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

D

DBUtil - class bioroot.DBUtil.

Utility class to hold database relevant methods and fields, some from Hall and Brown The following is a collection of stuff for interacting with a SQL database First open a connection by calling connectMySQL, then get results with executeSQL, then close the connection with closeConnection.

DBUtil() - Constructor for class bioroot.DBUtil

DBUtil(String) - Constructor for class bioroot.DBUtil

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

Specify decoding.

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

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

Don't break lines when encoding (violates strict Base64 specification)

DeleteMeNow - class bioroot.DeleteMeNow.

DeleteMeNow() - Constructor for class bioroot.DeleteMeNow

Delme2 - class util.apps.Delme2.

Delme2() - Constructor for class util.apps.Delme2

DelmeAligner - class gata.aligner.DelmeAligner.

DelmeAligner() - Constructor for class gata.aligner.DelmeAligner

DestypeIntensityCalculator - class trans.qc.DestypeIntensityCalculator.

DestypeIntensityCalculator() - Constructor for class trans.qc.DestypeIntensityCalculator

DmelCGNameCoordinatePrinter - class trans.anno.DmelCGNameCoordinatePrinter.

Prints genome coordinates for Dmel Rel 4 GFF3 CG names.

DmelCGNameCoordinatePrinter(String[]) - Constructor for class trans.anno.DmelCGNameCoordinatePrinter

DmelRel4Extractor - class util.bio.parsers.gff.DmelRel4Extractor.

Class for building gene models from GFF3Features, specifically tailored to release 4.0 drosophila melanogaster GFF.

DmelRel4Extractor() - Constructor for class util.bio.parsers.gff.DmelRel4Extractor

DrosGeneCollFileParser - class util.bio.parsers.DrosGeneCollFileParser.

Parses and extracts a unique set of gene names from a drosophila gene collection file.

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

dH - Static variable in class util.bio.calc.NucleicAcid

delta H values for dinucleotide pairs.

dS - Static variable in class util.bio.calc.NucleicAcid

delta S values for dinucleotide pairs.

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

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

Very low-level access to decoding ASCII characters in the form of a byte array.

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

Decodes data from Base64 notation, automatically detecting gzip-compressed data and decompressing it.

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

Convenience method for reading a base64-encoded file and decoding it.

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

Convenience method for decoding data to a file.

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

Attempts to decode Base64 data and deserialize a Java Object within.

defaults - Variable in class util.apps.JQSub

delete(String, String, Map) - Method in class com.amazon.s3.AWSAuthConnection

Deletes an object from S3.

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

delete(String[]) - Method in class util.amazon.S3Manager

Attempts to delete keyed objects from S3.

delete(String) - Method in class util.amazon.S3Manager

Attempts to delete keyed object from S3.

deleteAntibody(AntibodyBean, UserBean, DBUtil) - Static method in class bioroot.antibody.AntibodyModify

Attempts to delete an antibody, if sucessful, returns a "" String, otherwise an error message.

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

Scans a hashmap for an antibody prep to delete returns the index number

deleteBucket(String, Map) - Method in class com.amazon.s3.AWSAuthConnection

Deletes a bucket.

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

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

Deletes a directories contents, and then the directory.

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

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

Attempts to delete a file.

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

Attempts to delete a file.

deleteFiles(File[]) - Static method in class util.gen.IO

Attempts to delete the array of File.

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

Deletes files in a given directory with a given extension.

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

Deletes files in a given directory with a given prefix, that are older cutoff.

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

Looks in the given directory for files ending with given String and deletes them.

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

Deletes files in a given directory that don't end in a given extension.

deleteIntersectingIntervals() - Method in class trans.main.IntervalFilter

deleteOligo(OligoBean, UserBean, DBUtil) - Static method in class bioroot.oligo.OligoModify

Attempts to delete an oligo, if sucessful, returns a "" String, otherwise an error message.

deletePlasmid(PlasmidBean, UserBean, DBUtil) - Static method in class bioroot.plasmid.PlasmidModify

Attempts to delete an plasmid, if sucessful, returns a "" String, otherwise an error message.

deleteSpecificIntervals() - Method in class trans.main.IntervalFilter

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

deleteStrain(StrainBean, UserBean, DBUtil) - Static method in class bioroot.strain.StrainModify

Attempts to delete an strain, if sucessful, returns a "" String, otherwise an error message.

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

Scans a hashmap for a use dilution to delete returns the index string or null.

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

The delimiter echoed back from the request.

demoUserId - Static variable in class bioroot.Util

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

Returns the difference of each pair.

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

Returns the difference of each pair.

