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

E

ENCODE - Static variable in class com.amazon.thirdparty.Base64

Specify encoding.

ENZYMES - Static variable in class bioroot.oligo.OligoBase

Email - class util.gen.Email.

Email(String, String, String, String) - Constructor for class util.gen.Email

Enzyme - class util.bio.digest.Enzyme.

Restriction enzyme information.

Enzyme(String, String, String, String, String) - Constructor for class util.bio.digest.Enzyme

ExonIntron - class util.bio.annotation.ExonIntron.

ExonIntron info.

ExonIntron(int, int) - Constructor for class util.bio.annotation.ExonIntron

ExonIntron(int, int, String) - Constructor for class util.bio.annotation.ExonIntron

ExonIntron(Gff3Feature) - Constructor for class util.bio.annotation.ExonIntron

ExonScoreExtractor - class trans.roc.ExonScoreExtractor.

Extracts scores from xxx.bar files for particular groups of exons.

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

ExportIntergenicRegions - class util.bio.annotation.ExportIntergenicRegions.

ExportIntergenicRegions(String[]) - Constructor for class util.bio.annotation.ExportIntergenicRegions

ExportIntervalData - class trans.main.ExportIntervalData.

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

ExportIntronicRegions - class util.bio.annotation.ExportIntronicRegions.

ExportIntronicRegions(String[]) - Constructor for class util.bio.annotation.ExportIntronicRegions

ExpressedGene - class expr.ExpressedGene.

ExpressedGene(String, Coordinates, float[]) - Constructor for class expr.ExpressedGene

ExpressionScores2CoordinatesViaGFF - class expr.ExpressionScores2CoordinatesViaGFF.

ExpressionScores2CoordinatesViaGFF() - Constructor for class expr.ExpressionScores2CoordinatesViaGFF

ExtractGffFeatures - class util.bio.parsers.gff.ExtractGffFeatures.

ExtractGffFeatures(String[]) - Constructor for class util.bio.parsers.gff.ExtractGffFeatures

ExtractNonOverlappingWindows - class trans.roc.ExtractNonOverlappingWindows.

Parses out non overlapping RocWindows.

ExtractNonOverlappingWindows(File) - Constructor for class trans.roc.ExtractNonOverlappingWindows

ExtractSaveSgrScores - class trans.roc.ExtractSaveSgrScores.

Application for extracting and saving the scores from a .sgr file as a serialized float[].

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

ExtractScoresForRoc - class trans.roc.ExtractScoresForRoc.

Assignes values from an sgr file to a collection of RocWindows.

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

ExtractWords - class bioroot.parsers.ExtractWords.

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

eTag - Variable in class com.amazon.s3.ListEntry

The object's ETag, which can be used for conditional GETs.

encodeBytes(byte[]) - Static method in class com.amazon.thirdparty.Base64

Encodes a byte array into Base64 notation.

encodeBytes(byte[], int) - Static method in class com.amazon.thirdparty.Base64

Encodes a byte array into Base64 notation.

encodeBytes(byte[], int, int) - Static method in class com.amazon.thirdparty.Base64

Encodes a byte array into Base64 notation.

encodeBytes(byte[], int, int, int) - Static method in class com.amazon.thirdparty.Base64

Encodes a byte array into Base64 notation.

encodeFromFile(String) - Static method in class com.amazon.thirdparty.Base64

Convenience method for reading a binary file and base64-encoding it.

encodeObject(Serializable) - Static method in class com.amazon.thirdparty.Base64

Serializes an object and returns the Base64-encoded version of that serialized object.

encodeObject(Serializable, int) - Static method in class com.amazon.thirdparty.Base64

Serializes an object and returns the Base64-encoded version of that serialized object.

encodeToFile(byte[], String) - Static method in class com.amazon.thirdparty.Base64

Convenience method for encoding data to a file.

encryptedCredentialsFile - Variable in class cgar.CommitFiles

engineDigest() - Method in class util.gen.MD5

engineGetDigestLength() - Method in class util.gen.MD5

engineReset() - Method in class util.gen.MD5

engineUpdate(byte) - Method in class util.gen.MD5

engineUpdate(byte[], int, int) - Method in class util.gen.MD5

entries - Variable in class com.amazon.s3.ListAllMyBucketsResponse

A list of Bucket objects, one for each of this account's buckets.

