Package | Description |
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com.compomics.util.experiment.identification |
This package contains experiment classes related to identifications.
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com.compomics.util.experiment.identification.matches |
This package contains experiment classes releated to matches.
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com.compomics.util.preferences |
Modifier and Type | Class and Description |
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class |
PeptideAssumption
This object will models the assumption made by an advocate.
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class |
TagAssumption
This class represent a tag assumption made by an identification algorithm
based on a sequence tag.
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Modifier and Type | Method and Description |
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static NeutralLossesMap |
SpectrumAnnotator.getDefaultLosses(SpectrumIdentificationAssumption spectrumIdentificationAssumption,
AminoAcidPattern.MatchingType matchingType,
double mzTolerance)
Returns the possible neutral losses expected by default for a given
peptide.
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Modifier and Type | Method and Description |
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SpectrumIdentificationAssumption |
SpectrumMatch.getFirstHit(int advocateId)
Returns the first hit obtained using the specified advocate.
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Modifier and Type | Method and Description |
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ArrayList<SpectrumIdentificationAssumption> |
SpectrumMatch.getAllAssumptions()
Return all assumptions for all identification algorithms as a list.
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HashMap<Double,ArrayList<SpectrumIdentificationAssumption>> |
SpectrumMatch.getAllAssumptions(int advocateId)
Return all assumptions for the specified search engine indexed by their
e-value.
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Modifier and Type | Method and Description |
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void |
SpectrumMatch.addHit(int otherAdvocateId,
SpectrumIdentificationAssumption otherAssumption,
boolean ascendingScore)
Add a first hit.
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void |
SpectrumMatch.removeAssumption(SpectrumIdentificationAssumption assumption)
Removes an assumption from the mapping.
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void |
SpectrumMatch.setFirstHit(int advocateId,
SpectrumIdentificationAssumption bestAssumption)
Sets the best assumption according to the search engine.
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Constructor and Description |
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SpectrumMatch(String spectrumKey,
SpectrumIdentificationAssumption assumption)
Constructor for the spectrum match.
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Modifier and Type | Method and Description |
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void |
AnnotationPreferences.setCurrentSettings(SpectrumIdentificationAssumption spectrumIdentificationAssumption,
boolean newSpectrum,
AminoAcidPattern.MatchingType matchingType,
double mzTolerance)
Sets the annotation settings for the current peptide and precursor
charge.
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