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 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

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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