com.compomics.util.experiment.identification.matches

Class ProteinMatch

java.lang.Object

com.compomics.util.experiment.personalization.ExperimentObject

com.compomics.util.experiment.identification.IdentificationMatch

com.compomics.util.experiment.identification.matches.ProteinMatch

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable

public class ProteinMatch
extends IdentificationMatch

This class models a protein 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

Field Summary

Fields

Modifier and Type	Field and Description
static double	maxX The maximal share of 'X' allowed in a peptide sequence.
static java.lang.String	PROTEIN_KEY_SPLITTER The splitter in the key between spectrumFile and spectrumTitle.

Constructor Summary

Constructors

Constructor and Description
ProteinMatch() Constructor for the protein match.
ProteinMatch(Peptide peptide, java.lang.String peptideMatchKey) Constructor for the protein match.
ProteinMatch(java.lang.String proteinAccession) Constructor for the protein match.

Method Summary

Methods

Modifier and Type	Method and Description
void	addPeptideMatch(java.lang.String peptideMatchKey) Add a subordinated peptide key.
void	addTheoreticProtein(java.lang.String proteinAccession) Setter for the matching protein.
boolean	contains(ProteinMatch proteinMatch) Returns a boolean indicating whether the protein match contains another set of theoretic proteins.
boolean	contains(java.lang.String aProtein) Returns a boolean indicating whether a protein was found in this protein match.
static boolean	contains(java.lang.String sharedKey, java.lang.String uniqueKey) Returns a boolean indicating whether a protein match contains another set of matches.
static java.lang.String[]	getAccessions(java.lang.String key) Returns a list of accessions from the given key.
static java.util.ArrayList<java.lang.String>	getCommonProteins(java.lang.String group1, java.lang.String group2) Returns the common proteins between two protein groups.
java.lang.String	getKey() returns the key of a match.
java.lang.String	getMainMatch() Returns the main match accession after protein inference.
int	getNProteins() Returns the number of proteins for this match.
static int	getNProteins(java.lang.String matchKey) Returns the number of proteins for the match corresponding to the given.
static java.util.ArrayList<java.lang.String>	getOtherProteins(java.lang.String group1, java.lang.String group2) Returns the proteins in a group (group1) which are not in another group (group2).
int	getPeptideCount() Returns the number of peptides found.
java.util.ArrayList<java.lang.String>	getPeptideMatches() Getter for the peptide keys.
static java.lang.String	getProteinMatchKey(Peptide peptide) Convenience method which returns the protein key of a peptide.
java.util.ArrayList<java.lang.String>	getTheoreticProteinsAccessions() Returns the accessions of the possible theoretic proteins.
IdentificationMatch.MatchType	getType() Returns the type of match.
boolean	hasEnzymaticPeptide(java.lang.String accession, Enzyme enzyme, AminoAcidPattern.MatchingType matchingType, java.lang.Double massTolerance) Indicates whether the protein group has an enzymatic peptide when considering the given accession as main accession.
boolean	isDecoy() Method indicates if the protein match is a decoy one.
static boolean	isDecoy(java.lang.String key) Convenience method indicating whether a match is decoy based on the match key.
void	setMainMatch(java.lang.String mainMatch) Sets the main protein accession after protein inference.

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

Field Detail

PROTEIN_KEY_SPLITTER

public static final java.lang.String PROTEIN_KEY_SPLITTER

The splitter in the key between spectrumFile and spectrumTitle.

See Also:

Constant Field Values

maxX

public static final double maxX

The maximal share of 'X' allowed in a peptide sequence. 0.25 means that less than 25% the amino acids can be 'X'

See Also:

Constant Field Values

Constructor Detail

ProteinMatch

public ProteinMatch()

Constructor for the protein match.

ProteinMatch

public ProteinMatch(java.lang.String proteinAccession)
             throws java.lang.IllegalArgumentException

Constructor for the protein match.

Parameters:

proteinAccession - the matching protein

Throws:

java.lang.IllegalArgumentException

ProteinMatch

public ProteinMatch(Peptide peptide,
            java.lang.String peptideMatchKey)
             throws java.io.IOException,
                    java.sql.SQLException,
                    java.lang.ClassNotFoundException,
                    java.lang.InterruptedException

Constructor for the protein match. Note: proteins must be set for the peptide

Parameters:

peptide - the corresponding peptide match

peptideMatchKey - the key of the peptide match

Throws:

java.io.IOException

java.sql.SQLException

java.lang.ClassNotFoundException

java.lang.InterruptedException

Method Detail

getTheoreticProteinsAccessions

public java.util.ArrayList<java.lang.String> getTheoreticProteinsAccessions()

Returns the accessions of the possible theoretic proteins.

