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

R

REDigest - class util.bio.digest.REDigest.

StandAlone class to perform a restriction digestion on a sequence, a hack, uses as a template.

REDigest() - Constructor for class util.bio.digest.REDigest

RandomRegions - class trans.anno.RandomRegions.

Use to generate random regions of a defined length from a file of regions (chrom, start, stop).

RandomRegions(File) - Constructor for class trans.anno.RandomRegions

RandomRegions(File, File) - Constructor for class trans.anno.RandomRegions

RandomizeLabels - class trans.main.RandomizeLabels.

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

RankSample - class util.gen.RankSample.

RankSample(int, float) - Constructor for class util.gen.RankSample

RankSampleIndexComparator - class util.gen.RankSampleIndexComparator.

Sorts by index, small to large.

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

RankSampleValueComparator - class util.gen.RankSampleValueComparator.

Sorts by value, small to large.

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

RankedFloatArray - class util.gen.RankedFloatArray.

RankedFloatArray(boolean, float[]) - Constructor for class util.gen.RankedFloatArray

RankedSetAnalysis - class trans.graphics.RankedSetAnalysis.

Performs set analysis on genomic regions with a visual display.

RankedSetAnalysis(String[]) - Constructor for class trans.graphics.RankedSetAnalysis

RankedSetDrawFrame - class trans.graphics.RankedSetDrawFrame.

Frame for RankedSetAnalysis.

RankedSetDrawFrame(RankedSetAnalysis) - Constructor for class trans.graphics.RankedSetDrawFrame

RankedSetDrawPanel - class trans.graphics.RankedSetDrawPanel.

Panel with the meat for RankedSetAnalysis

RankedSetDrawPanel(RankedSetAnalysis) - Constructor for class trans.graphics.RankedSetDrawPanel

ReadZip - class util.gen.ReadZip.

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

ReagentBean - class bioroot.ReagentBean.

ReagentBean() - Constructor for class bioroot.ReagentBean

Region - class trans.anno.Region.

Represents a genomic region.

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

RegionComparator - class trans.anno.RegionComparator.

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

Regions2Intervals - class trans.misc.Regions2Intervals.

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

Regions2Intervals() - Constructor for class trans.misc.Regions2Intervals

RenameRWSResults - class util.apps.RenameRWSResults.

Takes the output of RocWindowScanner from the cluster and renames the file

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

RenameWords - class bioroot.parsers.RenameWords.

RenameWords(String[]) - Constructor for class bioroot.parsers.RenameWords

RepeatMaskerToGFF - class util.bio.converters.RepeatMaskerToGFF.

Converts a RepeatMasker output to GFF annotation.

RepeatMaskerToGFF(String[]) - Constructor for class util.bio.converters.RepeatMaskerToGFF

ReplaceWindowScores - class trans.main.ReplaceWindowScores.

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

Response - class com.amazon.s3.Response.

The parent class of all other Responses.

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

RocWindow - class trans.roc.RocWindow.

For holding information about a region for ROC analysis.

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

RocWindowScanner - class trans.roc.RocWindowScanner.

Scans a window array over a range of thresholds and intersects with a list of positives to generate the false positive rate, true positive rate, and false discovery rates.

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

RotateCelFile - class trans.cel.RotateCelFile.

RotateCelFile() - Constructor for class trans.cel.RotateCelFile

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

Returns an array of float[numToSample] populated with randomly picked values from x.

randomize(int) - Method in class expr.CorrelationMaps

randomize(RandomizeLabels.ArrayName[]) - Method in class trans.main.RandomizeLabels

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

Randomizes the array by permutating indexes and swapping.

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

Randomizes the intensities, not between replicas.

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

Randomizes the first array by permutating indexes and swapping.

rangeCheck(double, StringBuffer) - Method in class trans.qc.StatFlag

Checks min max to see if value is contained withing, adds a 'Warning' line to the StringBuffer if so.

rank(float[]) - Method in class util.gen.SpearmanCorrelation

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

Ranks a sorted array of WilcoxonSamplePairs based on absoluteDifference.

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

Ranks a sorted array of WilcoxonSamples based on value.

rankSamples(RankSample[]) - Method in class util.gen.SpearmanCorrelation

Ranks a sorted array of RankSample based on value.

rankedIntersection(GenomicRegion[]) - Static method in class trans.graphics.RankedSetAnalysis

Calculates the number of hits in the ranked matched list.

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

Returns the ratio of each pair.

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

Returns the ratio of each pair, averages replicas.

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

Returns the ratio of each pair.

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

Returns the ratio of each pair.

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

Returns the ratio of each pair.

read() - Method in class com.amazon.thirdparty.Base64.InputStream

Reads enough of the input stream to convert to/from Base64 and returns the next byte.

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

Calls Base64.InputStream.read() repeatedly until the end of stream is reached or len bytes are read.

readBinary(File) - Static method in class util.bio.annotation.Coordinates

Reads a binary Coordinate[] file.

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

Reads a binary sequence file returning gatc or n, lower case.

