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java.lang.Objectcom.compomics.util.experiment.personalization.ExperimentObject
com.compomics.util.experiment.identification.IdentificationMatch
com.compomics.util.experiment.identification.matches.SpectrumMatch
public class SpectrumMatch
This class models a spectrum match.
Nested Class Summary |
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Nested classes/interfaces inherited from class com.compomics.util.experiment.identification.IdentificationMatch |
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IdentificationMatch.MatchType |
Constructor Summary | |
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SpectrumMatch()
Constructor for the spectrum match. |
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SpectrumMatch(String spectrumKey)
Constructor for the spectrum match. |
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SpectrumMatch(String spectrumKey,
PeptideAssumption assumption)
Constructor for the spectrum match. |
Method Summary | |
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void |
addHit(int otherAdvocateId,
PeptideAssumption otherAssumption)
Add a first hit. |
ArrayList<Integer> |
getAdvocates()
Returns all advocates used referenced by their index. |
ArrayList<PeptideAssumption> |
getAllAssumptions()
Return all assumptions for all search engines as a list. |
HashMap<Double,ArrayList<PeptideAssumption>> |
getAllAssumptions(int advocateId)
Return all assumptions for the specified search engine indexed by their e-value. |
PeptideAssumption |
getBestAssumption()
Getter for the best assumption. |
PeptideAssumption |
getFirstHit(int advocateId)
Returns the first hit obtained using the specified advocate. |
String |
getKey()
returns the key of a match. |
Integer |
getSpectrumNumber()
Returns the spectrum number in the spectrum file. |
IdentificationMatch.MatchType |
getType()
Returns the type of match. |
boolean |
hasAssumption()
Indicates whether the spectrum match contains a peptide assumption from a search engine. |
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) |
void |
removeAssumption(PeptideAssumption peptideAssumption)
Removes an assumption from the mapping |
void |
setBestAssumption(PeptideAssumption bestAssumption)
Setter for the best assumption. |
void |
setFirstHit(int advocateId,
PeptideAssumption peptideAssumption)
Sets the best peptideAssumption according to the search engine. |
void |
setKey(String newKey)
Replaces the new key. |
void |
setSpectrumNumber(Integer spectrumNumber)
Sets the spectrum number in the spectrum file |
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 SpectrumMatch()
public SpectrumMatch(String spectrumKey, PeptideAssumption assumption)
spectrumKey
- The matched spectrumKeyassumption
- The matching peptide assumptionpublic SpectrumMatch(String spectrumKey)
spectrumKey
- The matched spectrum keyMethod Detail |
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public PeptideAssumption getBestAssumption()
public void setBestAssumption(PeptideAssumption bestAssumption)
bestAssumption
- the best assumption for the spectrumpublic String getKey()
IdentificationMatch
getKey
in class IdentificationMatch
public HashMap<Double,ArrayList<PeptideAssumption>> getAllAssumptions(int advocateId)
advocateId
- the desired advocate ID
public 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 index
public void setFirstHit(int advocateId, PeptideAssumption peptideAssumption)
advocateId
- the search engine indexpeptideAssumption
- the best assumptionpublic ArrayList<Integer> getAdvocates()
public IdentificationMatch.MatchType getType()
IdentificationMatch
getType
in class IdentificationMatch
public void setKey(String newKey)
newKey
- the new keypublic Integer getSpectrumNumber()
public void setSpectrumNumber(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 advocate
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