org.expasy.mzjava.proteomics.ms.ident

Class PeptideMatch

java.lang.Object

org.expasy.mzjava.proteomics.ms.ident.PeptideMatch

All Implemented Interfaces:

Comparable<PeptideMatch>, SymbolSequence<AminoAcid>

public class PeptideMatch
extends Object
implements SymbolSequence<AminoAcid>, Comparable<PeptideMatch>

PeptideMatch stores the match information from a peptide spectrum match

Version:

1.0

Author:

Oliver Horlacher

Constructor Summary

Constructors

Constructor and Description
PeptideMatch(AminoAcid... sequence) Create a peptide match given an amino acid sequence
PeptideMatch(List<AminoAcid> sequence) Create a peptide match given an amino acid sequence
PeptideMatch(PeptideSpectrum peptideSpectrum, String scoreName, double score) Construct a PeptideMatch from a peptide spectrum and score.
PeptideMatch(String peptideSequence) Create a peptide match given an amino acid sequence
PeptideMatch(SymbolSequence<AminoAcid> sequence) Create a peptide match given an amino acid esequence

Method Summary

Methods

Modifier and Type	Method and Description
ModificationMatch	addModificationMatch(int index, double modificationMass) Convenience method for adding a ModificationMatch.
ModificationMatch	addModificationMatch(int index, Modification modification) Convenience method for adding a ModificationMatch.
void	addModificationMatch(int index, ModificationMatch modificationMatch) Add a the modificationMatch to the side chain of residue at index
ModificationMatch	addModificationMatch(ModAttachment modAttachment, double modificationMass) Convenience method for adding a ModificationMatch.
ModificationMatch	addModificationMatch(ModAttachment modAttachment, Modification modification) Convenience method for adding a ModificationMatch.
void	addModificationMatch(ModAttachment modAttachment, ModificationMatch modificationMatch) Add a the modificationMatch to either end of the this peptide match.
void	addProteinMatch(PeptideProteinMatch proteinMatch) Add a protein match to this PeptideMatch
void	addProteinMatches(Collection<PeptideProteinMatch> matchCollection) Add all the accessions in proteinAC to this PeptideMatch
void	addScore(String name, double value) Add the score to the score map
int	compareTo(PeptideMatch o)
boolean	containsOnlyProteinMatch(Pattern pattern) Returns true if this PeptideMatch contains only ProteinMatch's that have an accession in which the regex pattern can be found.
boolean	containsOnlyProteinMatch(String regex) Returns true if this PeptideMatch contains only ProteinMatch's that have an accession in which the regex pattern can be found.
boolean	containsProtein(String proteinAcs) Returns true if this PeptideMatch contains the proteinAcs protein accession, false otherwise.
boolean	containsProteinMatch(Pattern pattern) Returns true if this PeptideMatch contains a ProteinMatch that has an accession in which the regex pattern can be found.
boolean	containsProteinMatch(String regex) Returns true if this PeptideMatch contains a ProteinMatch that has an accession in which the regex pattern can be found.
boolean	equals(Object o)
com.google.common.base.Optional<Double>	getMassDiff() Returns the difference between the theoretical and experimental mass.
int	getModificationCount() Returns the number of modifications that theis peptide match has.
List<ModificationMatch>	getModifications(int index, Set<ModAttachment> attachments) Returns a list containing all ModificationMatch for the residue at index that are attached by a ModAttachment contained in the attachments set.
List<ModificationMatch>	getModifications(Set<ModAttachment> attachments) Return a list containing all ModificationMatch for ModAttachment's in the attachments set.
double	getNeutralPeptideMass()
com.google.common.base.Optional<Integer>	getNumMatchedIons() Return the number of ions that are were matched
com.google.common.base.Optional<Integer>	getNumMissedCleavages() Return the number of missed cleavages that the Peptide contains
List<PeptideProteinMatch>	getProteinMatches() Return a reference to the protein accession list
com.google.common.base.Optional<Integer>	getRank() Return the rank of this PeptideMatch
double	getScore(String scoreName) Return the score that is associtaed with scoreName
gnu.trove.map.TObjectDoubleMap<String>	getScoreMap() Returns a reference to the score map
AminoAcid	getSymbol(int index) Returns the symbol at the specified position in this symbol sequence.
com.google.common.base.Optional<Integer>	getTotalNumIons() Return the total number of ions that were generated for the Peptide
int	hashCode()
boolean	hasScore(String scoreName) Returns true if there is a score for scoreName
com.google.common.base.Optional<Boolean>	isRejected() Returns true if this PeptideMatch was rejected, false otherwise
boolean	sameModPeptide(PeptideMatch match) Returns true if this PeptideMatch and match have the same peptide sequence and modifications.
void	setMassDiff(com.google.common.base.Optional<Double> massDiff) Set the difference between the the theoretical and experimental mass
void	setNeutralPeptideMass(double neutralPeptideMass)
void	setNumMatchedIons(com.google.common.base.Optional<Integer> numMatchedIons) Set the number of ions that were matched
void	setNumMissedCleavages(com.google.common.base.Optional<Integer> numMissedCleavages) Set the number of missed cleavages that the Peptide contains
void	setRank(com.google.common.base.Optional<Integer> rank) Set the rank of this PeptideMatch
void	setRejected(com.google.common.base.Optional<Boolean> rejected) Set whether this PeptideMatch was rejected or not
void	setTotalNumIons(com.google.common.base.Optional<Integer> totalNumIons) Set the total number of ion that were generated for the Peptide
int	size() Returns the number of symbols in this symbol sequence.
Peptide	toBarePeptide() Convert this PeptideMatch to a peptide containing only the bare peptide sequence.
Peptide	toPeptide() Convert this PeptideMatch to a peptide
Peptide	toPeptide(ModificationMatchResolver modMatchResolver) Convert this PeptideMatch to a peptide using the supplied modificationMatchResolver to convert ModificationMatch instances to Modifications.
String	toString()
String	toSymbolString() String containing the Symbols

