Package | Description |
---|---|
org.biojava.nbio.core.sequence.io | |
org.biojava.nbio.structure.io |
Input and Output of Structures
|
Modifier and Type | Class and Description |
---|---|
class |
GenericFastaHeaderParser<S extends AbstractSequence<C>,C extends Compound>
The default fasta header parser where some headers are well defined based on the source
database which allows us to set the source of the protein sequence and the identifier
that can be used in future implementations to load features from external sources
If the user has a custom header with local data then they can create their own implementation
of a FastaHeaderParserInterface
GenBank gi|gi-number|gb|accession|locus
ENA Data Library gi|gi-number|emb|accession|locus
DDBJ, DNA Database of Japan gi|gi-number|dbj|accession|locus
NBRF PIR pir||entry
Protein Research Foundation prf||name
SWISS-PROT sp|accession|name
Brookhaven Protein Data Bank (1) pdb|entry|chain
Brookhaven Protein Data Bank (2) entry:chain|PDBID|CHAIN|SEQUENCE
PDB EBI PDB:1ECY_A mol:protein length:142 ECOTIN
Patents pat|country|number
GenInfo Backbone Id bbs|number
General database identifier gnl|database|identifier
NCBI Reference Sequence ref|accession|locus
Local Sequence identifier lcl|identifier
|
class |
GenericGenbankHeaderParser<S extends AbstractSequence<C>,C extends Compound> |
class |
PlainFastaHeaderParser<S extends AbstractSequence<C>,C extends Compound>
The plain fasta header takes everything in the header as a single entity.
|
Constructor and Description |
---|
FastaReader(File file,
SequenceHeaderParserInterface<S,C> headerParser,
SequenceCreatorInterface<C> sequenceCreator)
If you are going to use the FileProxyProteinSequenceCreator then you
need to use this constructor because we need details about
the location of the file.
|
FastaReader(InputStream is,
SequenceHeaderParserInterface<S,C> headerParser,
SequenceCreatorInterface<C> sequenceCreator)
If you are going to use FileProxyProteinSequenceCreator then do not use this constructor because we need details about
local file offsets for quick reads.
|
GenbankReader(File file,
SequenceHeaderParserInterface<S,C> headerParser,
SequenceCreatorInterface<C> sequenceCreator)
If you are going to use the FileProxyProteinSequenceCreator then you
need to use this constructor because we need details about
the location of the file.
|
GenbankReader(InputStream is,
SequenceHeaderParserInterface<S,C> headerParser,
SequenceCreatorInterface<C> sequenceCreator)
If you are going to use FileProxyProteinSequenceCreator then do not use this constructor because we need details about
local file offsets for quick reads.
|
Constructor and Description |
---|
FastaStructureParser(File file,
SequenceHeaderParserInterface<ProteinSequence,AminoAcidCompound> headerParser,
SequenceCreatorInterface<AminoAcidCompound> sequenceCreator,
AtomCache cache) |
FastaStructureParser(InputStream is,
SequenceHeaderParserInterface<ProteinSequence,AminoAcidCompound> headerParser,
SequenceCreatorInterface<AminoAcidCompound> sequenceCreator,
AtomCache cache) |
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