com.compomics.util.experiment.identification.matches

Class SpectrumMatch

java.lang.Object

com.compomics.util.experiment.personalization.ExperimentObject

com.compomics.util.experiment.identification.IdentificationMatch

com.compomics.util.experiment.identification.matches.SpectrumMatch

All Implemented Interfaces:

Serializable, Cloneable

public class SpectrumMatch
extends IdentificationMatch

This class models a spectrum match.

Author:

Marc Vaudel

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from class com.compomics.util.experiment.identification.IdentificationMatch

IdentificationMatch.MatchType

Constructor Summary

Constructors

Constructor and Description
SpectrumMatch() Constructor for the spectrum match.
SpectrumMatch(String spectrumKey) Constructor for the spectrum match.
SpectrumMatch(String spectrumKey, SpectrumIdentificationAssumption assumption) Constructor for the spectrum match.

Method Summary

Methods

Modifier and Type	Method and Description
void	addHit(int otherAdvocateId, SpectrumIdentificationAssumption otherAssumption, boolean ascendingScore) Add a first hit.
ArrayList<Integer>	getAdvocates() Returns all advocates used referenced by their index.
ArrayList<SpectrumIdentificationAssumption>	getAllAssumptions() Return all assumptions for all identification algorithms as a list.
HashMap<Double,ArrayList<SpectrumIdentificationAssumption>>	getAllAssumptions(int advocateId) Return all assumptions for the specified search engine indexed by their e-value.
PeptideAssumption	getBestPeptideAssumption() Getter for the best peptide assumption.
TagAssumption	getBestTagAssumption() Getter for the best tag assumption.
SpectrumIdentificationAssumption	getFirstHit(int advocateId) Returns the first hit obtained using the specified advocate.
ArrayList<SpectrumIdentificationAssumption>	getFirstHits(int advocateId) Returns a list of the top scoring assumptions for the given advocate.
String	getKey() Returns the key of a match.
SpectrumMatch	getPeptidesFromTags(ProteinTree proteinTree, AminoAcidPattern.MatchingType matchingType, Double massTolerance, boolean scoreInAscendingOrder, ArrayList<String> fixedModifications, ArrayList<String> variableModifications, boolean ascendingScore, boolean reportFixedPtms) Creates a peptide based spectrum match where peptide assumptions are deduced from tag assumptions.
Integer	getSpectrumNumber() Returns the spectrum number in the spectrum file.
IdentificationMatch.MatchType	getType() Returns the type of match.
boolean	hasAssumption() Indicates whether the spectrum match contains a peptide assumption from a search engine.
boolean	hasAssumption(int advocateId) Indicates whether the spectrum match contains a peptide assumption for the given advocate (for example a search engine, see the Advocate class)
void	removeAssumption(SpectrumIdentificationAssumption assumption) Removes an assumption from the mapping.
void	setBestPeptideAssumption(PeptideAssumption bestAssumption) Setter for the best peptide assumption.
void	setBestTagAssumption(TagAssumption bestTagAsssumption) Setter for the best tag assumption.
void	setFirstHit(int advocateId, SpectrumIdentificationAssumption bestAssumption) Sets the best assumption according to the search engine.
void	setKey(String newKey) Replaces the new key.
void	setSpectrumNumber(Integer spectrumNumber) Sets the spectrum number in the spectrum file.

Methods inherited from class com.compomics.util.experiment.personalization.ExperimentObject

addUrParam, getParameterKey, getUrParam

Methods inherited from class java.lang.Object

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

Constructor Detail

SpectrumMatch

public SpectrumMatch()

Constructor for the spectrum match.

SpectrumMatch

public SpectrumMatch(String spectrumKey,
             SpectrumIdentificationAssumption assumption)

Constructor for the spectrum match.

Parameters:

spectrumKey - The matched spectrumKey

assumption - The matching assumption

SpectrumMatch

public SpectrumMatch(String spectrumKey)

Constructor for the spectrum match.

Parameters:

spectrumKey - The matched spectrum key

Method Detail

getBestPeptideAssumption

public PeptideAssumption getBestPeptideAssumption()

Getter for the best peptide assumption.

Returns:

the best peptide assumption for the spectrum

setBestPeptideAssumption

public void setBestPeptideAssumption(PeptideAssumption bestAssumption)

Setter for the best peptide assumption.

Parameters:

bestAssumption - the best peptide assumption for the spectrum

getBestTagAssumption

public TagAssumption getBestTagAssumption()

Getter for the best tag assumption.

Returns:

the best tag assumption for the spectrum

setBestTagAssumption

public void setBestTagAssumption(TagAssumption bestTagAsssumption)

Setter for the best tag assumption.

