno.BindingRegionComparator.

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

BindingRegionGraphPrinter - class trans.main.BindingRegionGraphPrinter.

For printing chromosome specific .sgr files from IntervalPloter .txt picks files.

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

BindingRegionsToGff3 - class trans.anno.BindingRegionsToGff3.

Converts a Binding GenomicRegion file into GFF3 format.

BindingRegionsToGff3() - Constructor for class trans.anno.BindingRegionsToGff3

BindingRegionsToIntervals - class trans.anno.BindingRegionsToIntervals.

Converts binding regions to intervals setting the binding region as the best window and adds 2kb on either side.

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

Blast - class gata.aligner.Blast.

Blast(AlignParams) - Constructor for class gata.aligner.Blast

Blast - class util.bio.wrappers.Blast.

Template to fire and fetch results from the ncbi bl2seq program.

Blast() - Constructor for class util.bio.wrappers.Blast

BlastFilterResult - class trans.tpmap.BlastFilterResult.

Container for a blast result: chromosome, numMatches, exactMatches, oneBPMismatches, startExactMatch.

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

BlastMatcher - class bioroot.BlastMatcher.

BlastMatcher(ResultSet) - Constructor for class bioroot.BlastMatcher

Constructor passed a ResultSet containing an id, name, and sequence; watch order!

BlastMatcher(String) - Constructor for class bioroot.BlastMatcher

BlastResult - class util.bio.wrappers.BlastResult.

Information related to a blast results.

BlastResult() - Constructor for class util.bio.wrappers.BlastResult

Box - class trans.graphics.Box.

Box for IntervalPlotter.

Box(double, double, double, Color) - Constructor for class trans.graphics.Box

BrowseButtonAction - class gata.aligner.BrowseButtonAction.

BrowseButtonAction(JTextField, JFrame, JFileChooser) - Constructor for class gata.aligner.BrowseButtonAction

Bucket - class com.amazon.s3.Bucket.

A class representing a single bucket.

Bucket() - Constructor for class com.amazon.s3.Bucket

Bucket(String, Date) - Constructor for class com.amazon.s3.Bucket

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

baseNumber(char) - Static method in class util.bio.calc.NucleicAcid

Returns 0 for a, 1 for c, 2 for g, 3 for t, -1 for everything else.

baseOverlapsWindow(int, Windows2HeatMapSgr.Window) - Static method in class igb.util.Windows2HeatMapSgr

Is a given base contained within the window?

baseOverlapsWindow(int, Window) - Method in class trans.main.WindowBlockMaker

Is a given base contained within the window?

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

Runs through an array of Sgr[] noting whether it falls in the positive regions or not positive regions

bioroot - package bioroot

bioroot.antibody - package bioroot.antibody

bioroot.oligo - package bioroot.oligo

bioroot.parsers - package bioroot.parsers

bioroot.plasmid - package bioroot.plasmid

bioroot.strain - package bioroot.strain

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

Resets the positive regions to their instantiation state.

blastFASTAFiles(File, File) - Method in class util.bio.wrappers.BL2Seq

Uses BLAST bl2seq program to align two sequences found in the seq files, won't work on windows?

blastForOneBPRepeats(String, String, File) - Static method in class trans.tpmap.TPMapOligoBlastFilter

This has been tweaked to find 1bp mismatches in a 25mer to a genome.

blastIt(String) - Method in class gata.aligner.Blast

blastIt(String, String) - Method in class util.bio.wrappers.SimpleBlast

blastResultToHTML(BlastResult) - Static method in class bioroot.Search

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

Assumes regions are on the same chromosome, and the end base is included, not interbase numbering.

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

Assumes regions are on the same chromosome, and the end base is included, not interbase numbering.

breakAndSaveCelp(File, MapFeature[]) - Static method in class trans.cel.CelProcessor

Given a float[] celp file and the corresponding MapFeature[] will make a minimal

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

breakSaveFeatureArray(ArrayList, MapFeature[], File) - Static method in class trans.cel.CelProcessor

Use this method to break and save a celp float[] file into chromosomal components in a directory named after the celpFile minus the .celp extension.

breakSaveIntensityValues(ArrayList, int[], String) - Static method in class trans.tpmap.MapSplitter

Use this method to break a int[] array into different int[] by chromosome.

breakSaveIntensityValues(ArrayList, float[], String) - Static method in class trans.tpmap.MapSplitter

Use this method to break a float[] array into different float[] by chromosome.

breakSaveIntensityValues(ArrayList, int[][], String) - Static method in class trans.tpmap.MapSplitter

Use this method to break a int[][] array into different int[][] by chromosome.

breakSaveIntensityValues(ArrayList, float[][], String) - Static method in class trans.tpmap.MapSplitter

Use this method to break a float[][] array into different float[][] by chromosome.

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

bucket - Variable in class util.amazon.S3Manager

bucketName - Variable in class cgar.CommitFiles

bucketName - Variable in class util.amazon.S3Manager

buildAndPrintIntrons() - Method in class util.bio.annotation.ExportIntronicRegions

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

Converts a String of "grp1=/my/Dir1,grp2=/my/Dir2, etc that contains directories into a LinkedHashMap.

buildExecuteDoc(Primer3Pick[]) - Method in class util.bio.wrappers.Primer3Wrapper

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

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

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

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

Converts a String of "grp1=/my/file1,grp1=/my/old/file2,grp2=/my/file2, grp2=/my/new/file3,grp3=/my/new/dir/,/my/default etc" to a File[][] where the files have been broken by grouping into different File[].

buildGeneGrp(Gff3Feature) - Method in class util.bio.parsers.gff.DmelRel4Extractor

Creates a new gene group, call this last after having loaded the exons, transcripts, and translations.

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

buildGenericFeature(Gff3Feature) - Method in class util.bio.parsers.gff.DmelRel4Extractor

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

buildHTMLTableRows(String[], String[][], boolean) - Static method in class bioroot.Util

Build HTML table rows.

buildSqlStatement(UserBean, String) - Static method in class bioroot.Archive

Creates a sql statement for super users and standard users returns null for everyone else, lab specific.

buildSqlStatement(String, UserBean, DBUtil, boolean) - Static method in class bioroot.DBUtil

Creates a sql statement given a UserBean and a boolean as to whether to add a DESC to the order by where appropriate.

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

Builds a tpmap file from a mummer results file

buildTabTableRows(String[][]) - Static method in class bioroot.Archive

Build tab delimited table rows.

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

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

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

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

bunZip2(File, File) - Static method in class util.gen.IO

Use to read in xxx.bz2 files directly to a String[].