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Packages that use SequenceFormat | |
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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 |
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Classes in org.biojava.bio.program.phred that implement SequenceFormat | |
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class |
PhredFormat
Format object representing Phred Quality files. |
Uses of SequenceFormat in org.biojava.bio.program.ssaha |
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Constructors in org.biojava.bio.program.ssaha with parameters of type SequenceFormat | |
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SequenceStreamer.FileStreamer(SequenceFormat format,
SymbolTokenization toke,
File f)
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SequenceStreamer.FileStreamer(SequenceFormat format,
SymbolTokenization toke,
List files)
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Uses of SequenceFormat in org.biojava.bio.seq.db |
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Methods in org.biojava.bio.seq.db that return SequenceFormat | |
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SequenceFormat |
BioIndex.getFormat()
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SequenceFormat |
EmblCDROMIndexStore.getFormat()
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SequenceFormat |
IndexStore.getFormat()
Retrieve the format of the index file. |
SequenceFormat |
TabIndexStore.getFormat()
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protected abstract SequenceFormat |
WebSequenceDB.getSequenceFormat()
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protected SequenceFormat |
SwissprotSequenceDB.getSequenceFormat()
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protected SequenceFormat |
GenbankSequenceDB.getSequenceFormat()
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SequenceFormat |
NCBISequenceDB.getSequenceFormat()
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protected SequenceFormat |
GenpeptSequenceDB.getSequenceFormat()
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Methods in org.biojava.bio.seq.db with parameters of type SequenceFormat | |
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void |
NCBISequenceDB.setSequenceFormat(SequenceFormat format)
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Constructors in org.biojava.bio.seq.db with parameters of type SequenceFormat | |
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EmblCDROMIndexStore(File pathPrefix,
File divisionLkp,
File entryNamIdx,
SequenceFormat format,
SequenceBuilderFactory factory,
SymbolTokenization parser)
Creates a new EmblCDROMIndexStore backed by a
random access binary index. |
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EmblCDROMIndexStore(File divisionLkp,
File entryNamIdx,
SequenceFormat format,
SequenceBuilderFactory factory,
SymbolTokenization parser)
Creates a new EmblCDROMIndexStore backed by a
random access binary index. |
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NCBISequenceDB(String database,
SequenceFormat format)
Parameterized constructor |
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NCBISequenceDB(String server,
String CGI,
String database,
SequenceFormat format)
Parameterized constructor |
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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 |
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Classes in org.biojava.bio.seq.io that implement SequenceFormat | |
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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 | |
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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 | |
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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 | |
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StreamReader(BufferedReader reader,
SequenceFormat format,
SymbolTokenization symParser,
SequenceBuilderFactory sf)
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StreamReader(InputStream is,
SequenceFormat format,
SymbolTokenization symParser,
SequenceBuilderFactory sf)
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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 |
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Subinterfaces of SequenceFormat in org.biojavax.bio.seq.io | |
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interface |
RichSequenceFormat
Allows a file format to be read/written as RichSequences. |
Classes in org.biojavax.bio.seq.io that implement SequenceFormat | |
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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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