public class SingleProteinSequenceProvider extends Object implements SequenceProvider
Constructor and Description |
---|
SingleProteinSequenceProvider(Protein protein)
Constructor.
|
Modifier and Type | Method and Description |
---|---|
Collection<String> |
getAccessions()
Returns all accessions loaded in the provider.
|
HashSet<String> |
getDecoyAccessions()
Returns the decoy accessions.
|
String |
getHeader(String proteinAccession)
Returns the FASTA header of the protein as found in the FASTA file.
|
String |
getSequence(String proteinAccession)
Returns the protein sequence for the given accession.
|
String |
getSubsequence(String accession,
int start,
int end)
Returns the subsequence of the sequence of a given protein.
|
public SingleProteinSequenceProvider(Protein protein)
protein
- the proteinpublic Collection<String> getAccessions()
SequenceProvider
getAccessions
in interface SequenceProvider
public HashSet<String> getDecoyAccessions()
SequenceProvider
getDecoyAccessions
in interface SequenceProvider
public String getSequence(String proteinAccession)
SequenceProvider
getSequence
in interface SequenceProvider
proteinAccession
- the accession of the proteinpublic String getSubsequence(String accession, int start, int end)
SequenceProvider
getSubsequence
in interface SequenceProvider
accession
- the accession of the proteinstart
- the start indexend
- the end indexpublic String getHeader(String proteinAccession)
SequenceProvider
getHeader
in interface SequenceProvider
proteinAccession
- the accession of the proteinCopyright © 2018. All rights reserved.