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

To test your hash.

readSimpleGrBarFile(File) - Static method in class trans.misc.Util

This is a complete hack of Gregg Helt's IGB code to parse bar files.

readTagValPairs(DataInput, int) - Static method in class trans.misc.Util

Dummy method used for parsing binary stream.

reallyRedrawAnnotationPanel(AnnoSpecParams) - Method in class gata.menu.GATAFrame

redrawAlignPanel() - Method in class gata.menu.GATAFrame

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

redrawAnnotationPanels() - Method in class gata.menu.GATAFrame

basically draws annotation twice, once to estimate the size, the second time for real

redrawGlyphPanel(AnnoSpecParams) - Method in class gata.plotter.AlignPanel

reformatSeq(int[][], String, String) - Static method in class gata.plotter.ConservedSeqs

Reformats a sequence given and int[][] containing start stops

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

Calculates a relative difference.

relativeDifferenceToLog2Ratio(float[]) - Static method in class util.gen.Num

Converter

relativeDifferenceToLog2Ratio(double) - Static method in class util.gen.Num

Converter

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

Calculates relative differences.

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

Returns the relative difference of each pair, averages replicas.

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

Throws out data lines that are immediately adjacent and have the same sequence.

removeDuplicateMappingOligos(File) - Method in class trans.tpmap.TPMapDuplicateFilter

Removes any oligo that is found more than once in the bpmap file.

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

Removes the extension from each File in the directory.

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

Removes an extension if found xxx.txt -> xxx.

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

Removes windows that contain < minNumberOligos.

removeLowQualitySegs(int[][]) - Method in class selex.SeqRead

removeMaskedRegions() - Method in class trans.roc.RocWindowScanner

Remove windows that intersect the masked regions.

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

Removes any NaN or Infinite

removeOddSizedSegs(ArrayList) - Method in class selex.SeqRead

removeParent(StrainBean, HashMap, DBUtil) - Static method in class bioroot.strain.NewStrain

removePlasmid(AntibodyBean, HashMap, DBUtil) - Static method in class bioroot.antibody.AntibodyBase

removePlasmid(StrainBean, HashMap, DBUtil) - Static method in class bioroot.strain.NewStrain

removeStrain(AntibodyBean, HashMap, DBUtil) - Static method in class bioroot.antibody.AntibodyBase

removeStrain(HashMap, PlasmidBean, DBUtil) - Static method in class bioroot.plasmid.NewPlasmid

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

Removes zero values and their assoicated values from all arrays.

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

Remove zero values from float array.

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

Provide a float[2][0], will remove zeros from both and there matched pair.

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

Replaces the File pointers to the converted xxx.cela files preserving the input structure.

renameFile(String, String) - Static method in class bioroot.antibody.AntibodyBase

Copies an old file and renames it to tempRndmWrd_name.

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

Renames files containing the toReplace with replaceWith using String.replaceAll(String, String)

renameToACels(File[][]) - Method in class trans.main.T2Parameter

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

Attempts to match the end of the word with the match, case insensitive, replaces it if found, otherwise returns null.

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

reset() - Method in class bioroot.Feature

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

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

resetOrderNumber(HttpServletRequest) - Method in class bioroot.TableHeading

Sets orderNumber from parameter provided, the Param can be converted to an int that is >0.

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

Scans the bins to determine the optimal start and stop for the next round.

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

Runs thru an enzyme array attempting to cut a particular sequence

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

Returns an arraylist of enzymes found to cut the sequence

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

Restriction map a sequence.

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

Resumes encoding of the stream.

reverseAntibodyBeans(AntibodyBean[]) - Static method in class bioroot.antibody.AntibodyBase

Reverses the order of an array of PlasmidBeans.

reverseCompDNA(String) - Static method in class meme.MemeParser

takes DNA seq and reverse comps it ambiguous symbols OK.

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

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

Takes a DNA seq and reverse comps it, ambiguous symbols OK.

reverseOligoBeans(OligoBean[]) - Static method in class bioroot.oligo.OligoBase

Reverses the order of an array of OligoBean.

reversePlasmidBeans(PlasmidBean[]) - Static method in class bioroot.plasmid.PlasmidBase

Reverses the order of an array of PlasmidBeans.

reverseStrainBeans(StrainBean[]) - Static method in class bioroot.strain.StrainBase

Reverses the order of an array of StrainBeans.

rotateCelFile(File, int) - Static method in class trans.cel.RotateCelFile

Rotates a text version cel file 90 degrees clockwise.

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

Rotates a square matrix 90 degrees Clock Wise?

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

Rotates a square matrix 90 degrees CounterClockWise?

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

Rounds a double[] based on number of desired decimals, ie 1 = x.x, 2 = x.xx limited to 6

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

Rounds a double based on number of desired decimals, ie 1 = x.x, 2 = x.xx limited to 6

run() - Method in class gata.aligner.AlignerThread

runMummerExactMatcher(File) - Method in class trans.tpmap.MummerMapper

Runs MUMMER to find perfect matches