org.expasy.mzjava.proteomics.ms.ident

Class PeptideProteinMatch

java.lang.Object

org.expasy.mzjava.proteomics.ms.ident.PeptideProteinMatch

public class PeptideProteinMatch
extends Object

Class that stores the information where a peptide matches to a protein.

Has fields for the protein accession, the previous amino acid and the next amino acid. Has two fields which indicate the position of the peptide in the protein (start and end) Peptides that are at the N-term or C-term have "-" as the previous or next amino acid. "?" indicates that the amino acid is unknown

The previous and next AA are wrapped in com.google.common.base.Optional so that it is possible to differentiate between an unknown AA and when the information is not provided.

Version:

sqrt -1

Author:

Oliver Horlacher

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	PeptideProteinMatch.HitType

Constructor Summary

Constructors

Constructor and Description
PeptideProteinMatch(String accession, com.google.common.base.Optional<String> searchDatabase, com.google.common.base.Optional<String> previousAA, com.google.common.base.Optional<String> nextAA, int start, int end, PeptideProteinMatch.HitType hitType) Constructor, none of the parameters can be null The previous and next AA are wrapped in com.google.common.base.Optional so that it is possible to differentiate between a unknown AA and when the information is not available.
PeptideProteinMatch(String accession, com.google.common.base.Optional<String> searchDatabase, com.google.common.base.Optional<String> previousAA, com.google.common.base.Optional<String> nextAA, PeptideProteinMatch.HitType hitType) Constructor, none of the parameters can be null.

Method Summary

Methods

Modifier and Type	Method and Description
boolean	equals(Object o)
String	getAccession() Returns the protein accession number
int	getEnd() Returns the end position of the peptide within the protein.
PeptideProteinMatch.HitType	getHitType() Returns the HitType.
com.google.common.base.Optional<String>	getNextAA() Returns the amino acid that occurs after the end of the peptide.
com.google.common.base.Optional<String>	getPreviousAA() Returns the amino acid that occurs before the start of the peptide.
com.google.common.base.Optional<String>	getSearchDatabase() Returns the search database contains this match.
int	getStart() Returns the start position of the peptide within the protein.
int	hashCode()
boolean	isCTerm() Returns true if the peptide in on the C-Term of the protein, false otherwise
boolean	isNTerm() Returns true if the peptide in on the N-Term of the protein, false otherwise

Methods inherited from class java.lang.Object

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

Constructor Detail

PeptideProteinMatch

public PeptideProteinMatch(String accession,
                   com.google.common.base.Optional<String> searchDatabase,
                   com.google.common.base.Optional<String> previousAA,
                   com.google.common.base.Optional<String> nextAA,
                   PeptideProteinMatch.HitType hitType)

Constructor, none of the parameters can be null.

The previous and next AA are wrapped in com.google.common.base.Optional so that it is possible to differentiate between a unknown AA and when the information is not available.

Parameters:

accession - the protein accession

searchDatabase - the search database

previousAA - the previous amino acid if the peptide is at the N-Term of the protein use "-", if the previous amino acid is unknown use "?" and if the AA information is not given use Optional.absent

nextAA - the next amino acid if the peptide is at the C-Term of the protein use "-", if the next amino acid is unknown use "?" and if the AA information is not given use Optional.absent

hitType - indicate what kind of hit it was. It can be: {TARGET, DECOY, UNKNOWN}

PeptideProteinMatch

public PeptideProteinMatch(String accession,
                   com.google.common.base.Optional<String> searchDatabase,
                   com.google.common.base.Optional<String> previousAA,
                   com.google.common.base.Optional<String> nextAA,
                   int start,
                   int end,
                   PeptideProteinMatch.HitType hitType)

Constructor, none of the parameters can be null

The previous and next AA are wrapped in com.google.common.base.Optional so that it is possible to differentiate between a unknown AA and when the information is not available.

Parameters:

accession - the protein accession

searchDatabase - the search database

previousAA - the previous amino acid if the peptide is at the N-Term of the protein use "-", if the previous amino acid is unknown use "?" and if the AA information is not given use Optional.absent

nextAA - the next amino acid if the peptide is at the C-Term of the protein use "-", if the next amino acid is unknown use "?" and if the AA information is not given use Optional.absent

start - the start position of the peptide within the protein

end - the end position of the peptide within the protein

Method Detail

getAccession

public String getAccession()

Returns the protein accession number

Returns:

the protein accession number

isNTerm

public boolean isNTerm()

Returns true if the peptide in on the N-Term of the protein, false otherwise

Returns:

true if the peptide in on the N-Term of the protein, false otherwise

isCTerm

public boolean isCTerm()

Returns true if the peptide in on the C-Term of the protein, false otherwise

Returns:

true if the peptide in on the C-Term of the protein, false otherwise

getPreviousAA

public com.google.common.base.Optional<String> getPreviousAA()

Returns the amino acid that occurs before the start of the peptide. If the peptide is N-Term on the protein "-" is returned.

Returns:

the amino acid that occurs before the start of the peptide. If the peptide is N-Term on the protein "-" is returned.

getNextAA

public com.google.common.base.Optional<String> getNextAA()

Returns the amino acid that occurs after the end of the peptide. If the peptide is C-Term on the protein "-" is returned.

Returns:

the amino acid that occurs after the end of the peptide. If the peptide is C-Term on the protein "-" is returned.

getStart

public int getStart()

Returns the start position of the peptide within the protein. If the value is not defined, it will be -1.

Returns:

the start position of the peptide within the protein. If the value is not defined, it will be -1.

getEnd

public int getEnd()

Returns the end position of the peptide within the protein. If the value is not defined, it will be -1.

Returns:

the end position of the peptide within the protein. If the value is not defined, it will be -1.

getHitType

public PeptideProteinMatch.HitType getHitType()

Returns the HitType. It can be: {TARGET, DECOY, UNKNOWN}

Returns:

the HitType. It can be: {TARGET, DECOY, UNKNOWN}

getSearchDatabase

public com.google.common.base.Optional<String> getSearchDatabase()

Returns the search database contains this match. If the value is not defined, null

Returns:

the search database contains this match. If the value is not defined, null

equals

public boolean equals(Object o)

Overrides:

equals in class Object

hashCode

public int hashCode()

Overrides:

hashCode in class Object