public class SpectrumMatch extends IdentificationMatch
IdentificationMatch.MatchType
Constructor and Description |
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SpectrumMatch()
Constructor for the spectrum match.
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SpectrumMatch(java.lang.String spectrumKey)
Constructor for the spectrum match.
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SpectrumMatch(java.lang.String spectrumKey,
PeptideAssumption assumption)
Constructor for the spectrum match.
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Modifier and Type | Method and Description |
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void |
addHit(int otherAdvocateId,
PeptideAssumption otherAssumption)
Add a first hit.
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java.util.ArrayList<java.lang.Integer> |
getAdvocates()
Returns all advocates used referenced by their index.
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java.util.ArrayList<PeptideAssumption> |
getAllAssumptions()
Return all assumptions for all search engines as a list.
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java.util.HashMap<java.lang.Double,java.util.ArrayList<PeptideAssumption>> |
getAllAssumptions(int advocateId)
Return all assumptions for the specified search engine indexed by their
e-value.
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PeptideAssumption |
getBestAssumption()
Getter for the best assumption.
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PeptideAssumption |
getFirstHit(int advocateId)
Returns the first hit obtained using the specified advocate.
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java.lang.String |
getKey()
returns the key of a match.
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java.lang.Integer |
getSpectrumNumber()
Returns the spectrum number in the spectrum file.
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IdentificationMatch.MatchType |
getType()
Returns the type of match.
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boolean |
hasAssumption()
Indicates whether the spectrum match contains a peptide assumption from a
search engine.
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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)
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void |
removeAssumption(PeptideAssumption peptideAssumption)
Removes an assumption from the mapping
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void |
setBestAssumption(PeptideAssumption bestAssumption)
Setter for the best assumption.
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void |
setFirstHit(int advocateId,
PeptideAssumption peptideAssumption)
Sets the best peptideAssumption according to the search engine.
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void |
setKey(java.lang.String newKey)
Replaces the new key.
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void |
setSpectrumNumber(java.lang.Integer spectrumNumber)
Sets the spectrum number in the spectrum file
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addUrParam, getParameterKey, getUrParam
public SpectrumMatch()
public SpectrumMatch(java.lang.String spectrumKey, PeptideAssumption assumption)
spectrumKey
- The matched spectrumKeyassumption
- The matching peptide assumptionpublic SpectrumMatch(java.lang.String spectrumKey)
spectrumKey
- The matched spectrum keypublic PeptideAssumption getBestAssumption()
public void setBestAssumption(PeptideAssumption bestAssumption)
bestAssumption
- the best assumption for the spectrumpublic java.lang.String getKey()
IdentificationMatch
getKey
in class IdentificationMatch
public java.util.HashMap<java.lang.Double,java.util.ArrayList<PeptideAssumption>> getAllAssumptions(int advocateId)
advocateId
- the desired advocate IDpublic java.util.ArrayList<PeptideAssumption> getAllAssumptions()
public void addHit(int otherAdvocateId, PeptideAssumption otherAssumption)
otherAdvocateId
- The index of the new advocateotherAssumption
- The new peptide assumptionpublic PeptideAssumption getFirstHit(int advocateId)
advocateId
- the specified advocate indexpublic void setFirstHit(int advocateId, PeptideAssumption peptideAssumption)
advocateId
- the search engine indexpeptideAssumption
- the best assumptionpublic java.util.ArrayList<java.lang.Integer> getAdvocates()
public IdentificationMatch.MatchType getType()
IdentificationMatch
getType
in class IdentificationMatch
public void setKey(java.lang.String newKey)
newKey
- the new keypublic java.lang.Integer getSpectrumNumber()
public void setSpectrumNumber(java.lang.Integer spectrumNumber)
spectrumNumber
- the spectrum number in the spectrum filepublic void removeAssumption(PeptideAssumption peptideAssumption)
peptideAssumption
- the peptide assumption to removepublic boolean hasAssumption()
public boolean hasAssumption(int advocateId)
advocateId
- The index of the advocateCopyright © 2013. All Rights Reserved.