Uses of Interface org.biojava.bio.seq.io.SequenceFormat (BioJava-1.5-beta API)

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

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