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

A List of ListEntry objects representing the objects in the given bucket.

estimatePValue(double) - Static method in class util.bio.calc.Alignment

Calculates the standard normal cumulative distribution given a z-ratio.

executeCommandLine(String[]) - Static method in class util.gen.IO

Executes tokenized params on command line, use full paths.

executeCommandLine(String[], File) - Static method in class util.gen.IO

Executes tokenized params on command line, use full paths.

executeCommandLine(String[], File, String[]) - Static method in class util.gen.IO

Executes tokenized params on command line, use full paths.

executeCommandLineReturnAll(String[]) - Static method in class util.gen.IO

Executes tokenized params on command line, use full paths.

executeSQL(String) - Method in class bioroot.DBUtil

executeSQL(String) - Method in class util.gen.SQL

executeSQLAdvance(String) - Method in class bioroot.DBUtil

Execute and advance the ResultSet.

executeSQLAdvance(String) - Method in class util.gen.SQL

Execute and advance the ResultSet.

executeSQLUpdate(String) - Method in class bioroot.DBUtil

Fires SQL Update statement returning true if no problems were encountered.

executeSQLUpdate(String) - Method in class util.gen.SQL

Fires SQL Update statement returning true if no problems were encountered.

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

Executes a String of shell script commands via a temp file.

expandFlatTopPeak() - Method in class trans.main.PeakPicker

Attempts to expand the leftIndex and rightIndex

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

Converts a float[] to float[][], must be certain about the number of rows and colmns!

exportIntergenicRegions() - Method in class util.bio.annotation.ExportIntergenicRegions

expr - package expr

Classes and tools related to expression array analysis.

extract(File, boolean) - Method in class util.bio.parsers.gff.DmelRel4Extractor

extract1lqFile(File, File) - Method in class trans.qc.CoordinateExtractor1lq

Fetches coordinates for DESTYPEs of 0, 3, -3, 6, or -6 (Control) and PM -111, 111.

extract1lqFile(File, File) - Static method in class trans.qc.Parser1lq

Fetches coordinates for DESTYPEs of 0, 3, -3, 6, or -6 (Control) and PM -111, 111.

extract1lqFiles() - Method in class trans.qc.CoordinateExtractor1lq

Extracts control oligo information from 1lq files.

extract1lqFiles() - Method in class trans.qc.Parser1lq

Extracts control oligo information from 1lq files.

extractCGNames(ArrayList) - Static method in class trans.anno.AnnotateRegions

Extracts the names of each gene group returning an ArrayList of Strings.

extractCGNames(ArrayList) - Static method in class trans.anno.AnnotateRegionsWithGeneList

Extracts the names of each gene group returning an ArrayList of Strings.

extractChrFiles(File) - Static method in class trans.tpmap.WindowMaker

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

Attempts to extract chr1,2,3...22 or chrX,Y,M,MT from the String.

extractFileName(String) - Static method in class meme.UtilMeme

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

Extracts all files with a given extension from a comma delimited string of files and directories.

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

Extracts all files from a comma delimited string of files and directories.

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

Extracts the full path file names of all the files and directories in a given directory.

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

Extracts the full path file names of all the files in a given directory with a given extension (ie txt or .txt).

extractFiles(String[], String) - Static method in class util.gen.IO

Given full path file or directory names, extracts all files given an extension.

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

Extracts the full path file names of all the files in a given directory with a given extension.

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

Extracts the full path file names of all the files in a given directory with a given extension.

extractGeneGroups(HashMap, String[]) - Static method in class trans.roc.ParsePatternedWindows

Pulls out a sub set of GeneGroups with the names in the geneList.

extractGeneGrps(ArrayList, boolean) - Static method in class trans.anno.BindingRegion

Returns summary line or name for each GeneGrp in ArrayList

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

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

Ditto to extractIDFromConcat but works on String[] returning IDs as a String[].

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

Takes a String like testSlide:33328:testslide desc...:1 or test: gip: 2, splits on the : and looks for ID in the last String[x], if not found it returns zero, otherwise it returns a parsed int.

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

Takes a String like 1: testSlide: 33328:testslide desc etc or 2: test: gip, splits on the : and looks for ID in the first String[x], if not found it returns zero, otherwise it returns a parsed int.

extractLogin(String) - Static method in class bioroot.AccountManagement

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

Assumes the windows are sorted

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

Extracts out the normalized values regenerating the original float[][] except the scores have been quantile normalized.

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

Extracts the full path file names of all the files not directories in a given directory.

extractScores() - Method in class trans.roc.ExonScoreExtractor

extractSegs(ArrayList) - Method in class selex.SeqRead

extractStartEnds(ExonIntron[]) - Static method in class gata.main.GATAUtil

Deep copies start stops from ExonIntron objects to an ArrayList

extractStartEnds(ExonIntron[]) - Static method in class util.bio.annotation.GeneGroup

extractStartEndsInts(ExonIntron[]) - Static method in class gata.main.GATAUtil

extractStartEndsInts(ExonIntron[]) - Static method in class util.bio.annotation.GeneGroup

extractSubRegionOligos(int, int) - Method in class trans.main.Interval

Given a bp start and bp end as well as a larger Oligo[] returns a sub array of the oligos flanking and including the start and end.

extractType() - Method in class bioroot.UserRegistrationBean