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java.lang.Objectcom.compomics.util.experiment.personalization.ExperimentObject
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(PeptideMatch peptideMatch)
Constructor for the protein match |
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ProteinMatch(Protein protein)
Constructor for the protein match |
Method Summary | |
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void |
addPeptideMatch(PeptideMatch peptideMatch)
add a subordinated peptide match |
void |
addTheoreticProtein(Protein protein)
setter for the matching protein |
boolean |
contains(Protein aProtein)
Returns a boolean indicating whether a protein was found in this protein match |
boolean |
contains(ProteinMatch proteinMatch)
Returns a boolean indicating whether the protein match contains another set of theoretic proteins. |
ProteinMatch |
getComplementMatch(ProteinMatch proteinMatch)
returns a proteinMatch complementary to the protein match given Example: if the protein match was identified on proteins A, B and C; if the given match was identified on A; the method returns a protein match with B and C. |
String |
getKey()
Returns the index of the protein match |
Protein |
getMainMatch()
Returns the main match after protein inference |
int |
getNProteins()
Returns the number of proteins for this match |
int |
getPeptideCount()
Returns the number of peptides found |
HashMap<String,PeptideMatch> |
getPeptideMatches()
getter for the peptide matches |
static String |
getProteinMatchKey(Peptide peptide)
Convenience method which returns the protein key of a peptide |
int |
getSpectrumCount()
method to get the spectrum count for this protein match |
Protein |
getTheoreticProtein(String accession)
getter for the matching protein |
Set<String> |
getTheoreticProteinsAccessions()
Returns the accessions of the possible theoretic proteins |
boolean |
isDecoy()
methods indicates if the protein match is a decoy one |
void |
setMainMatch(Protein mainMatch)
Sets the main protein after protein inference |
Methods inherited from class com.compomics.util.experiment.personalization.ExperimentObject |
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addUrParam, 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(Protein protein)
protein
- the matching proteinpublic ProteinMatch(PeptideMatch peptideMatch)
peptideMatch
- The corresponding peptide matchesMethod Detail |
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public Protein getTheoreticProtein(String accession)
public Set<String> getTheoreticProteinsAccessions()
public void addTheoreticProtein(Protein protein)
protein
- the matching proteinpublic Protein getMainMatch()
public void setMainMatch(Protein mainMatch)
mainMatch
- the main matchpublic HashMap<String,PeptideMatch> getPeptideMatches()
public void addPeptideMatch(PeptideMatch peptideMatch)
peptideMatch
- a peptide matchpublic int getSpectrumCount()
public int getPeptideCount()
public boolean isDecoy()
public String getKey()
public static String getProteinMatchKey(Peptide peptide)
peptide
- the considered peptide
public int getNProteins()
public boolean contains(ProteinMatch proteinMatch)
proteinMatch
- another protein match
public boolean contains(Protein aProtein)
aProtein
- the inspected protein
public ProteinMatch getComplementMatch(ProteinMatch proteinMatch) throws Exception
proteinMatch
- the given protein match
Exception
- Exception thrown when two spectrum matches from the same search engine are attached to the same spectrum
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