A B C D E F G H I L M N O P Q R S T U V W X

A

accept(Object, Object) - Method in class ssbind.FilterByValue

accept(Object, Object) - Method in class ssbind.SubHitFilter

addHitProperty(Object, Object) - Method in class ssbind.Echoer

addHitProperty(Object, Object) - Method in class ssbind.ListSubjects

addHitProperty(Object, Object) - Method in class ssbind.PropertyEchoer

addSearchProperty(Object, Object) - Method in class ssbind.Echoer

addSearchProperty(Object, Object) - Method in class ssbind.PropertyEchoer

addSubHitProperty(Object, Object) - Method in class ssbind.AlignmentBuilder

addSubHitProperty(Object, Object) - Method in class ssbind.Echoer

addSubHitProperty(Object, Object) - Method in class ssbind.PropertyEchoer

addSubHitProperty(Object, Object) - Method in class ssbind.SubHitBuilder

addSubHitProperty(Object, Object) - Method in class ssbind.SubHitFilter

ALIGNMENT - Static variable in class ssbind.AlignmentBuilder

AlignmentBuilder - Class in ssbind

This filter intercepts the querySequence and subjectSequence events to build an alignment.

AlignmentBuilder(SearchContentHandler) - Constructor for class ssbind.AlignmentBuilder

annodb - package annodb

arrangeSBs() - Method in class symbol.PatternDemo

B

backtrack(int, int) - Method in class symbol.PatternDemo

BeadDemo - Class in seqviewer

BeadDemo demonstrates various some of the FeatureRenders which extend AbstractBeadFeatureRenderer.

BeadDemo() - Constructor for class seqviewer.BeadDemo

biosql - package biosql

Blast2HTML - Class in eventbasedparsing

Example application for converting a Blast - like SAX stream to HTML.

Blast2HTML() - Constructor for class eventbasedparsing.Blast2HTML

BlastLike2XML - Class in eventbasedparsing

Blast2XML is an application for the conversion native output from BLAST-like bioinformatics software into an XML format.

BlastLike2XML() - Constructor for class eventbasedparsing.BlastLike2XML

BlastLike2XML - Class in nativeapps

Deprecated. Prior to the biojava1.1 release - use equivalent class in the demo package eventbasedparsing. Classes in this package were deprecated because nativeapps is an unhelpful name.

BlastLike2XML() - Constructor for class nativeapps.BlastLike2XML

Deprecated.

BlastParser - Class in blastxml

BlastParser() - Constructor for class blastxml.BlastParser

blastxml - package blastxml

C

calculate(Location, Location) - Method in interface symbol.TestLocation.BooleanBinaryOp

calculate(Location, Location) - Method in interface symbol.TestLocation.LocationBinaryOp

CircLocTest - package CircLocTest

CircularEmblViewer - Class in seqviewer

Demo for the circular viewer code that loads an embl file.

CircularEmblViewer() - Constructor for class seqviewer.CircularEmblViewer

CircularLocationTester - Class in CircLocTest

This program was developed to test the CircularLocation class.

CircularLocationTester() - Constructor for class CircLocTest.CircularLocationTester

configureBlastN(PrintWriter) - Static method in class eventbasedparsing.Blast2HTML

configureBlastP(PrintWriter) - Static method in class eventbasedparsing.Blast2HTML

configureRenderer(String, PrintWriter) - Static method in class eventbasedparsing.Blast2HTML

CountHits - Class in ssbind

Prints out a count of the total number of hits in a report.

CountHits() - Constructor for class ssbind.CountHits

CountSubHits - Class in ssbind

Prints out a count of the total number of sub hits in a report.

CountSubHits() - Constructor for class ssbind.CountSubHits

createCasino() - Static method in class dp.Dice

CreateDNAFastaHashTable - Class in ssaha

CreateDNAFastaHashTable() - Constructor for class ssaha.CreateDNAFastaHashTable

CreateDNAFastaHashTableCompact - Class in ssaha

Build a SSAHAj hash table

CreateDNAFastaHashTableCompact() - Constructor for class ssaha.CreateDNAFastaHashTableCompact

CreateDNAFastaHashTableLarge - Class in ssaha

CreateDNAFastaHashTableLarge() - Constructor for class ssaha.CreateDNAFastaHashTableLarge

CreateEmblHashTable - Class in ssaha

CreateEmblHashTable() - Constructor for class ssaha.CreateEmblHashTable

CreateEmblHashTableLarge - Class in ssaha

CreateEmblHashTableLarge() - Constructor for class ssaha.CreateEmblHashTableLarge

CreateFAIndex - Class in indexing

CreateFAIndex() - Constructor for class indexing.CreateFAIndex

CreateIndex - Class in indexing

CreateIndex() - Constructor for class indexing.CreateIndex

CreateIndexDB - Class in annodb

Creates an index DB.