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

displayName - Variable in class com.amazon.s3.Owner

doGet(HttpServletRequest, HttpServletResponse) - Method in class bioroot.AccountManagement

doGet(HttpServletRequest, HttpServletResponse) - Method in class bioroot.Archive

doGet(HttpServletRequest, HttpServletResponse) - Method in class bioroot.CellType

doGet(HttpServletRequest, HttpServletResponse) - Method in class bioroot.Contact

doGet(HttpServletRequest, HttpServletResponse) - Method in class bioroot.Gene

doGet(HttpServletRequest, HttpServletResponse) - Method in class bioroot.Login

doGet(HttpServletRequest, HttpServletResponse) - Method in class bioroot.Logout

doGet(HttpServletRequest, HttpServletResponse) - Method in class bioroot.Marker

doGet(HttpServletRequest, HttpServletResponse) - Method in class bioroot.Organism

doGet(HttpServletRequest, HttpServletResponse) - Method in class bioroot.Search

doGet(HttpServletRequest, HttpServletResponse) - Method in class bioroot.UserRegistration

doGet(HttpServletRequest, HttpServletResponse) - Method in class bioroot.antibody.AntibodyBase

doGet(HttpServletRequest, HttpServletResponse) - Method in class bioroot.antibody.AntibodyModify

doGet(HttpServletRequest, HttpServletResponse) - Method in class bioroot.antibody.AntibodySpreadSheet

doGet(HttpServletRequest, HttpServletResponse) - Method in class bioroot.antibody.AntibodyViewPreferences

doGet(HttpServletRequest, HttpServletResponse) - Method in class bioroot.antibody.NewAntibody

doGet(HttpServletRequest, HttpServletResponse) - Method in class bioroot.oligo.NewOligo

doGet(HttpServletRequest, HttpServletResponse) - Method in class bioroot.oligo.OligoBase

doGet(HttpServletRequest, HttpServletResponse) - Method in class bioroot.oligo.OligoModify

doGet(HttpServletRequest, HttpServletResponse) - Method in class bioroot.oligo.OligoSpreadSheet

doGet(HttpServletRequest, HttpServletResponse) - Method in class bioroot.oligo.OligoUpload

doGet(HttpServletRequest, HttpServletResponse) - Method in class bioroot.oligo.OligoViewPreferences

doGet(HttpServletRequest, HttpServletResponse) - Method in class bioroot.plasmid.NewPlasmid

doGet(HttpServletRequest, HttpServletResponse) - Method in class bioroot.plasmid.PlasmidBase

doGet(HttpServletRequest, HttpServletResponse) - Method in class bioroot.plasmid.PlasmidModify

doGet(HttpServletRequest, HttpServletResponse) - Method in class bioroot.plasmid.PlasmidSpreadSheet

doGet(HttpServletRequest, HttpServletResponse) - Method in class bioroot.plasmid.PlasmidUpload

doGet(HttpServletRequest, HttpServletResponse) - Method in class bioroot.plasmid.PlasmidViewPreferences

doGet(HttpServletRequest, HttpServletResponse) - Method in class bioroot.strain.NewStrain

doGet(HttpServletRequest, HttpServletResponse) - Method in class bioroot.strain.StrainBase

doGet(HttpServletRequest, HttpServletResponse) - Method in class bioroot.strain.StrainModify

doGet(HttpServletRequest, HttpServletResponse) - Method in class bioroot.strain.StrainSpreadSheet

doGet(HttpServletRequest, HttpServletResponse) - Method in class bioroot.strain.StrainUpload

doGet(HttpServletRequest, HttpServletResponse) - Method in class bioroot.strain.StrainViewPreferences

doPost(HttpServletRequest, HttpServletResponse) - Method in class bioroot.AccountManagement

doPost(HttpServletRequest, HttpServletResponse) - Method in class bioroot.Archive

doPost(HttpServletRequest, HttpServletResponse) - Method in class bioroot.CellType

doPost(HttpServletRequest, HttpServletResponse) - Method in class bioroot.Contact

doPost(HttpServletRequest, HttpServletResponse) - Method in class bioroot.Gene

doPost(HttpServletRequest, HttpServletResponse) - Method in class bioroot.Login

doPost(HttpServletRequest, HttpServletResponse) - Method in class bioroot.Marker

doPost(HttpServletRequest, HttpServletResponse) - Method in class bioroot.Organism

doPost(HttpServletRequest, HttpServletResponse) - Method in class bioroot.Search

doPost(HttpServletRequest, HttpServletResponse) - Method in class bioroot.UserRegistration

