Package | Description |
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com.compomics.util.experiment |
Gene factory classes.
|
com.compomics.util.experiment.identification.psm_scoring |
Main PSM scoring class.
|
Modifier and Type | Method and Description |
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static ShotgunProtocol |
ShotgunProtocol.inferProtocolFromSearchSettings(SearchParameters searchParameters)
Backward compatibility inferring the protocol from search settings.
|
Modifier and Type | Method and Description |
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static double |
PsmScores.getDecreasingScore(Peptide peptide,
Integer peptideCharge,
MSnSpectrum spectrum,
ShotgunProtocol shotgunProtocol,
IdentificationParameters identificationParameters,
SpecificAnnotationSettings specificAnnotationPreferences,
int scoreIndex)
Scores the match between the given peptide and spectrum using the given
score.
|
static double |
PsmScores.getScore(Peptide peptide,
Integer peptideCharge,
MSnSpectrum spectrum,
ShotgunProtocol shotgunProtocol,
IdentificationParameters identificationParameters,
SpecificAnnotationSettings specificAnnotationPreferences,
int scoreIndex)
Scores the match between the given peptide and spectrum using the given
score.
|
static double |
PsmScores.getScore(Peptide peptide,
Integer peptideCharge,
MSnSpectrum spectrum,
ShotgunProtocol shotgunProtocol,
IdentificationParameters identificationParameters,
SpecificAnnotationSettings specificAnnotationPreferences,
PsmScores psmScore)
Scores the match between the given peptide and spectrum using the given
score.
|
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