CreateIndexDB() - Constructor for class annodb.CreateIndexDB

CreateSPIndex - Class in indexing

CreateSPIndex() - Constructor for class indexing.CreateSPIndex

createSymbolList(int) - Static method in class dist.Tools

Creates a random DNA sequence.

createSymbolList(int) - Static method in class symbol.Tools

Creates a random DNA sequence.

CreateUnigeneFlat - Class in unigene

CreateUnigeneFlat() - Constructor for class unigene.CreateUnigeneFlat

D

das - package das

Dice - Class in dp

This demo file is a simulation of the "The occasionally dishonest casino" example from the book by R.

Dice() - Constructor for class dp.Dice

dist - package dist

dp - package dp

DP demonstration programs.

DummyFromGFF - Class in biosql

DummyFromGFF() - Constructor for class biosql.DummyFromGFF

dump(Location[], TestLocation.BooleanBinaryOp) - Static method in class symbol.TestLocation

dump(Location[], TestLocation.LocationBinaryOp) - Static method in class symbol.TestLocation

E

Echoer - Class in ssbind

Echo the event stream to stdout with prety indenting.

Echoer() - Constructor for class ssbind.Echoer

EmblToGffFasta - Class in gff

Converts an EMBL file into a fasta file for the sequence and a GFF file for the features.

EmblToGffFasta() - Constructor for class gff.EmblToGffFasta

EmblViewer - Class in seqviewer

EmblViewer() - Constructor for class seqviewer.EmblViewer

EmblViewer2 - Class in seqviewer

EmblViewer2() - Constructor for class seqviewer.EmblViewer2

endHeader() - Method in class ssbind.Echoer

endHit() - Method in class ssbind.Echoer

endSearch(String) - Method in class ssaha.ResultPrinter

endSearch() - Method in class ssbind.CountHits

endSearch() - Method in class ssbind.CountSubHits

endSearch() - Method in class ssbind.Echoer

endSubHit() - Method in class ssbind.AlignmentBuilder

endSubHit() - Method in class ssbind.Echoer

endSubHit() - Method in class ssbind.SubHitBuilder

endSubHit() - Method in class ssbind.SubHitFilter

eventbasedparsing - package eventbasedparsing

F

Fasta2XML - Class in eventbasedparsing

Fasta2XML preliminary demo program.

Fasta2XML() - Constructor for class eventbasedparsing.Fasta2XML

FastBeadDemo - Class in seqviewer

FastBeadDemo is just the same as BeadDemo, except that it uses TranslatedSequencePanel as its SequenceRenderContext.

FastBeadDemo() - Constructor for class seqviewer.FastBeadDemo

FetchSeq - Class in seq

Fetch sequences by accession from the NCBI efetch server and dump them as genbank.

FetchSeq() - Constructor for class seq.FetchSeq

fillMatrix() - Method in class symbol.PatternDemo

FilterByValue - Class in ssbind

Filter complete sub hits by the numerical value of some property.

FilterByValue(SearchContentHandler) - Constructor for class ssbind.FilterByValue

G

GappedViewer - Class in seqviewer

--class description--

GappedViewer() - Constructor for class seqviewer.GappedViewer

GCContent - Class in seq

Counts the GC content of a sequence in fasta format

GCContent() - Constructor for class seq.GCContent

GenbankToGffFasta - Class in gff

Converts a Genbank file into a fasta file for the sequence and a GFF file for the features.

GenbankToGffFasta() - Constructor for class gff.GenbankToGffFasta

getKeyName() - Method in class ssbind.FilterByValue

getKeyName() - Method in class ssbind.PropertyEchoer

getMatch() - Method in class symbol.MatrixValue

getMatrixValues() - Method in class symbol.MatrixValue

getMaxVal() - Method in class ssbind.FilterByValue

getMinVal() - Method in class ssbind.FilterByValue

getMoreSearches() - Method in class ssbind.Echoer

getPrefix() - Method in class ssbind.Echoer

getScore() - Method in class symbol.MatrixValue

getTotalHits() - Method in class symbol.PatternDemo

gff - package gff

GFFCompare - Class in gff

GFFCompare() - Constructor for class gff.GFFCompare

GFFFilter - Class in gff

This tests the parsing and writing of GFF features.

