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java.lang.Objectcom.compomics.util.experiment.personalization.ExperimentObject
com.compomics.util.experiment.identification.IdentificationMatch
com.compomics.util.experiment.identification.matches.ProteinMatch
public class ProteinMatch
This class models a protein match.
Created by IntelliJ IDEA. User: Marc Date: Jun 18, 2010 Time: 8:59:02 AM
Constructor Summary | |
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ProteinMatch()
Constructor for the protein match |
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ProteinMatch(Peptide peptide)
Constructor for the protein match |
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ProteinMatch(String proteinAccession)
Constructor for the protein match |
Method Summary | |
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void |
addPeptideMatch(String peptideMatchKey)
add a subordinated peptide match |
void |
addTheoreticProtein(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(String aProtein)
Returns a boolean indicating whether a protein was found in this protein match |
static boolean |
contains(String sharedKey,
String uniqueKey)
Returns a boolean indicating whether a protein match contains another set of matches. |
static String[] |
getAccessions(String key)
Returns a list of accessions from the given key |
String |
getKey()
returns the key of a match |
String |
getMainMatch()
Returns the main match accession after protein inference |
int |
getNProteins()
Returns the number of proteins for this match |
static int |
getNProteins(String matchKey)
Returns the number of proteins for the match corresponding to the given key |
int |
getPeptideCount()
Returns the number of peptides found |
ArrayList<String> |
getPeptideMatches()
getter for the peptide matches |
static String |
getProteinMatchKey(Peptide peptide)
Convenience method which returns the protein key of a peptide |
ArrayList<String> |
getTheoreticProteinsAccessions()
Returns the accessions of the possible theoretic proteins |
boolean |
isDecoy()
methods indicates if the protein match is a decoy one |
static boolean |
isDecoy(String key)
Convenience method indicating whether a match is decoy based on the match key |
void |
setMainMatch(String mainMatch)
Sets the main protein accession after protein inference |
Methods inherited from class com.compomics.util.experiment.personalization.ExperimentObject |
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addUrParam, getParameterKey, getUrParam |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public ProteinMatch()
public ProteinMatch(String proteinAccession)
proteinAccession
- the matching proteinpublic ProteinMatch(Peptide peptide)
peptide
- The corresponding peptide matchMethod Detail |
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public ArrayList<String> getTheoreticProteinsAccessions()
public void addTheoreticProtein(String proteinAccession)
proteinAccession
- the matching proteinpublic String getMainMatch()
public void setMainMatch(String mainMatch)
mainMatch
- the main matchpublic ArrayList<String> getPeptideMatches()
public void addPeptideMatch(String peptideMatchKey)
peptideMatchKey
- a peptide matchpublic int getPeptideCount()
public boolean isDecoy()
public static boolean isDecoy(String key)
key
- the match key
public String getKey()
IdentificationMatch
getKey
in class IdentificationMatch
public static String getProteinMatchKey(Peptide peptide)
peptide
- the considered peptide
public static int getNProteins(String matchKey)
matchKey
- the given key
public int getNProteins()
public static boolean contains(String sharedKey, String uniqueKey)
sharedKey
- the key of the protein of interestuniqueKey
- the key of the protein supposedly contained
public boolean contains(ProteinMatch proteinMatch)
proteinMatch
- another protein match
public boolean contains(String aProtein)
aProtein
- the inspected protein
public static String[] getAccessions(String key)
key
- the given key
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