Package com.compomics.util.experiment.identification.protein_sequences

Class SingleProteinSequenceProvider

java.lang.Object

com.compomics.util.experiment.identification.protein_sequences.SingleProteinSequenceProvider

All Implemented Interfaces:

SequenceProvider

public class SingleProteinSequenceProvider
extends Object
implements SequenceProvider

Sequence provider for a single protein.

Author:

Marc Vaudel

Constructor Summary

Constructors

Constructor	Description
SingleProteinSequenceProvider()	Empty default constructor.
SingleProteinSequenceProvider(Protein protein)	Constructor.

Method Summary

Modifier and Type	Method	Description
Collection<String>	getAccessions()	Returns all accessions loaded in the provider.
HashSet<String>	getDecoyAccessions()	Returns the decoy accessions.
String	getHeaderAsString(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.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details

SingleProteinSequenceProvider

public SingleProteinSequenceProvider()

Empty default constructor.

SingleProteinSequenceProvider

public SingleProteinSequenceProvider(Protein protein)

Constructor.

Parameters:

protein - the protein

Method Details

getAccessions

public Collection<String> getAccessions()

Description copied from interface: SequenceProvider

Returns all accessions loaded in the provider.

Specified by:

getAccessions in interface SequenceProvider

Returns:

all accessions loaded in the provider

getDecoyAccessions

public HashSet<String> getDecoyAccessions()

Description copied from interface: SequenceProvider

Returns the decoy accessions.

Specified by:

getDecoyAccessions in interface SequenceProvider

Returns:

the decoy accessions

getSequence

public String getSequence(String proteinAccession)

Description copied from interface: SequenceProvider

Returns the protein sequence for the given accession.

Specified by:

getSequence in interface SequenceProvider

Parameters:

proteinAccession - the accession of the protein

Returns:

the sequence of the protein

getSubsequence

public String getSubsequence(String accession,
 int start,
 int end)

Description copied from interface: SequenceProvider

Returns the subsequence of the sequence of a given protein. Indexes are 0-based like for strings and no exception is thrown if indexes are out of bounds, the substring is trimmed.

Specified by:

getSubsequence in interface SequenceProvider

Parameters:

accession - the accession of the protein

start - the start index

end - the end index

Returns:

the subsequence as string

getHeaderAsString

public String getHeaderAsString(String proteinAccession)

Description copied from interface: SequenceProvider

Returns the FASTA header of the protein as found in the FASTA file.

Specified by:

getHeaderAsString in interface SequenceProvider

Parameters:

proteinAccession - the accession of the protein

Returns:

the FASTA header of the protein as found in the FASTA file