GFFFilter() - Constructor for class gff.GFFFilter

GFFMask - Class in gff

GFFMask() - Constructor for class gff.GFFMask

GFFToFeatures - Class in gff

This tests the gff code to check that we can read in features, add them to a sequence, and then print something out.

GFFToFeatures() - Constructor for class gff.GFFToFeatures

Grep - Class in tagvalue

Grep() - Constructor for class tagvalue.Grep

H

hit(int, int, int, int) - Method in class ssaha.ResultPrinter

I

indent() - Method in class ssbind.Echoer

Index - Class in tagvalue

Index() - Constructor for class tagvalue.Index

IndexFastaDB - Class in search

IndexFastaDB will perform Biojava indexing of DNA or protein Fasta format files, creating an IndexedSequenceDB-compliant database.

IndexFastaDB() - Constructor for class search.IndexFastaDB

indexing - package indexing

initialVector(int, int) - Method in class symbol.PatternDemo

L

LargeSequenceTest - Class in biosql

LargeSequenceTest() - Constructor for class biosql.LargeSequenceTest

ListIDs - Class in indexing

ListIDs() - Constructor for class indexing.ListIDs

ListQueries - Class in ssbind

Lists all query sequence names in the report.

ListQueries() - Constructor for class ssbind.ListQueries

ListSubjects - Class in ssbind

Lists all subject sequence names in the report.

ListSubjects() - Constructor for class ssbind.ListSubjects

loadGFF(String) - Static method in class biosql.DummyFromGFF

M

main(String[]) - Static method in class annodb.CreateIndexDB

main(String[]) - Static method in class biosql.DummyFromGFF

main(String[]) - Static method in class biosql.LargeSequenceTest

main(String[]) - Static method in class biosql.SeqDumper

main(String[]) - Static method in class biosql.SeqEMBL

main(String[]) - Static method in class biosql.SeqGFF

main(String[]) - Static method in class biosql.SequenceTest

main(String[]) - Static method in class biosql.UploadFlat

main(String[]) - Static method in class blastxml.BlastParser

args[0] is assumed to be the name of a Blast output file

main(String[]) - Static method in class CircLocTest.CircularLocationTester

main(String[]) - Static method in class das.TestDAS

main(String[]) - Static method in class das.TestDASG

main(String[]) - Static method in class das.TestDASH

main(String[]) - Static method in class das.TestDSN

main(String[]) - Static method in class dist.TestDistribution

main(String[]) - Static method in class dist.TestOrderNAlphabet

main(String[]) - Static method in class dist.TestOrderNDistribution

main(String[]) - Static method in class dp.Dice

main(String[]) - Static method in class dp.PairwiseAlignment

main(String[]) - Static method in class dp.PatternFinder

main(String[]) - Static method in class dp.SearchProfile

main(String[]) - Static method in class dp.ViterbiAlign

main(String[]) - Static method in class eventbasedparsing.Blast2HTML

main(String[]) - Static method in class eventbasedparsing.BlastLike2XML

Converts an file containing the output from bioinformatics software with a "blast-like" format into an XML format.

main(String[]) - Static method in class eventbasedparsing.Fasta2XML

main(String[]) - Static method in class eventbasedparsing.Pdb2XML

Converts an file containing the output from bioinformatics software with a "pdb like" format into an XML format.

main(String[]) - Static method in class eventbasedparsing.TutorialEx1

Takes an XML doc as input and parses it

main(String[]) - Static method in class gff.EmblToGffFasta

main(String[]) - Static method in class gff.GenbankToGffFasta

main(String[]) - Static method in class gff.GFFCompare

main(String[]) - Static method in class gff.GFFFilter

main(String[]) - Static method in class gff.GFFMask

main(String[]) - Static method in class gff.GFFToFeatures

main(String[]) - Static method in class gff.SwissprotToGffFasta

main(String[]) - Static method in class gff.XFF2GFF

main(String[]) - Static method in class indexing.CreateFAIndex

main(String[]) - Static method in class indexing.CreateIndex

main(String[]) - Static method in class indexing.CreateSPIndex

main(String[]) - Static method in class indexing.ListIDs

main(String[]) - Static method in class indexing.ReadRaw

main(String[]) - Static method in class indexing.ReadRawSecondary

main(String[]) - Static method in class nativeapps.BlastLike2XML

Deprecated. Converts an file containing the output from bioinformatics software with a "blast-like" format into an XML format.

