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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
addFeatureProperty(Object, Object) - Method in class game.SeqIOTatler
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
addSequenceProperty(Object, Object) - Method in class game.SeqIOTatler
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
addSymbols(Alphabet, Symbol[], int, int) - Method in class game.SeqIOTatler
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
AlignProteins - Class in performance
  An example that aligns two protein structures.
AlignProteins() - Constructor for class performance.AlignProteins
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 `FeatureRender`s 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

calcPhiPsi(Structure) - Method in class structure.PhiPsiCalculation
  calculate Phi and Psi angles for the AminoAcids in the first chain of a structure
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
endFeature() - Method in class game.SeqIOTatler
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
endSequence() - Method in class game.SeqIOTatler
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

game - package game
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
getStructureFromFile(String) - Static method in class performance.AlignProteins
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
LoadStructure - Class in structure
  a simple demo to demonstrating how to load a PDB file
LoadStructure() - Constructor for class structure.LoadStructure
loadStructure(String) - Method in class structure.LoadStructure
loadStructureById() - Method in class structure.LoadStructure
  access a structure from a directory by using a PDB code.

## 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 game.TestGAME
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 performance.AlignProteins
main(String[]) - Static method in class performance.ReadFasta
  The program takes two args: the first is the file name of the Fasta file.
main(String[]) - Static method in class performance.ReadFastaX
main(String[]) - Static method in class performance.ReadFastaX2
main(String[]) - Static method in class performance.ReverseComplement
main(String[]) - Static method in class performance.SmithWatermanExample
  This method computes a pairwise local alignment between two given sequences and prints the result on the standard output stream.
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 structure.LoadStructure
main(String[]) - Static method in class structure.PDBView
main(String[]) - Static method in class structure.PhiPsiCalculation
main(String[]) - Static method in class structure.SuperimposeStructures
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.
PDBView - Class in structure
  A simple utility class that checks if JMol is installed, and if yes loads the PDB file that has been given as an argument
PDBView() - Constructor for class structure.PDBView
performance - package performance
PhiPsiCalculation - Class in structure
  a demo showing how to calculate Phi and Psi angles for a protein structure.
PhiPsiCalculation() - Constructor for class structure.PhiPsiCalculation
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
printHelp() - Static method in class structure.PDBView
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

ReadFasta - Class in performance
  Read a FASTA file and print the length of all sequences in the file.
ReadFasta() - Constructor for class performance.ReadFasta
ReadFastaX - Class in performance
  Read a FASTA file and print the length of all sequences in the file.
ReadFastaX() - Constructor for class performance.ReadFastaX
ReadFastaX2 - Class in performance
  Demo class that reads all chromosomes of Drosophila and prints out their sizes.
ReadFastaX2() - Constructor for class performance.ReadFastaX2
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.
readStructureFromStream() - Method in class structure.LoadStructure
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 performance
  Read DNA sequence and write their reverse complement.
ReverseComplement() - Constructor for class performance.ReverseComplement
ReverseComplement - Class in seq
  Demo of reverse complementing a fasta DNA file
ReverseComplement() - Constructor for class seq.ReverseComplement
run() - Method in class structure.SuperimposeStructures

## 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
SeqIOTatler - Class in game
  dumps events being passed to the class
SeqIOTatler() - Constructor for class game.SeqIOTatler
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
setName(String) - Method in class game.SeqIOTatler
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
setText(String) - Method in class performance.UserDisplay
show(String) - Method in class structure.PDBView
sidFailure() - Method in class symbol.PatternDemo
SimpleAssemblyTest - Class in seq
SimpleAssemblyTest() - Constructor for class seq.SimpleAssemblyTest
SmithWatermanExample - Class in performance
SmithWatermanExample() - Constructor for class performance.SmithWatermanExample
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
startFeature(Feature.Template) - Method in class game.SeqIOTatler
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
startSequence() - Method in class game.SeqIOTatler
startSubHit() - Method in class ssbind.CountSubHits
startSubHit() - Method in class ssbind.Echoer
startSubHit() - Method in class ssbind.SubHitBuilder
startSubHit() - Method in class ssbind.SubHitFilter
structure - package structure
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
SuperimposeStructures - Class in structure
  A demo that show how to calculate structure superimpositions
SuperimposeStructures() - Constructor for class structure.SuperimposeStructures
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
TestGAME - Class in game
TestGAME() - Constructor for class game.TestGAME
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
UserDisplay - Class in performance
UserDisplay() - Constructor for class performance.UserDisplay

## 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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