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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)
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SequenceStreamer.FileStreamer(SequenceFormat format,
SymbolTokenization toke,
java.io.File f)
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Uses of SequenceFormat in org.biojava.bio.seq.db |
Methods in org.biojava.bio.seq.db that return SequenceFormat | |
SequenceFormat |
EmblCDROMIndexStore.getFormat()
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SequenceFormat |
TabIndexStore.getFormat()
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protected SequenceFormat |
GenpeptSequenceDB.getSequenceFormat()
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SequenceFormat |
IndexStore.getFormat()
Retrieve the format of the index file. |
SequenceFormat |
NCBISequenceDB.getSequenceFormat()
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protected SequenceFormat |
SwissprotSequenceDB.getSequenceFormat()
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protected abstract SequenceFormat |
WebSequenceDB.getSequenceFormat()
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SequenceFormat |
BioIndex.getFormat()
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protected SequenceFormat |
GenbankSequenceDB.getSequenceFormat()
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Methods in org.biojava.bio.seq.db with parameters of type SequenceFormat | |
void |
NCBISequenceDB.setSequenceFormat(SequenceFormat format)
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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. |
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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. |
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TabIndexStore(java.io.File storeFile,
java.io.File indexFile,
java.lang.String name,
SequenceFormat format,
SequenceBuilderFactory sbFactory,
SymbolTokenization symbolParser)
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NCBISequenceDB(java.lang.String database,
SequenceFormat format)
Parameterized constructor |
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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)
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StreamReader(java.io.BufferedReader reader,
SequenceFormat format,
SymbolTokenization symParser,
SequenceBuilderFactory sf)
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StreamWriter(java.io.OutputStream os,
SequenceFormat format)
Generate a new StreamWriter to the stream os and using format. |
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