main(String[]) - Static method in class nativeapps.Pdb2XML

Deprecated. Converts an file containing the output from bioinformatics software with a "blast-like" format into an XML format.

main(String[]) - Static method in class process.ProcessToolsTest

main(String[]) - Static method in class prot.TestDigestIO

main(String[]) - Static method in class search.IndexFastaDB

main(String[]) - Static method in class seq.FetchSeq

Run the program

main(String[]) - Static method in class seq.GCContent

Run the program

main(String[]) - Static method in class seq.MotifFinder2

Run the Program

main(String[]) - Static method in class seq.ReverseComplement

Run the program

main(String[]) - Static method in class seq.SimpleAssemblyTest

main(String[]) - Static method in class seq.TestEmbl

main(String[]) - Static method in class seq.TestEmbl2

main(String[]) - Static method in class seq.TestGenbank

main(String[]) - Static method in class seq.TestRefSeqPrt

main(String[]) - Static method in class seq.TestSubSequence

main(String[]) - Static method in class seq.TestSwissprot

main(String[]) - Static method in class seq.TestTranslation

main(String[]) - Static method in class seq.UniProtDemo

main(String[]) - Static method in class seqviewer.BeadDemo

main(String[]) - Static method in class seqviewer.CircularEmblViewer

main(String[]) - Static method in class seqviewer.EmblViewer

main(String[]) - Static method in class seqviewer.EmblViewer2

main(String[]) - Static method in class seqviewer.FastBeadDemo

main(String[]) - Static method in class seqviewer.GappedViewer

main(String[]) - Static method in class seqviewer.TraceViewer

main(String[]) - Static method in class ssaha.CreateDNAFastaHashTable

main(String[]) - Static method in class ssaha.CreateDNAFastaHashTableCompact

main(String[]) - Static method in class ssaha.CreateDNAFastaHashTableLarge

main(String[]) - Static method in class ssaha.CreateEmblHashTable

main(String[]) - Static method in class ssaha.CreateEmblHashTableLarge

main(String[]) - Static method in class ssaha.SSAHA

main(String[]) - Static method in class ssaha.SSAHALarge

main(String[]) - Static method in class ssaha.SSAHASeq

main(String[]) - Static method in class ssaha.SSAHASeqLarge

main(String[]) - Static method in class ssbind.ProcessBlastReport

main(String[]) - Static method in class symbol.PatternDemo

main(String[]) - Static method in class symbol.TestAlphabetIndexers

main(String[]) - Static method in class symbol.TestAmbiguity

main(String[]) - Static method in class symbol.TestGappedSymbolList

main(String[]) - Static method in class symbol.TestIndexedIntegers

main(String[]) - Static method in class symbol.TestLocation

main(String[]) - Static method in class symbol.TestOrderNSymbolList

main(String[]) - Static method in class symbol.TestSimpleAlignment

main(String[]) - Static method in class symbol.TestWindowedSymbolList

main(String[]) - Static method in class symbol.WindowCount

main(String[]) - Static method in class tagvalue.Grep

main(String[]) - Static method in class tagvalue.Index

main(String[]) - Static method in class tagvalue.Parse

main(String[]) - Static method in class tagvalue.ParseEmbl

main(String[]) - Static method in class tagvalue.ParseSwissprot

main(String[]) - Static method in class tagvalue.PrintFormat

main(String[]) - Static method in class unigene.CreateUnigeneFlat

main(String[]) - Static method in class unigene.ParseLibInfo

main(String[]) - Static method in class unigene.ParseUnigene

main(String[]) - Static method in class unigene.SearchUnigeneFlat

main(String[]) - Static method in class xff.TestXFFStreaming

MatrixValue - Class in symbol

This class provides data for the some matrix's found in the dp demos.

MatrixValue() - Constructor for class symbol.MatrixValue

MatrixValue(int, boolean) - Constructor for class symbol.MatrixValue

MotifFinder2 - Class in seq

Modified version of MotifFinder.java This program will search a fasta file for a motif.