Methods inherited from class java.lang.Object

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

Constructor Detail

PeptideMatch

public PeptideMatch(AminoAcid... sequence)

Create a peptide match given an amino acid sequence

Parameters:

sequence - the amino acid sequence

PeptideMatch

public PeptideMatch(List<AminoAcid> sequence)

Create a peptide match given an amino acid sequence

Parameters:

sequence - the amino acid sequence

PeptideMatch

public PeptideMatch(String peptideSequence)

Create a peptide match given an amino acid sequence

Parameters:

peptideSequence - the amino acid sequence

PeptideMatch

public PeptideMatch(SymbolSequence<AminoAcid> sequence)

Create a peptide match given an amino acid esequence

Parameters:

sequence - the amino acid sequence

PeptideMatch

public PeptideMatch(PeptideSpectrum peptideSpectrum,
            String scoreName,
            double score)

Construct a PeptideMatch from a peptide spectrum and score.

This constructor sets the score and copies the peptide and protein information.

Parameters:

peptideSpectrum - the peptideSequence for which the PeptideMatch is to be created

scoreName - the name of the score

score - the score

Method Detail

addScore

public void addScore(String name,
            double value)

Add the score to the score map

Parameters:

name - the name of the score

value - the value of the score

getScoreMap

public gnu.trove.map.TObjectDoubleMap<String> getScoreMap()

Returns a reference to the score map

Returns:

a reference to the score map

hasScore

public boolean hasScore(String scoreName)

Returns true if there is a score for scoreName

Parameters:

scoreName - the name of the score to test fore

Returns:

true if there is a score for scoreName

getScore

public double getScore(String scoreName)

Return the score that is associtaed with scoreName

Parameters:

scoreName - the name of the score

Returns:

the score that is associtaed with scoreName

Throws:

IllegalArgumentException - if there is no score associated with scoreName

getRank

public com.google.common.base.Optional<Integer> getRank()

Return the rank of this PeptideMatch

Returns:

the rank of this PeptideMatch

setRank

public void setRank(com.google.common.base.Optional<Integer> rank)

Set the rank of this PeptideMatch

Parameters:

rank - the rank of the PeptideMatch

getNumMatchedIons

public com.google.common.base.Optional<Integer> getNumMatchedIons()

Return the number of ions that are were matched

Returns:

the number of ions that are were matched

setNumMatchedIons

public void setNumMatchedIons(com.google.common.base.Optional<Integer> numMatchedIons)

Set the number of ions that were matched

Parameters:

numMatchedIons - the number of ions tha twere matched

getTotalNumIons

public com.google.common.base.Optional<Integer> getTotalNumIons()

Return the total number of ions that were generated for the Peptide

Returns:

the total number of ions that were generated for the Peptide

setTotalNumIons

public void setTotalNumIons(com.google.common.base.Optional<Integer> totalNumIons)

Set the total number of ion that were generated for the Peptide

Parameters:

totalNumIons - the total number of ions

getMassDiff

public com.google.common.base.Optional<Double> getMassDiff()

Returns the difference between the theoretical and experimental mass.