Returns:

the accessions of the possible theoretic proteins

addTheoreticProtein

public void addTheoreticProtein(java.lang.String proteinAccession)

Setter for the matching protein.

Parameters:

proteinAccession - the matching protein

getMainMatch

public java.lang.String getMainMatch()

Returns the main match accession after protein inference.

Returns:

the main match accession after protein inference

setMainMatch

public void setMainMatch(java.lang.String mainMatch)

Sets the main protein accession after protein inference.

Parameters:

mainMatch - the main match

getPeptideMatches

public java.util.ArrayList<java.lang.String> getPeptideMatches()

Getter for the peptide keys.

Returns:

subordinated peptide keys

addPeptideMatch

public void addPeptideMatch(java.lang.String peptideMatchKey)

Add a subordinated peptide key.

Parameters:

peptideMatchKey - a peptide key

getPeptideCount

public int getPeptideCount()

Returns the number of peptides found.

Returns:

the number of peptides found

isDecoy

public boolean isDecoy()

Method indicates if the protein match is a decoy one.

Returns:

boolean indicating if the protein match is a decoy one

isDecoy

public static boolean isDecoy(java.lang.String key)

Convenience method indicating whether a match is decoy based on the match key. Note: the sequence database should be loaded in the sequence factory

Parameters:

key - the match key

Returns:

a boolean indicating whether a match is decoy

getKey

public java.lang.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

getProteinMatchKey

public static java.lang.String getProteinMatchKey(Peptide peptide)
                                           throws java.io.IOException,
                                                  java.sql.SQLException,
                                                  java.lang.ClassNotFoundException,
                                                  java.lang.InterruptedException

Convenience method which returns the protein key of a peptide. Note: proteins must be set for the peptide.

Parameters:

peptide - the considered peptide

Returns:

the protein match key

Throws:

java.io.IOException

java.sql.SQLException

java.lang.ClassNotFoundException

java.lang.InterruptedException

getNProteins

public static int getNProteins(java.lang.String matchKey)

Returns the number of proteins for the match corresponding to the given. key.

Parameters:

matchKey - the given key

Returns:

the number of proteins for this match

getNProteins

public int getNProteins()

Returns the number of proteins for this match.

Returns:

the number of proteins for this match

contains

public static boolean contains(java.lang.String sharedKey,
               java.lang.String uniqueKey)

Returns a boolean indicating whether a protein match contains another set of matches.

Parameters:

sharedKey - the key of the protein of interest

uniqueKey - the key of the protein supposedly contained

Returns:

a boolean indicating whether a protein match contains another set of matches.

getOtherProteins

public static java.util.ArrayList<java.lang.String> getOtherProteins(java.lang.String group1,
                                                     java.lang.String group2)

Returns the proteins in a group (group1) which are not in another group (group2).

Parameters:

group1 - the key of the shared group

group2 - the key of the unique group

Returns:

list of the accessions in the search group which are not in the unique group

getCommonProteins

public static java.util.ArrayList<java.lang.String> getCommonProteins(java.lang.String group1,
                                                      java.lang.String group2)

Returns the common proteins between two protein groups.

Parameters:

group1 - key of the first group

group2 - key of the second group

Returns:

a list of common keys

contains

public boolean contains(ProteinMatch proteinMatch)

Returns a boolean indicating whether the protein match contains another set of theoretic proteins.

Parameters:

proteinMatch - another protein match

Returns:

a boolean indicating whether the protein match contains another set of theoretic proteins

contains

public boolean contains(java.lang.String aProtein)

Returns a boolean indicating whether a protein was found in this protein match.

Parameters:

aProtein - the inspected protein

Returns:

a boolean indicating whether a protein was found in this protein match

getAccessions

public static java.lang.String[] getAccessions(java.lang.String key)

Returns a list of accessions from the given key.

Parameters:

key - the given key

Returns:

the corresponding list of accessions

hasEnzymaticPeptide

public boolean hasEnzymaticPeptide(java.lang.String accession,
                          Enzyme enzyme,
                          AminoAcidPattern.MatchingType matchingType,
                          java.lang.Double massTolerance)
                            throws java.io.IOException,
                                   java.lang.IllegalArgumentException,
                                   java.lang.InterruptedException,
                                   java.io.FileNotFoundException,
                                   java.lang.ClassNotFoundException

Indicates whether the protein group has an enzymatic peptide when considering the given accession as main accession.

Parameters:

accession - the candidate main accession

enzyme - the enzyme used

matchingType - the matching type

massTolerance - the mass tolerance for matching type 'indistiguishibleAminoAcids'. Can be null otherwise

Returns:

true if the main accession generates an enzymatic peptide

Throws:

java.io.IOException

java.lang.IllegalArgumentException

java.lang.InterruptedException

java.io.FileNotFoundException

java.lang.ClassNotFoundException

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