Package | Description |
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com.compomics.util.experiment.biology |
Experiment classes related to biological entities.
|
com.compomics.util.experiment.identification |
Experiment classes related to identifications.
|
com.compomics.util.experiment.identification.psm_scoring |
Main PSM scoring class.
|
com.compomics.util.experiment.identification.search_parameters_cli |
Identification search parameters.
|
com.compomics.util.experiment.io.identifications |
Experiment identification classes.
|
com.compomics.util.gui.searchsettings |
Search settings dialog.
|
com.compomics.util.preferences |
Utilities preferences classes.
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com.compomics.util.pride |
Objects related to mapping to PRIDE.
|
Modifier and Type | Method and Description |
---|---|
ArrayList<String> |
PTMFactory.loadBackedUpModifications(SearchParameters searchParameters,
boolean overwrite)
Verifies that the modifications backed-up in the search parameters are
loaded and alerts the user in case conflicts are found.
|
Modifier and Type | Method and Description |
---|---|
static SearchParameters |
SearchParameters.getIdentificationParameters(File file)
Loads the identification parameters from a serialized file.
|
Modifier and Type | Method and Description |
---|---|
boolean |
SearchParameters.equals(SearchParameters otherSearchParameters)
Returns true of the search parameter objects have identical settings.
|
static void |
SearchParameters.saveIdentificationParameters(SearchParameters identificationParameters,
File file)
Saves the identification parameters to a serialized file.
|
Modifier and Type | Method and Description |
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static double |
PsmScores.getDecreasingScore(Peptide peptide,
MSnSpectrum spectrum,
HashMap<Ion.IonType,ArrayList<Integer>> iontypes,
NeutralLossesMap neutralLosses,
ArrayList<Integer> charges,
int identificationCharge,
SearchParameters searchParameters,
int scoreIndex)
Scores the match between the given peptide and spectrum using an m/z
fidelity score.
|
static double |
PsmScores.getScore(Peptide peptide,
MSnSpectrum spectrum,
HashMap<Ion.IonType,ArrayList<Integer>> iontypes,
NeutralLossesMap neutralLosses,
ArrayList<Integer> charges,
int identificationCharge,
SearchParameters searchParameters,
int scoreIndex)
Scores the match between the given peptide and spectrum using an m/z
fidelity score.
|
static double |
PsmScores.getScore(Peptide peptide,
MSnSpectrum spectrum,
HashMap<Ion.IonType,ArrayList<Integer>> iontypes,
NeutralLossesMap neutralLosses,
ArrayList<Integer> charges,
int identificationCharge,
SearchParameters searchParameters,
PsmScores psmScore)
Scores the match between the given peptide and spectrum using an m/z
fidelity score.
|
Modifier and Type | Method and Description |
---|---|
SearchParameters |
IdentificationParametersInputBean.getSearchParameters()
Returns the search parameters.
|
Modifier and Type | Method and Description |
---|---|
static SearchParameters |
IdentificationParametersReader.getSearchParameters(Properties aProps,
File userModsFile)
Deprecated.
Conversion methods which converts an old school set of identification
properties into a SearchParameters instance.
|
Modifier and Type | Method and Description |
---|---|
static String |
MzIdentMLIdfileSearchParametersConverter.getSearchParameters(File mzIdentMLFile,
SearchParameters searchParameters,
String species,
WaitingHandler waitingHandler)
Constructor.
|
Modifier and Type | Method and Description |
---|---|
SearchParameters |
SearchSettingsDialogParent.getSearchParameters()
Returns the search parameters.
|
SearchParameters |
SearchSettingsDialog.getSearchParameters()
Returns a SearchParameters instance based on the user input in the GUI.
|
Modifier and Type | Method and Description |
---|---|
void |
SearchSettingsDialogParent.setSearchParameters(SearchParameters searchParameters)
Set the search parameters.
|
Constructor and Description |
---|
SearchSettingsDialog(JFrame parentFrame,
SearchSettingsDialogParent searchSettingsDialogParent,
SearchParameters searchParameters,
Image normalIcon,
Image waitingIcon,
boolean setVisible,
boolean modal)
Creates a new SearchSettingsDialog.
|
Modifier and Type | Method and Description |
---|---|
static SequenceMatchingPreferences |
SequenceMatchingPreferences.getDefaultSequenceMatching(SearchParameters searchParameters)
Returns default preferences from amino acid matching.
|
void |
AnnotationPreferences.setPreferencesFromSearchParameters(SearchParameters searchParameters)
Updates the annotation parameters based on the search parameters
|
Modifier and Type | Method and Description |
---|---|
static PtmToPrideMap |
PtmToPrideMap.loadPtmToPrideMap(SearchParameters searchParameters)
Loads the PRIDE to PTM map from the user folder or creates a new one if
the file is not present.
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Copyright © 2014. All rights reserved.