## 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.
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
`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, 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
`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
`void` `NCBISequenceDB.setSequenceFormat(SequenceFormat format)`

Constructors in org.biojava.bio.seq.db with parameters of type SequenceFormat
`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
`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
`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
`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(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
`interface` `RichSequenceFormat` Allows a file format to be read/written as RichSequences.

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