MotifFinder2() - Constructor for class seq.MotifFinder2

N

nativeapps - package nativeapps

nullModel - Static variable in class dp.SearchProfile

O

ONEMILLION - Static variable in class symbol.PatternDemo

outdent() - Method in class ssbind.Echoer

output(Double, AtomicSymbol) - Static method in class symbol.WindowCount

P

PairwiseAlignment - Class in dp

This demo file is a simple implementation of pairwise-alignment.

PairwiseAlignment() - Constructor for class dp.PairwiseAlignment

Parse - Class in tagvalue

Parse() - Constructor for class tagvalue.Parse

ParseEmbl - Class in tagvalue

ParseEmbl() - Constructor for class tagvalue.ParseEmbl

ParseLibInfo - Class in unigene

ParseLibInfo() - Constructor for class unigene.ParseLibInfo

ParseSwissprot - Class in tagvalue

ParseSwissprot() - Constructor for class tagvalue.ParseSwissprot

ParseUnigene - Class in unigene

ParseUnigene() - Constructor for class unigene.ParseUnigene

PatternDemo - Class in symbol

PatternDemo(Sequence, SymbolList, String, String, String) - Constructor for class symbol.PatternDemo

PatternFinder - Class in dp

PatternFinder() - Constructor for class dp.PatternFinder

Pdb2XML - Class in eventbasedparsing

Pdb2XML is an application for the conversion native output from BLAST-like bioinformatics software into an XML format.

Pdb2XML() - Constructor for class eventbasedparsing.Pdb2XML

Pdb2XML - Class in nativeapps

Deprecated. Prior to the biojava1.1 release - use equivalent class in the demo package eventbasedparsing. Classes in this package were deprecated because nativeapps is an unhelpful name.

Pdb2XML() - Constructor for class nativeapps.Pdb2XML

Deprecated.

printAlignment() - Method in class symbol.PatternDemo

printFeatures(FeatureHolder, PrintStream, String) - Static method in class das.TestDAS

printFeatures(FeatureHolder, FeatureFilter, PrintStream, String) - Static method in class das.TestDASG

printFeatures(FeatureHolder, FeatureFilter, PrintStream, String) - Static method in class das.TestDASH

printFeatures(FeatureHolder) - Static method in class seq.SimpleAssemblyTest

printFeatures(FeatureHolder, PrintWriter, String) - Static method in class seq.SimpleAssemblyTest

printFeatures(FeatureHolder, FeatureFilter, PrintStream, String) - Static method in class seq.TestEmbl2

printFeatures(FeatureHolder, PrintStream, String) - Static method in class seq.TestSubSequence

PrintFormat - Class in tagvalue

PrintFormat() - Constructor for class tagvalue.PrintFormat

printHit() - Method in class symbol.PatternDemo

printMatrix(int) - Method in class symbol.PatternDemo

printPath() - Method in class symbol.PatternDemo

printScores() - Method in class symbol.PatternDemo

printUsage() - Static method in class ssaha.CreateDNAFastaHashTableCompact

probePaths(int, int) - Method in class symbol.PatternDemo

process - package process

ProcessBlastReport - Class in ssbind

Driver script that parses a blast report and pumps the result through a configurable chain of filters and handlers.

ProcessBlastReport() - Constructor for class ssbind.ProcessBlastReport

ProcessToolsTest - Class in process

ProcessToolsTest() - Constructor for class process.ProcessToolsTest

processWindowEvent(WindowEvent) - Method in class CircLocTest.TestFrame

PropertyEchoer - Class in ssbind

Print out the value of a single property.

PropertyEchoer() - Constructor for class ssbind.PropertyEchoer

prot - package prot

Q

QUERY - Static variable in class ssbind.AlignmentBuilder

R

ReadRaw - Class in indexing

ReadRaw() - Constructor for class indexing.ReadRaw

ReadRawSecondary - Class in indexing

ReadRawSecondary() - Constructor for class indexing.ReadRawSecondary

readSequenceDB(File, Alphabet) - Static method in class dp.SearchProfile

readSequenceDB(File, Alphabet) - Static method in class symbol.WindowCount

Create a sequence database from a fasta file.

