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

Packages that use SequenceFormat

Package	Description
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.
org.biojavax.bio.seq.io	Classes to support the I/O of RichSequence and Bioentry objects.

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

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

Modifier and Type	Class	Description
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

Constructor	Description
FileStreamer(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 SequenceFormat

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

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

Modifier and Type	Method	Description
void	NCBISequenceDB.setSequenceFormat(SequenceFormat format)

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

Constructor	Description
EmblCDROMIndexStore(File pathPrefix, File divisionLkp, File entryNamIdx, SequenceFormat format, SequenceBuilderFactory factory, SymbolTokenization parser)	Creates a new EmblCDROMIndexStore backed by a random access binary index.
EmblCDROMIndexStore(File divisionLkp, File entryNamIdx, SequenceFormat format, SequenceBuilderFactory factory, SymbolTokenization parser)	Creates a new EmblCDROMIndexStore backed by a random access binary index.
NCBISequenceDB(String server, String CGI, String database, SequenceFormat format)	Parameterized constructor
NCBISequenceDB(String database, SequenceFormat format)	Parameterized constructor
TabIndexStore(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 SequenceFormat

Modifier and Type	Class	Description
class	EmblLikeFormat	Deprecated. Use org.biojavax.bio.seq.io.EMBLFormat instead
class	FastaFormat	Deprecated. Use org.biojavax.bio.seq.io.FastaFormat
class	GAMEFormat	A rudimentary read-only GAME 1.2 Format object.
class	GenbankFormat	Deprecated. Use org.biojavax.bio.seq.io.GenbankFormat
class	GenbankXmlFormat	Deprecated. Use org.biojavax.bio.seq.io.INSDseqFormat
class	GenpeptFormat	Deprecated. Use org.biojavax.bio.seq.io framework instead

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

Modifier and Type	Method	Description
static SequenceFormat	SeqIOTools.getSequenceFormat(int identifier)	Deprecated. 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

Modifier and Type	Method	Description
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

Constructor	Description
StreamReader(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.io

Modifier and Type	Interface	Description
interface	RichSequenceFormat	Allows a file format to be read/written as RichSequences.

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

Modifier and Type	Class	Description
class	EMBLFormat	Format reader for EMBL files.
class	EMBLxmlFormat	Format reader for EMBLxml files.
class	FastaFormat	Format object representing FASTA files.
class	GenbankFormat	Format reader for GenBank files.
class	INSDseqFormat	Format reader for INSDseq files.
static class	RichSequenceFormat.BasicFormat	Provides a basic format with simple things like line-widths precoded.
static class	RichSequenceFormat.HeaderlessFormat	Provides the basic implementation required for simple header/footer-less files such as Genbank.
class	UniProtFormat	Format reader for UniProt files.
class	UniProtXMLFormat	Format reader for UniProtXML files.