Package | Description |
---|---|
com.compomics.util.experiment.identification.identification_parameters |
Parameters settings for the spectrum identification algorithms.
|
com.compomics.util.experiment.identification.parameters_cli |
Identification search parameters.
|
com.compomics.util.experiment.identification.psm_scoring |
Main PSM scoring class.
|
com.compomics.util.gui.parameters |
GUI classes for parameters, settings and preferences.
|
com.compomics.util.gui.parameters.identification_parameters |
GUI classes for parameters, settings and preferences used for identification.
|
com.compomics.util.preferences |
Utilities preferences classes.
|
Modifier and Type | Method and Description |
---|---|
IdentificationParameters |
IdentificationParametersFactory.getIdentificationParameters(String name)
Returns the identification parameters corresponding to the given name.
|
Modifier and Type | Method and Description |
---|---|
void |
IdentificationParametersFactory.addIdentificationParameters(IdentificationParameters identificationParameters)
Adds the given identification parameters to the factory.
|
void |
IdentificationParametersFactory.updateIdentificationParameters(IdentificationParameters oldParameters,
IdentificationParameters newParameters)
Replaces old parameters by new.
|
Modifier and Type | Method and Description |
---|---|
IdentificationParameters |
IdentificationParametersInputBean.getIdentificationParameters()
Returns the identification parameters.
|
Modifier and Type | Method and Description |
---|---|
void |
IdentificationParametersInputBean.setIdentificationParameters(IdentificationParameters identificationParameters)
Sets the identification parameters.
|
Modifier and Type | Method and Description |
---|---|
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 |
---|---|
IdentificationParameters |
IdentificationParametersSelectionDialog.getIdentificationParameters()
Deprecated.
Returns the selected identification parameters.
|
IdentificationParameters |
IdentificationParametersOverviewDialog.getIdentificationParameters()
Returns the selected identification parameters.
|
IdentificationParameters |
IdentificationParametersEditionDialog.getIdentificationParameters()
Returns the identification parameters as set by the user.
|
Constructor and Description |
---|
IdentificationParametersEditionDialog(Dialog owner,
Frame parentFrame,
IdentificationParameters identificationParameters,
ConfigurationFile configurationFile,
Image normalIcon,
Image waitingIcon,
LastSelectedFolder lastSelectedFolder,
ValidationQCPreferencesDialogParent validationQCPreferencesDialogParent,
boolean editable)
Creates a new IdentificationParametersEditionDialog with a dialog as
owner.
|
IdentificationParametersEditionDialog(Frame parentFrame,
IdentificationParameters identificationParameters,
ConfigurationFile configurationFile,
Image normalIcon,
Image waitingIcon,
LastSelectedFolder lastSelectedFolder,
ValidationQCPreferencesDialogParent validationQCPreferencesDialogParent,
boolean editable)
Creates a new IdentificationParametersEditionDialog with a frame as
owner.
|
IdentificationParametersSelectionDialog(Frame parentFrame,
Dialog owner,
IdentificationParameters identificationParameters,
IdentificationParametersSelectionDialog.StartupMode startupMode,
ConfigurationFile configurationFile,
Image normalIcon,
Image waitingIcon,
LastSelectedFolder lastSelectedFolder,
ValidationQCPreferencesDialogParent validationQCPreferencesDialogParent,
boolean editable)
Deprecated.
Constructor with a dialog as owner.
|
IdentificationParametersSelectionDialog(Frame parentFrame,
IdentificationParameters identificationParameters,
IdentificationParametersSelectionDialog.StartupMode startupMode,
ConfigurationFile configurationFile,
Image normalIcon,
Image waitingIcon,
LastSelectedFolder lastSelectedFolder,
ValidationQCPreferencesDialogParent validationQCPreferencesDialogParent,
boolean editable)
Deprecated.
Constructor with a frame as owner.
|
OldProcessingPreferencesDialog(Frame parent,
boolean editable,
IdentificationParameters identificationParameters,
PSProcessingPreferences processingPreferences)
Creates a new parameters dialog.
|
OldProcessingPreferencesDialog(JDialog parent,
boolean editable,
IdentificationParameters identificationParameters,
PSProcessingPreferences processingPreferences)
Creates a new parameters dialog.
|
Modifier and Type | Method and Description |
---|---|
void |
IdentificationParametersNameDialog.updateParameters(IdentificationParameters identificationParameters)
Updates the given identification parameters attributes.
|
Constructor and Description |
---|
IdentificationParametersNameDialog(Dialog owner,
Frame parentFrame,
IdentificationParameters identificationParameters,
boolean editable)
Creates a new IdentificationParametersNameDialog with a dialog as owner.
|
IdentificationParametersNameDialog(Frame parentFrame,
IdentificationParameters identificationParameters,
boolean editable)
Creates a new IdentificationParametersNameDialog with a frame as owner.
|
Modifier and Type | Method and Description |
---|---|
static IdentificationParameters |
IdentificationParameters.getIdentificationParameters(File identificationParametersFile)
Loads the identification parameters from a file.
|
Modifier and Type | Method and Description |
---|---|
boolean |
IdentificationParameters.equals(IdentificationParameters otherIdentificationParameters)
Returns true if the identification parameter objects have identical
settings.
|
boolean |
IdentificationParameters.equalsExceptValidationPreferences(IdentificationParameters otherIdentificationParameters)
Returns true if the identification parameter objects have identical
settings except for the validation preferences.
|
static void |
IdentificationParameters.saveIdentificationParameters(IdentificationParameters identificationParameters,
File identificationParametersFile)
Saves the identification parameters to a file.
|
Copyright © 2016. All rights reserved.