resetPath(Collection) - Method in class symbol.PatternDemo

resetScores() - Method in class symbol.PatternDemo

ResultPrinter - Class in ssaha

ResultPrinter(DataStore) - Constructor for class ssaha.ResultPrinter

ReverseComplement - Class in seq

Demo of reverse complementing a fasta DNA file

ReverseComplement() - Constructor for class seq.ReverseComplement

S

search - package search

SEARCH_SUB_HIT - Static variable in class ssbind.SubHitBuilder

SearchProfile - Class in dp

SearchProfile() - Constructor for class dp.SearchProfile

SearchUnigeneFlat - Class in unigene

SearchUnigeneFlat() - Constructor for class unigene.SearchUnigeneFlat

seq - package seq

SeqDumper - Class in biosql

SeqDumper() - Constructor for class biosql.SeqDumper

SeqEMBL - Class in biosql

SeqEMBL() - Constructor for class biosql.SeqEMBL

SeqGFF - Class in biosql

SeqGFF() - Constructor for class biosql.SeqGFF

SequenceTest - Class in biosql

SequenceTest() - Constructor for class biosql.SequenceTest

seqviewer - package seqviewer

setDatabaseID(String) - Method in class ssbind.Echoer

setFileSeqIndices() - Method in class symbol.PatternDemo

setKeyName(String) - Method in class ssbind.FilterByValue

setKeyName(String) - Method in class ssbind.PropertyEchoer

setMaxVal(double) - Method in class ssbind.FilterByValue

setMinVal(double) - Method in class ssbind.FilterByValue

setMoreSearches(boolean) - Method in class ssbind.Echoer

setQueryID(String) - Method in class ssbind.Echoer

setQuerySeq(String) - Method in class ssbind.Echoer

setQuerySeq(String) - Method in class ssbind.ListQueries

setSubjectDB(String) - Method in class ssbind.Echoer

sidFailure() - Method in class symbol.PatternDemo

SimpleAssemblyTest - Class in seq

SimpleAssemblyTest() - Constructor for class seq.SimpleAssemblyTest

sp - Static variable in class seqviewer.EmblViewer

sp - Static variable in class seqviewer.EmblViewer2

ssaha - package ssaha

SSAHA - Class in ssaha

SSAHA() - Constructor for class ssaha.SSAHA

SSAHALarge - Class in ssaha

SSAHALarge() - Constructor for class ssaha.SSAHALarge

SSAHASeq - Class in ssaha

SSAHASeq() - Constructor for class ssaha.SSAHASeq

SSAHASeqLarge - Class in ssaha

SSAHASeqLarge() - Constructor for class ssaha.SSAHASeqLarge

ssbind - package ssbind

startBacktrack() - Method in class symbol.PatternDemo

startHeader() - Method in class ssbind.Echoer

startHit() - Method in class ssbind.CountHits

startHit() - Method in class ssbind.Echoer

startSearch(String) - Method in class ssaha.ResultPrinter

startSearch() - Method in class ssbind.CountHits

startSearch() - Method in class ssbind.CountSubHits

startSearch() - Method in class ssbind.Echoer

startSearch() - Method in class symbol.PatternDemo

startSubHit() - Method in class ssbind.CountSubHits

startSubHit() - Method in class ssbind.Echoer

startSubHit() - Method in class ssbind.SubHitBuilder

startSubHit() - Method in class ssbind.SubHitFilter

SubHitBuilder - Class in ssbind

Build SeqSimilaritySearchSubHit instances from the sub hit info.

SubHitBuilder(SearchContentHandler) - Constructor for class ssbind.SubHitBuilder

SubHitFilter - Class in ssbind

Abstract base class for things that will allow or disallow whole sub hit messages through to the next handler.

SubHitFilter(SearchContentHandler) - Constructor for class ssbind.SubHitFilter

SUBJECT - Static variable in class ssbind.AlignmentBuilder

SwissprotToGffFasta - Class in gff

Converts a Swissprot file into a fasta file for the sequence and a GFF file for the features.

SwissprotToGffFasta() - Constructor for class gff.SwissprotToGffFasta

symbol - package symbol

T

tagvalue - package tagvalue

TestAlphabetIndexers - Class in symbol

TestAlphabetIndexers() - Constructor for class symbol.TestAlphabetIndexers

TestAmbiguity - Class in symbol

This demonstrates building an alignment from a set of sequences of the same length.

