Package | Description |
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com.compomics.util.experiment.identification.psm_scoring |
Main PSM scoring class.
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com.compomics.util.gui.parameters |
GUI classes for parameters, settings and preferences.
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com.compomics.util.preferences |
Utilities preferences classes.
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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.
|
Modifier and Type | Method and Description |
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IdentificationParameters |
IdentificationParametersDialog.getIdentificationParameters()
Returns the identification parameters as set by the user.
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Constructor and Description |
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IdentificationParametersDialog(Frame parentFrame,
IdentificationParameters identificationParameters,
ConfigurationFile configurationFile,
ArrayList<NeutralLoss> possibleNeutralLosses,
ArrayList<Integer> reporterIons,
Image normalIcon,
Image waitingIcon,
LastSelectedFolder lastSelectedFolder,
ValidationQCPreferencesDialogParent validationQCPreferencesDialogParent,
boolean editable)
Constructor.
|
ProcessingPreferencesDialog(Frame parent,
boolean editable,
IdentificationParameters identificationParameters,
PSProcessingPreferences processingPreferences)
Creates a new parameters dialog.
|
ProcessingPreferencesDialog(JDialog parent,
boolean editable,
IdentificationParameters identificationParameters,
PSProcessingPreferences processingPreferences)
Creates a new parameters dialog.
|
Modifier and Type | Method and Description |
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static IdentificationParameters |
IdentificationParameters.getDefaultIdentificationParameters()
Creates blank parameters.
|
static IdentificationParameters |
IdentificationParameters.getDefaultIdentificationParameters(SearchParameters searchParameters)
Returns default identification parameters based on given search
parameters.
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