public class ProteinMatch extends IdentificationMatch
IdentificationMatch.MatchType
NO_KEY
Constructor and Description |
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ProteinMatch()
Constructor for the protein match.
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ProteinMatch(Peptide peptide,
long peptideMatchKey)
Constructor for the protein match.
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ProteinMatch(String proteinAccession)
Constructor for the protein match.
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Modifier and Type | Method and Description |
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void |
addPeptideMatchKey(long peptideMatchKey)
Add a subordinated peptide key.
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void |
addPeptideMatchKeys(long[] newKeys)
Add a subordinated peptide key.
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boolean |
contains(String aProtein)
Returns a boolean indicating whether a protein was found in this protein
match.
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boolean |
containsPeptide(long peptideKey)
Returns a boolean indicating whether a peptide was found in this protein
match.
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String[] |
getAccessions()
Returns the accessions of the proteins in this match.
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long |
getKey()
Returns the key of a match.
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String |
getLeadingAccession()
Returns the leading accession for this match.
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int |
getNProteins()
Returns the number of proteins for this match.
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int |
getPeptideCount()
Returns the number of peptides found.
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long[] |
getPeptideMatchesKeys()
Getter for the peptide keys.
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static long |
getProteinMatchKey(Peptide peptide)
Convenience method which returns the protein key from a peptide.
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IdentificationMatch.MatchType |
getType()
Returns the type of match.
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boolean |
isDecoy()
Returns a boolean indicating whether the given match is decoy.
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void |
setAccessions(String[] newAccessions)
Sets the accessions of the proteins in this group.
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void |
setDecoy(boolean decoy)
Sets whether the given match is decoy
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void |
setLeadingAccession(String leadingAccession)
Sets the leading accession for this match.
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void |
setPeptideMatchesKeys(long[] peptideMatchKeys)
Sets the peptide keys for this protein match.
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addUrParam, asLong, clearParametersMap, getId, getUrParam, getUrParams, removeUrParam, setId, setUrParams
public ProteinMatch()
public ProteinMatch(String proteinAccession)
proteinAccession
- the matching proteinpublic ProteinMatch(Peptide peptide, long peptideMatchKey)
peptide
- the corresponding peptide matchpeptideMatchKey
- the key of the peptide matchpublic void setAccessions(String[] newAccessions)
newAccessions
- the accessions of the proteins in this grouppublic String[] getAccessions()
public String getLeadingAccession()
public void setLeadingAccession(String leadingAccession)
leadingAccession
- the leading accession for this matchpublic boolean isDecoy()
public void setDecoy(boolean decoy)
decoy
- a boolean indicating whether the given match is decoypublic long[] getPeptideMatchesKeys()
public void addPeptideMatchKey(long peptideMatchKey)
peptideMatchKey
- a peptide keypublic void addPeptideMatchKeys(long[] newKeys)
newKeys
- peptide keyspublic void setPeptideMatchesKeys(long[] peptideMatchKeys)
peptideMatchKeys
- the peptide match keyspublic int getPeptideCount()
public long getKey()
IdentificationMatch
getKey
in class IdentificationMatch
public static long getProteinMatchKey(Peptide peptide)
peptide
- the considered peptidepublic int getNProteins()
public boolean contains(String aProtein)
aProtein
- the protein accessionpublic boolean containsPeptide(long peptideKey)
peptideKey
- the peptide keypublic IdentificationMatch.MatchType getType()
IdentificationMatch
getType
in class IdentificationMatch
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