Parameters:

bestTagAsssumption - the best tag assumption for the spectrum

getKey

public String getKey()

Description copied from class: IdentificationMatch

Returns the key of a match.

Specified by:

getKey in class IdentificationMatch

Returns:

the key of a match

getAllAssumptions

public HashMap<Double,ArrayList<SpectrumIdentificationAssumption>> getAllAssumptions(int advocateId)

Return all assumptions for the specified search engine indexed by their e-value.

Parameters:

advocateId - the desired advocate ID

Returns:

all assumptions

getAllAssumptions

public ArrayList<SpectrumIdentificationAssumption> getAllAssumptions()

Return all assumptions for all identification algorithms as a list.

Returns:

all assumptions

addHit

public void addHit(int otherAdvocateId,
          SpectrumIdentificationAssumption otherAssumption,
          boolean ascendingScore)

Add a first hit.

Parameters:

otherAdvocateId - the index of the new advocate

otherAssumption - the new identification assumption

ascendingScore - indicates whether the score is ascending when hits get better

getFirstHit

public SpectrumIdentificationAssumption getFirstHit(int advocateId)

Returns the first hit obtained using the specified advocate.

Parameters:

advocateId - the specified advocate index

Returns:

the first hit

getFirstHits

public ArrayList<SpectrumIdentificationAssumption> getFirstHits(int advocateId)

Returns a list of the top scoring assumptions for the given advocate.

Parameters:

advocateId - the index of the advocate of interest

Returns:

a list of the top scoring assumptions for the given advocate

setFirstHit

public void setFirstHit(int advocateId,
               SpectrumIdentificationAssumption bestAssumption)

Sets the best assumption according to the search engine.

Parameters:

advocateId - the search engine index

bestAssumption - the best assumption

getAdvocates

public ArrayList<Integer> getAdvocates()

Returns all advocates used referenced by their index.

Returns:

all advocates used

getType

public IdentificationMatch.MatchType getType()

Description copied from class: IdentificationMatch

Returns the type of match.

Specified by:

getType in class IdentificationMatch

Returns:

the type of match

setKey

public void setKey(String newKey)

Replaces the new key. The key of the PSM should always be the same as the spectrum key it links to.

Parameters:

newKey - the new key

getSpectrumNumber

public Integer getSpectrumNumber()

Returns the spectrum number in the spectrum file. Returns null if not implemented (for versions older than 3.4.17 for instance).

Returns:

the spectrum number in the spectrum file

setSpectrumNumber

public void setSpectrumNumber(Integer spectrumNumber)

Sets the spectrum number in the spectrum file.

Parameters:

spectrumNumber - the spectrum number in the spectrum file

removeAssumption

public void removeAssumption(SpectrumIdentificationAssumption assumption)

Removes an assumption from the mapping. Note: this does not affect the first hit map.

Parameters:

assumption - the peptide assumption to remove

hasAssumption

public boolean hasAssumption()

Indicates whether the spectrum match contains a peptide assumption from a search engine.

Returns:

a boolean indicating whether the spectrum match contains an assumption

hasAssumption

public boolean hasAssumption(int advocateId)

Indicates whether the spectrum match contains a peptide assumption for the given advocate (for example a search engine, see the Advocate class)

Parameters:

advocateId - The index of the advocate

Returns:

a boolean indicating whether the spectrum match contains a peptide assumption for the given advocate

getPeptidesFromTags

public SpectrumMatch getPeptidesFromTags(ProteinTree proteinTree,
                                AminoAcidPattern.MatchingType matchingType,
                                Double massTolerance,
                                boolean scoreInAscendingOrder,
                                ArrayList<String> fixedModifications,
                                ArrayList<String> variableModifications,
                                boolean ascendingScore,
                                boolean reportFixedPtms)
                                  throws IOException,
                                         InterruptedException,
                                         ClassNotFoundException,
                                         SQLException

Creates a peptide based spectrum match where peptide assumptions are deduced from tag assumptions. The original tag assumption is added to the peptide match as refinement parameter

Parameters:

proteinTree - the protein tree to use to map tags to peptides

matchingType - the sequence matching type

massTolerance - the mass tolerance to use

scoreInAscendingOrder - boolean indicating whether the tag score is in the ascending order; ie the higher the score, the better the match.

fixedModifications - the fixed modifications to account for

variableModifications - the variable modifications to account for

ascendingScore - indicates whether the score is ascending when hits get better

reportFixedPtms - a boolean indicating whether fixed PTMs should be reported in the Peptide object

Returns:

a new spectrum match containing the peptide assumptions made from the tag assumptions.

Throws:

IOException

InterruptedException

ClassNotFoundException

SQLException