TestAmbiguity() - Constructor for class symbol.TestAmbiguity

TestDAS - Class in das

TestDAS() - Constructor for class das.TestDAS

TestDASG - Class in das

TestDASG() - Constructor for class das.TestDASG

TestDASH - Class in das

TestDASH() - Constructor for class das.TestDASH

TestDigestIO - Class in prot

TestDigestIO(String, String) - Constructor for class prot.TestDigestIO

Creates new TestDigest2

TestDistribution - Class in dist

TestDistribution() - Constructor for class dist.TestDistribution

TestDSN - Class in das

TestDSN() - Constructor for class das.TestDSN

TestEmbl - Class in seq

Demo reading an EMBL file

TestEmbl() - Constructor for class seq.TestEmbl

TestEmbl2 - Class in seq

Another EMBL demo

TestEmbl2() - Constructor for class seq.TestEmbl2

TestFrame - Class in CircLocTest

TestFrame() - Constructor for class CircLocTest.TestFrame

TestGappedSymbolList - Class in symbol

This demonstrates gapped sequences as a view onto an ungapped sequence.

TestGappedSymbolList() - Constructor for class symbol.TestGappedSymbolList

TestGenbank - Class in seq

Demo GenBank reading

TestGenbank() - Constructor for class seq.TestGenbank

TestIndexedIntegers - Class in symbol

TestIndexedIntegers() - Constructor for class symbol.TestIndexedIntegers

TestLocation - Class in symbol

TestLocation() - Constructor for class symbol.TestLocation

TestLocation.BooleanBinaryOp - Interface in symbol

TestLocation.LocationBinaryOp - Interface in symbol

TestOrderNAlphabet - Class in dist

Demonstration of the using training to obtain the distribution of a n-mer.

TestOrderNAlphabet() - Constructor for class dist.TestOrderNAlphabet

TestOrderNDistribution - Class in dist

Demonstration of the using OrderNDistribution

TestOrderNDistribution() - Constructor for class dist.TestOrderNDistribution

TestOrderNSymbolList - Class in symbol

Demonstration of the OrderNSymbolList class.

TestOrderNSymbolList() - Constructor for class symbol.TestOrderNSymbolList

TestRefSeqPrt - Class in seq

Demo of reading RefSeqProtein

TestRefSeqPrt() - Constructor for class seq.TestRefSeqPrt

TestSimpleAlignment - Class in symbol

This demonstrates building an alignment from a set of sequences of the same length.

TestSimpleAlignment() - Constructor for class symbol.TestSimpleAlignment

TestSubSequence - Class in seq

Demo the use of SubSequence

TestSubSequence() - Constructor for class seq.TestSubSequence

TestSwissprot - Class in seq

SwissProt format has been replaced by Uniprot format.

TestSwissprot() - Constructor for class seq.TestSwissprot

TestTranslation - Class in seq

TestTranslation() - Constructor for class seq.TestTranslation

TestWindowedSymbolList - Class in symbol

Demonstration of the WindowedSymbolList class.

TestWindowedSymbolList() - Constructor for class symbol.TestWindowedSymbolList

TestXFFStreaming - Class in xff

TestXFFStreaming() - Constructor for class xff.TestXFFStreaming

Tools - Class in dist

Common stuff that the demos rely on.

Tools() - Constructor for class dist.Tools

Tools - Class in symbol

Common stuff that the demos rely on.

Tools() - Constructor for class symbol.Tools

TraceViewer - Class in seqviewer

TraceViewer() - Constructor for class seqviewer.TraceViewer

TutorialEx1 - Class in eventbasedparsing

TutorialEx1() - Constructor for class eventbasedparsing.TutorialEx1

U

unigene - package unigene

UniProtDemo - Class in seq

UniProtDemo() - Constructor for class seq.UniProtDemo

updateScores() - Method in class symbol.PatternDemo

UploadFlat - Class in biosql

UploadFlat() - Constructor for class biosql.UploadFlat

usage() - Static method in class symbol.WindowCount

V

ViterbiAlign - Class in dp

This demonstrates aligning a sequence to a model.

ViterbiAlign() - Constructor for class dp.ViterbiAlign

W

WindowCount - Class in symbol

Title: WindowCount Description: A program to find the distribution of nmers in a fasta library Copyright: Copyright (c) 2001 Company: AgResearch

WindowCount() - Constructor for class symbol.WindowCount

X

X_AXIS - Static variable in class symbol.PatternDemo

xff - package xff

XFF2GFF - Class in gff

XFF2GFF() - Constructor for class gff.XFF2GFF

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