Returns:

the difference between the theoretical and experimental mass

setMassDiff

public void setMassDiff(com.google.common.base.Optional<Double> massDiff)

Set the difference between the the theoretical and experimental mass

Parameters:

massDiff - the mass difference

getNumMissedCleavages

public com.google.common.base.Optional<Integer> getNumMissedCleavages()

Return the number of missed cleavages that the Peptide contains

Returns:

the number of missed cleavages that the Peptide contains

setNumMissedCleavages

public void setNumMissedCleavages(com.google.common.base.Optional<Integer> numMissedCleavages)

Set the number of missed cleavages that the Peptide contains

Parameters:

numMissedCleavages - the number of missed cleavages

isRejected

public com.google.common.base.Optional<Boolean> isRejected()

Returns true if this PeptideMatch was rejected, false otherwise

Returns:

true if this PeptideMatch was rejected, false otherwise

setRejected

public void setRejected(com.google.common.base.Optional<Boolean> rejected)

Set whether this PeptideMatch was rejected or not

Parameters:

rejected - boolean to indicate wether the peptide was rejected or not

getNeutralPeptideMass

public double getNeutralPeptideMass()

setNeutralPeptideMass

public void setNeutralPeptideMass(double neutralPeptideMass)

addProteinMatch

public void addProteinMatch(PeptideProteinMatch proteinMatch)

Add a protein match to this PeptideMatch

Parameters:

proteinMatch - the protein accession to add

addProteinMatches

public void addProteinMatches(Collection<PeptideProteinMatch> matchCollection)

Add all the accessions in proteinAC to this PeptideMatch

Parameters:

matchCollection - collection containing the accessions to add

getProteinMatches

public List<PeptideProteinMatch> getProteinMatches()

Return a reference to the protein accession list

Returns:

a reference to the protein accession list

toString

public String toString()

Overrides:

toString in class Object

sameModPeptide

public boolean sameModPeptide(PeptideMatch match)

Returns true if this PeptideMatch and match have the same peptide sequence and modifications.

Parameters:

match - the PeptideMatch to test

Returns:

true if this PeptideMatch and match have the same peptide sequence and modifications

equals

public boolean equals(Object o)

Overrides:

equals in class Object

hashCode

public int hashCode()

Overrides:

hashCode in class Object

compareTo

public int compareTo(PeptideMatch o)

Specified by:

compareTo in interface Comparable<PeptideMatch>

getSymbol

public AminoAcid getSymbol(int index)

Description copied from interface: SymbolSequence

Returns the symbol at the specified position in this symbol sequence.

Specified by:

getSymbol in interface SymbolSequence<AminoAcid>

Parameters:

index - index of the symbol to return

Returns:

the symbol at the specified position in this symbol sequence

toSymbolString

public String toSymbolString()

Description copied from interface: SymbolSequence

String containing the Symbols

Specified by:

toSymbolString in interface SymbolSequence<AminoAcid>

Returns:

String containing the Symbols

size

public int size()

Description copied from interface: SymbolSequence

Returns the number of symbols in this symbol sequence. If this symbol sequence contains more than Integer.MAX_VALUE symbols, returns Integer.MAX_VALUE.

Specified by:

size in interface SymbolSequence<AminoAcid>

Returns:

the number of symbols in this symbol sequence

addModificationMatch

public void addModificationMatch(int index,
                        ModificationMatch modificationMatch)

Add a the modificationMatch to the side chain of residue at index

Parameters:

index - the index of the reside where the ModificationMatch is to be added

modificationMatch - the ModificationMatch that is to be added

addModificationMatch

public ModificationMatch addModificationMatch(int index,
                                     double modificationMass)

Convenience method for adding a ModificationMatch.

Parameters:

index - the index of the modification

modificationMass - the mass difference due to the modification

Returns:

the ModificationMatch that was added

addModificationMatch

public ModificationMatch addModificationMatch(int index,
                                     Modification modification)

Convenience method for adding a ModificationMatch.

