## 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, java.util.List files)`
`SequenceStreamer.FileStreamer(SequenceFormat format, SymbolTokenization toke, java.io.File f)`

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

Methods in org.biojava.bio.seq.db that return SequenceFormat
`SequenceFormat` `EmblCDROMIndexStore.getFormat()`
`SequenceFormat` `TabIndexStore.getFormat()`
`protected SequenceFormat` `GenpeptSequenceDB.getSequenceFormat()`
`SequenceFormat` `IndexStore.getFormat()` Retrieve the format of the index file.
`SequenceFormat` `NCBISequenceDB.getSequenceFormat()`
`protected SequenceFormat` `SwissprotSequenceDB.getSequenceFormat()`
`protected abstract SequenceFormat` `WebSequenceDB.getSequenceFormat()`
`SequenceFormat` `BioIndex.getFormat()`
`protected SequenceFormat` `GenbankSequenceDB.getSequenceFormat()`

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
`EmblCDROMIndexStore(java.io.File divisionLkp, java.io.File entryNamIdx, SequenceFormat format, SequenceBuilderFactory factory, SymbolTokenization parser)` Creates a new `EmblCDROMIndexStore` backed by a random access binary index.
`EmblCDROMIndexStore(java.io.File pathPrefix, java.io.File divisionLkp, java.io.File entryNamIdx, SequenceFormat format, SequenceBuilderFactory factory, SymbolTokenization parser)` Creates a new `EmblCDROMIndexStore` backed by a random access binary index.
`TabIndexStore(java.io.File storeFile, java.io.File indexFile, java.lang.String name, SequenceFormat format, SequenceBuilderFactory sbFactory, SymbolTokenization symbolParser)`
`NCBISequenceDB(java.lang.String database, SequenceFormat format)` Parameterized constructor
`NCBISequenceDB(java.lang.String server, java.lang.String CGI, java.lang.String database, SequenceFormat format)` Parameterized constructor

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.

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
`StreamReader(java.io.InputStream is, SequenceFormat format, SymbolTokenization symParser, SequenceBuilderFactory sf)`
`StreamReader(java.io.BufferedReader reader, SequenceFormat format, SymbolTokenization symParser, SequenceBuilderFactory sf)`
`StreamWriter(java.io.OutputStream os, SequenceFormat format)` Generate a new StreamWriter to the stream os and using format.