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 and 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 and Description
SequenceStreamer.FileStreamer(SequenceFormat format, SymbolTokenization toke, File f)
SequenceStreamer.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 and Description
SequenceFormat	TabIndexStore.getFormat()
SequenceFormat	IndexStore.getFormat() Retrieve the format of the index file.
SequenceFormat	EmblCDROMIndexStore.getFormat()
SequenceFormat	BioIndex.getFormat()
protected abstract SequenceFormat	WebSequenceDB.getSequenceFormat()
protected SequenceFormat	SwissprotSequenceDB.getSequenceFormat()
SequenceFormat	NCBISequenceDB.getSequenceFormat()
protected SequenceFormat	GenpeptSequenceDB.getSequenceFormat()
protected SequenceFormat	GenbankSequenceDB.getSequenceFormat()

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

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

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

Constructor and 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 database, SequenceFormat format) Parameterized constructor
NCBISequenceDB(String server, String CGI, 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 and 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 and 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 and 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 and 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 and 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 and Description
class	EMBLFormat Format reader for EMBL files.
class	EMBLxmlFormat Format reader for EMBLxml 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.