Parameters:

index - the index of the modification

modification - the modification

Returns:

the ModificationMatch that was added

addModificationMatch

public void addModificationMatch(ModAttachment modAttachment,
                        ModificationMatch modificationMatch)

Add a the modificationMatch to either end of the this peptide match. The end is specified busing the modAttachment

Parameters:

modAttachment - specifies which end of the peptide the modificationMatch is to be added

modificationMatch - the ModificationMatch that is to be added

addModificationMatch

public ModificationMatch addModificationMatch(ModAttachment modAttachment,
                                     double modificationMass)

Convenience method for adding a ModificationMatch.

Parameters:

modAttachment - the mod attachment is required to be either ModAttachment.N_TERM or ModAttachment.C_TERM

modificationMass - the mass difference due to the modification

Returns:

the ModificationMatch that was added

addModificationMatch

public ModificationMatch addModificationMatch(ModAttachment modAttachment,
                                     Modification modification)

Convenience method for adding a ModificationMatch.

Parameters:

modAttachment - the mod attachment is required to be either ModAttachment.N_TERM or ModAttachment.C_TERM

modification - the mass modification

Returns:

the ModificationMatch that was added

getModificationCount

public int getModificationCount()

Returns the number of modifications that theis peptide match has.

Returns:

the number of modifications that theis peptide match has

getModifications

public List<ModificationMatch> getModifications(Set<ModAttachment> attachments)

Return a list containing all ModificationMatch for ModAttachment's in the attachments set.

Parameters:

attachments - set containing the ModAttachments that are to be retrieved

Returns:

a list containing all ModificationMatch for ModAttachment's in the attachments set

getModifications

public List<ModificationMatch> getModifications(int index,
                                       Set<ModAttachment> attachments)

Returns a list containing all ModificationMatch for the residue at index that are attached by a ModAttachment contained in the attachments set.

Parameters:

index - the residue index

attachments - set containing the ModAttachments that are to be retrieved

Returns:

a list containing all ModificationMatch for the residue at index that are attached by a ModAttachment contained in the attachments set

toPeptide

public Peptide toPeptide()

Convert this PeptideMatch to a peptide

Returns:

the peptide

Throws:

UnresolvableModificationMatchException - if a modification match cannot be resolved to a modification

toPeptide

public Peptide toPeptide(ModificationMatchResolver modMatchResolver)

Convert this PeptideMatch to a peptide using the supplied modificationMatchResolver to convert ModificationMatch instances to Modifications.

Returns:

the peptide

Throws:

UnresolvableModificationMatchException - if a modification match cannot be resolved to a modification

toBarePeptide

public Peptide toBarePeptide()

Convert this PeptideMatch to a peptide containing only the bare peptide sequence.

Returns:

the peptide

containsProtein

public boolean containsProtein(String proteinAcs)

Returns true if this PeptideMatch contains the proteinAcs protein accession, false otherwise.

Parameters:

proteinAcs - the protein accession to test

Returns:

true if this PeptideMatch contains the proteinAcs protein accession, false otherwise

containsProteinMatch

public boolean containsProteinMatch(String regex)

Returns true if this PeptideMatch contains a ProteinMatch that has an accession in which the regex pattern can be found.

Parameters:

regex - the regex pattern

Returns:

Returns true if this PeptideMatch contains a ProteinMatch that has an accession in which the regex pattern can be found, false otherwise

containsOnlyProteinMatch

public boolean containsOnlyProteinMatch(String regex)

Returns true if this PeptideMatch contains only ProteinMatch's that have an accession in which the regex pattern can be found.

Parameters:

regex - the regex pattern

Returns:

Returns true if this PeptideMatch contains a ProteinMatch that has an accession in which the regex pattern can be found, false otherwise

containsProteinMatch

public boolean containsProteinMatch(Pattern pattern)

Returns true if this PeptideMatch contains a ProteinMatch that has an accession in which the regex pattern can be found.

Parameters:

pattern - the regex pattern

Returns:

Returns true if this PeptideMatch contains a ProteinMatch that has an accession in which the regex pattern can be found, false otherwise

containsOnlyProteinMatch

public boolean containsOnlyProteinMatch(Pattern pattern)

Returns true if this PeptideMatch contains only ProteinMatch's that have an accession in which the regex pattern can be found.

Parameters:

pattern - the regex pattern

Returns:

Returns true if this PeptideMatch contains only ProteinMatch's that has an accession in which the regex pattern can be found, false otherwise