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 TypeClassDescriptionclassFormat 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 SequenceFormatGenbankSequenceDB.getSequenceFormat()protected SequenceFormatGenpeptSequenceDB.getSequenceFormat()NCBISequenceDB.getSequenceFormat()protected SequenceFormatSwissprotSequenceDB.getSequenceFormat()protected abstract SequenceFormatWebSequenceDB.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 newEmblCDROMIndexStorebacked by a random access binary index.EmblCDROMIndexStore(File divisionLkp, File entryNamIdx, SequenceFormat format, SequenceBuilderFactory factory, SymbolTokenization parser) Creates a newEmblCDROMIndexStorebacked 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 TypeClassDescriptionclassDeprecated.Use org.biojavax.bio.seq.io.EMBLFormat insteadclassDeprecated.Use org.biojavax.bio.seq.io.FastaFormatclassA rudimentary read-only GAME 1.2 Format object.classDeprecated.Use org.biojavax.bio.seq.io.GenbankFormatclassDeprecated.Use org.biojavax.bio.seq.io.INSDseqFormatclassDeprecated.Use org.biojavax.bio.seq.io framework insteadMethods in org.biojava.bio.seq.io that return SequenceFormatModifier and TypeMethodDescriptionstatic SequenceFormatSeqIOTools.getSequenceFormat(int identifier) Deprecated.getSequenceFormataccepts a value which represents a sequence format and returns the relevantSequenceFormatobject.Methods in org.biojava.bio.seq.io with parameters of type SequenceFormatModifier and TypeMethodDescriptionstatic SequenceBuilderFactorySeqIOTools.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 TypeInterfaceDescriptioninterfaceAllows a file format to be read/written as RichSequences.Classes in org.biojavax.bio.seq.io that implement SequenceFormatModifier and TypeClassDescriptionclassFormat reader for EMBL files.classFormat reader for EMBLxml files.classFormat object representing FASTA files.classFormat reader for GenBank files.classFormat reader for INSDseq files.static classProvides a basic format with simple things like line-widths precoded.static classProvides the basic implementation required for simple header/footer-less files such as Genbank.classFormat reader for UniProt files.classFormat reader for UniProtXML files.