doPost(HttpServletRequest, HttpServletResponse) - Method in class bioroot.antibody.AntibodyBase

doPost(HttpServletRequest, HttpServletResponse) - Method in class bioroot.antibody.AntibodyModify

doPost(HttpServletRequest, HttpServletResponse) - Method in class bioroot.antibody.AntibodySpreadSheet

doPost(HttpServletRequest, HttpServletResponse) - Method in class bioroot.antibody.AntibodyViewPreferences

doPost(HttpServletRequest, HttpServletResponse) - Method in class bioroot.antibody.NewAntibody

doPost(HttpServletRequest, HttpServletResponse) - Method in class bioroot.oligo.NewOligo

doPost(HttpServletRequest, HttpServletResponse) - Method in class bioroot.oligo.OligoBase

doPost(HttpServletRequest, HttpServletResponse) - Method in class bioroot.oligo.OligoModify

doPost(HttpServletRequest, HttpServletResponse) - Method in class bioroot.oligo.OligoSpreadSheet

doPost(HttpServletRequest, HttpServletResponse) - Method in class bioroot.oligo.OligoUpload

doPost(HttpServletRequest, HttpServletResponse) - Method in class bioroot.oligo.OligoViewPreferences

doPost(HttpServletRequest, HttpServletResponse) - Method in class bioroot.plasmid.NewPlasmid

doPost(HttpServletRequest, HttpServletResponse) - Method in class bioroot.plasmid.PlasmidBase

doPost(HttpServletRequest, HttpServletResponse) - Method in class bioroot.plasmid.PlasmidModify

doPost(HttpServletRequest, HttpServletResponse) - Method in class bioroot.plasmid.PlasmidSpreadSheet

doPost(HttpServletRequest, HttpServletResponse) - Method in class bioroot.plasmid.PlasmidUpload

doPost(HttpServletRequest, HttpServletResponse) - Method in class bioroot.plasmid.PlasmidViewPreferences

doPost(HttpServletRequest, HttpServletResponse) - Method in class bioroot.strain.NewStrain

doPost(HttpServletRequest, HttpServletResponse) - Method in class bioroot.strain.StrainBase

doPost(HttpServletRequest, HttpServletResponse) - Method in class bioroot.strain.StrainModify

doPost(HttpServletRequest, HttpServletResponse) - Method in class bioroot.strain.StrainSpreadSheet

doPost(HttpServletRequest, HttpServletResponse) - Method in class bioroot.strain.StrainUpload

doPost(HttpServletRequest, HttpServletResponse) - Method in class bioroot.strain.StrainViewPreferences

doubleArrayToString(double[], String) - Static method in class util.gen.Misc

Returns a String separated by separator for each double[i].

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

Converts an array of double to a String with a defined number of decimal places and a delimiter.

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

Converts an array of double to a String with a maximal number of defined decimal places and a delimiter.

download(File, String[], String[]) - Method in class util.amazon.S3Manager

Downloads the keyed objects into the directory as files.

download(String, File, String[], String[]) - Method in class util.amazon.S3Manager

Downloads files from S3 using a different thread.

download(File) - Method in class util.amazon.S3Manager

Uses the file name as the S3 key to fetch and save the file.

download(File[]) - Method in class util.amazon.S3Manager

Uses the file names as the S3 keys to fetch and save the files.

draw(double) - Method in class gata.geneGlyphs.GeneRepGlyph

draw(float, float, float, float, float, ArrayList, float, float, boolean) - Method in class gata.geneGlyphs.GenericGlyph

draw(double) - Method in class gata.geneGlyphs.TransGrpGlyph

draw(Graphics2D) - Method in class trans.graphics.Box

draw(Graphics2D, FontRenderContext, Font) - Method in class trans.graphics.GenomicRegionGlyph

draw(Graphics2D, FontRenderContext, Font) - Method in class trans.graphics.Graph

drawAlignment(Graphics2D) - Method in class gata.aligner.Alignment

Called every time the alignPanel is repaint() ed

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

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

Call each time parameters effecting GenericGlyphs change

drawGlyphPanel(Graphics2D) - Method in class gata.geneGlyphs.GlyphPanel

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

Call each time the scale changes or user alters a glyph viewablility

drawJLabel(Graphics2D, JLabel, float) - Static method in class util.gen.Swing

Draws a JLabel on a Graphics2D.

drawLabels(ArrayList, Font, Graphics2D) - Static method in class gata.main.GATAUtil

drawLines(Line2D.Double[], Graphics2D) - Static method in class gata.main.GATAUtil

draws Shapes

drawTransGrpGlyphs() - Method in class gata.geneGlyphs.GeneRepGlyph