Uses of Interface
org.biojava.bio.seq.io.SequenceFormat
Packages that use SequenceFormat
Package
Description
Parser for Phred output
SSAHA sequence searching API.
Collections of biological sequence data.
Classes and interfaces for processing and producing flat-file representations
of sequences.
Classes to support the I/O of RichSequence and
Bioentry objects.
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Uses of SequenceFormat in org.biojava.bio.program.phred
Classes in org.biojava.bio.program.phred that implement SequenceFormatModifier and TypeClassDescriptionclass
Format object representing Phred Quality files. -
Uses of SequenceFormat in org.biojava.bio.program.ssaha
Constructors in org.biojava.bio.program.ssaha with parameters of type SequenceFormatModifierConstructorDescriptionFileStreamer
(SequenceFormat format, SymbolTokenization toke, File f) FileStreamer
(SequenceFormat format, SymbolTokenization toke, List files) -
Uses of SequenceFormat in org.biojava.bio.seq.db
Methods in org.biojava.bio.seq.db that return SequenceFormatModifier and TypeMethodDescriptionBioIndex.getFormat()
EmblCDROMIndexStore.getFormat()
IndexStore.getFormat()
Retrieve the format of the index file.TabIndexStore.getFormat()
protected SequenceFormat
GenbankSequenceDB.getSequenceFormat()
protected SequenceFormat
GenpeptSequenceDB.getSequenceFormat()
NCBISequenceDB.getSequenceFormat()
protected SequenceFormat
SwissprotSequenceDB.getSequenceFormat()
protected abstract SequenceFormat
WebSequenceDB.getSequenceFormat()
Methods in org.biojava.bio.seq.db with parameters of type SequenceFormatConstructors in org.biojava.bio.seq.db with parameters of type SequenceFormatModifierConstructorDescriptionEmblCDROMIndexStore
(File pathPrefix, File divisionLkp, File entryNamIdx, SequenceFormat format, SequenceBuilderFactory factory, SymbolTokenization parser) Creates a newEmblCDROMIndexStore
backed by a random access binary index.EmblCDROMIndexStore
(File divisionLkp, File entryNamIdx, SequenceFormat format, SequenceBuilderFactory factory, SymbolTokenization parser) Creates a newEmblCDROMIndexStore
backed by a random access binary index.NCBISequenceDB
(String server, String CGI, String database, SequenceFormat format) Parameterized constructorNCBISequenceDB
(String database, SequenceFormat format) Parameterized constructorTabIndexStore
(File storeFile, File indexFile, String name, SequenceFormat format, SequenceBuilderFactory sbFactory, SymbolTokenization symbolParser) Create a new TabIndexStore. -
Uses of SequenceFormat in org.biojava.bio.seq.io
Classes in org.biojava.bio.seq.io that implement SequenceFormatModifier and TypeClassDescriptionclass
Deprecated.Use org.biojavax.bio.seq.io.EMBLFormat insteadclass
Deprecated.Use org.biojavax.bio.seq.io.FastaFormatclass
A rudimentary read-only GAME 1.2 Format object.class
Deprecated.Use org.biojavax.bio.seq.io.GenbankFormatclass
Deprecated.Use org.biojavax.bio.seq.io.INSDseqFormatclass
Deprecated.Use org.biojavax.bio.seq.io framework insteadMethods in org.biojava.bio.seq.io that return SequenceFormatModifier and TypeMethodDescriptionstatic SequenceFormat
SeqIOTools.getSequenceFormat
(int identifier) Deprecated.getSequenceFormat
accepts a value which represents a sequence format and returns the relevantSequenceFormat
object.Methods in org.biojava.bio.seq.io with parameters of type SequenceFormatModifier and TypeMethodDescriptionstatic SequenceBuilderFactory
SeqIOTools.formatToFactory
(SequenceFormat format, Alphabet alpha) Deprecated.as this essentially duplicates the operation available in the methodidentifyBuilderFactory
.Constructors in org.biojava.bio.seq.io with parameters of type SequenceFormatModifierConstructorDescriptionStreamReader
(BufferedReader reader, SequenceFormat format, SymbolTokenization symParser, SequenceBuilderFactory sf) StreamReader
(InputStream is, SequenceFormat format, SymbolTokenization symParser, SequenceBuilderFactory sf) StreamWriter
(OutputStream os, SequenceFormat format) Generate a new StreamWriter to the stream os and using format. -
Uses of SequenceFormat in org.biojavax.bio.seq.io
Subinterfaces of SequenceFormat in org.biojavax.bio.seq.ioModifier and TypeInterfaceDescriptioninterface
Allows a file format to be read/written as RichSequences.Classes in org.biojavax.bio.seq.io that implement SequenceFormatModifier and TypeClassDescriptionclass
Format reader for EMBL files.class
Format reader for EMBLxml files.class
Format object representing FASTA files.class
Format reader for GenBank files.class
Format reader for INSDseq files.static class
Provides a basic format with simple things like line-widths precoded.static class
Provides the basic implementation required for simple header/footer-less files such as Genbank.class
Format reader for UniProt files.class
Format reader for UniProtXML files.