Uses of Interface
org.biojava.bio.seq.io.SequenceFormat

Packages that use SequenceFormat

org.biojava.bio.program.phred	Parser for Phred output
org.biojava.bio.program.ssaha	SSAHA sequence searching API.
org.biojava.bio.seq.db	Collections of biological sequence data.
org.biojava.bio.seq.io	Classes and interfaces for processing and producing flat-file representations of sequences.

Uses of SequenceFormat in org.biojava.bio.program.phred

Classes in org.biojava.bio.program.phred that implement SequenceFormat

class

PhredFormat 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 SequenceFormat

SequenceStreamer.FileStreamer(SequenceFormat format, SymbolTokenization toke, List files)

SequenceStreamer.FileStreamer(SequenceFormat format, SymbolTokenization toke, File f)

Uses of SequenceFormat in org.biojava.bio.seq.db

Methods in org.biojava.bio.seq.db that return SequenceFormat

protected abstract SequenceFormat	WebSequenceDB.getSequenceFormat()
SequenceFormat	TabIndexStore.getFormat()
protected SequenceFormat	SwissprotSequenceDB.getSequenceFormat()
SequenceFormat	NCBISequenceDB.getSequenceFormat()
SequenceFormat	IndexStore.getFormat() Retrieve the format of the index file.
protected SequenceFormat	GenpeptSequenceDB.getSequenceFormat()
protected SequenceFormat	GenbankSequenceDB.getSequenceFormat()
SequenceFormat	EmblCDROMIndexStore.getFormat()
SequenceFormat	BioIndex.getFormat()

Methods in org.biojava.bio.seq.db with parameters of type SequenceFormat

void	NCBISequenceDB.setSequenceFormat(SequenceFormat format)

Constructors in org.biojava.bio.seq.db with parameters of type SequenceFormat

TabIndexStore(File storeFile, File indexFile, String name, SequenceFormat format, SequenceBuilderFactory sbFactory, SymbolTokenization symbolParser)
Create a new TabIndexStore.

NCBISequenceDB(String database, SequenceFormat format)
Parameterized constructor

NCBISequenceDB(String server, String CGI, String database, SequenceFormat format)
Parameterized constructor

EmblCDROMIndexStore(File divisionLkp, File entryNamIdx, SequenceFormat format, SequenceBuilderFactory factory, SymbolTokenization parser)
Creates a new EmblCDROMIndexStore backed by a random access binary index.

EmblCDROMIndexStore(File pathPrefix, File divisionLkp, File entryNamIdx, SequenceFormat format, SequenceBuilderFactory factory, SymbolTokenization parser)
Creates a new EmblCDROMIndexStore backed by a random access binary index.

Uses of SequenceFormat in org.biojava.bio.seq.io

Classes in org.biojava.bio.seq.io that implement SequenceFormat

class	EmblLikeFormat Format processor for handling EMBL records and similar files.
class	FastaFormat Format object representing FASTA files.
class	GAMEFormat A rudimentary read-only GAME 1.2 Format object.
class	GenbankFormat Format reader for GenBank files.
class	GenpeptFormat This class is necessitated by the deprecation of writeSequence(Sequence seq, String format, PrintStream os) method.

Methods in org.biojava.bio.seq.io that return SequenceFormat

static SequenceFormat

SeqIOTools.getSequenceFormat(int identifier) getSequenceFormat accepts a value which represents a sequence format and returns the relevant SequenceFormat object.

Methods in org.biojava.bio.seq.io with parameters of type SequenceFormat

static SequenceBuilderFactory

SeqIOTools.formatToFactory(SequenceFormat format, Alphabet alpha) Deprecated. as this essentially duplicates the operation available in the method identifyBuilderFactory.

Constructors in org.biojava.bio.seq.io with parameters of type SequenceFormat

StreamWriter(OutputStream os, SequenceFormat format)
Generate a new StreamWriter to the stream os and using format.

StreamReader(InputStream is, SequenceFormat format, SymbolTokenization symParser, SequenceBuilderFactory sf)

StreamReader(BufferedReader reader, SequenceFormat format, SymbolTokenization symParser, SequenceBuilderFactory sf)