Modifier and Type | Method and Description |
---|---|
static ShotgunProtocol |
ShotgunProtocol.inferProtocolFromSearchSettings(SearchParameters searchParameters)
Backward compatibility inferring the protocol from search settings.
|
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 |
---|---|
void |
PeptideAssumptionFilter.setFilterFromSearchParameters(SearchParameters searchParameters)
Updates the filter based on the search parameters.
|
Modifier and Type | Method and Description |
---|---|
static SearchParameters |
SearchParameters.getIdentificationParameters(File searchParametersFile)
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 searchParametersFile)
Saves the identification parameters to a serialized file.
|
void |
SearchParameters.setDefaultAdvancedSettings(SearchParameters searchParameters)
Set the advanced settings to the values in the given search parameters
object or to the default values of the advanced settings are not set for
a given advocate.
|
Constructor and Description |
---|
SearchParameters(SearchParameters searchParameters)
Constructor.
|
Modifier and Type | Method and Description |
---|---|
SearchParameters |
IdentificationParametersInputBean.getSearchParameters()
Returns the search parameters.
|
Modifier and Type | Method and Description |
---|---|
void |
AnnotationSettings.setPreferencesFromSearchParameters(SearchParameters searchParameters)
Updates the annotation parameters based on search parameters.
|
Constructor and Description |
---|
AnnotationSettings(SearchParameters searchParameters)
Constructor setting preferences from search parameters.
|
Modifier and Type | Method and Description |
---|---|
LinkedList<SpectrumMatch> |
IdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler,
SearchParameters searchParameters)
Retrieves all the identifications from an identification file as a list
of spectrum matches It is very important to close the file reader after
creation.
|
LinkedList<SpectrumMatch> |
IdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler,
SearchParameters searchParameters,
SequenceMatchingPreferences sequenceMatchingPreferences,
boolean expandAaCombinations)
Retrieves all the identifications from an identification file as a list
of spectrum matches It is very important to close the file reader after
creation.
|
static String |
MzIdentMLIdfileSearchParametersConverter.getSearchParameters(File mzIdentMLFile,
SearchParameters searchParameters,
String species,
WaitingHandler waitingHandler)
Constructor.
|
Modifier and Type | Method and Description |
---|---|
LinkedList<SpectrumMatch> |
TideIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler,
SearchParameters searchParameters) |
LinkedList<SpectrumMatch> |
PNovoIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler,
SearchParameters searchParameters) |
LinkedList<SpectrumMatch> |
PepxmlIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler,
SearchParameters searchParameters) |
LinkedList<SpectrumMatch> |
PepNovoIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler,
SearchParameters searchParameters) |
LinkedList<SpectrumMatch> |
NovorIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler,
SearchParameters searchParameters) |
LinkedList<SpectrumMatch> |
MzIdentMLIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler,
SearchParameters searchParameters) |
LinkedList<SpectrumMatch> |
MsAmandaIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler,
SearchParameters searchParameters) |
LinkedList<SpectrumMatch> |
DirecTagIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler,
SearchParameters searchParameters) |
LinkedList<SpectrumMatch> |
AndromedaIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler,
SearchParameters searchParameters) |
LinkedList<SpectrumMatch> |
TideIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler,
SearchParameters searchParameters,
SequenceMatchingPreferences sequenceMatchingPreferences,
boolean expandAaCombinations) |
LinkedList<SpectrumMatch> |
PNovoIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler,
SearchParameters searchParameters,
SequenceMatchingPreferences sequenceMatchingPreferences,
boolean expandAaCombinations) |
LinkedList<SpectrumMatch> |
PepxmlIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler,
SearchParameters searchParameters,
SequenceMatchingPreferences sequenceMatchingPreferences,
boolean expandAaCombinations) |
LinkedList<SpectrumMatch> |
PepNovoIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler,
SearchParameters searchParameters,
SequenceMatchingPreferences sequenceMatchingPreferences,
boolean expandAaCombinations) |
LinkedList<SpectrumMatch> |
NovorIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler,
SearchParameters searchParameters,
SequenceMatchingPreferences sequenceMatchingPreferences,
boolean expandAaCombinations) |
LinkedList<SpectrumMatch> |
MzIdentMLIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler,
SearchParameters searchParameters,
SequenceMatchingPreferences sequenceMatchingPreferences,
boolean expandAaCombinations) |
LinkedList<SpectrumMatch> |
MsAmandaIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler,
SearchParameters searchParameters,
SequenceMatchingPreferences sequenceMatchingPreferences,
boolean expandAaCombinations) |
LinkedList<SpectrumMatch> |
DirecTagIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler,
SearchParameters searchParameters,
SequenceMatchingPreferences sequenceMatchingPreferences,
boolean expandAaCombinations) |
LinkedList<SpectrumMatch> |
AndromedaIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler,
SearchParameters searchParameters,
SequenceMatchingPreferences sequenceMatchingPreferences,
boolean expandAaCombinations) |
Modifier and Type | Method and Description |
---|---|
SearchParameters |
SearchSettingsDialog.getSearchParameters()
Returns the search parameters object.
|
static SearchParameters |
SearchSettingsDialog.saveSearchParameters(JDialog parentDialog,
SearchParameters tempSearchParameters,
Advocate advocate,
IdentificationAlgorithmParameter identificationAlgorithmParameter,
LastSelectedFolder lastSelectedFolder)
Saves the search parameters to a file of the users choice.
|
Modifier and Type | Method and Description |
---|---|
static SearchParameters |
SearchSettingsDialog.saveSearchParameters(JDialog parentDialog,
SearchParameters tempSearchParameters,
Advocate advocate,
IdentificationAlgorithmParameter identificationAlgorithmParameter,
LastSelectedFolder lastSelectedFolder)
Saves the search parameters to a file of the users choice.
|
Constructor and Description |
---|
SearchSettingsDialog(JFrame parentFrame,
SearchParameters searchParameters,
Image normalIcon,
Image waitingIcon,
boolean setVisible,
boolean modal,
ConfigurationFile configurationFile,
LastSelectedFolder lastSelectedFolder,
boolean editable)
Creates a new SearchSettingsDialog.
|
Modifier and Type | Method and Description |
---|---|
SearchParameters |
PNovoSettingsDialog.getSearchParametersFromGUI()
Returns the search parameters as set in the GUI.
|
SearchParameters |
NovorSettingsDialog.getSearchParametersFromGUI()
Returns the search parameters as set in the GUI.
|
SearchParameters |
DirecTagSettingsDialog.getSearchParametersFromGUI()
Returns the search parameters as set in the GUI.
|
Constructor and Description |
---|
DirecTagSettingsDialog(JFrame parent,
SearchParameters searchParameters,
boolean modal)
Creates a new DirecTagSettingsDialog.
|
NovorSettingsDialog(JFrame parent,
SearchParameters searchParameters,
boolean modal)
Creates a new NovorSettingsDialog.
|
PNovoSettingsDialog(JFrame parent,
SearchParameters searchParameters,
boolean modal)
Creates a new PNovoSettingsDialog.
|
Modifier and Type | Method and Description |
---|---|
SearchParameters |
IdentificationParameters.getSearchParameters()
Returns the parameters used for the spectrum matching.
|
Modifier and Type | Method and Description |
---|---|
static IdentificationParameters |
IdentificationParameters.getDefaultIdentificationParameters(SearchParameters searchParameters)
Returns default identification parameters based on given search
parameters.
|
void |
IdentificationParameters.setParametersFromSearch(SearchParameters searchParameters)
Sets identification parameters based on given search parameters.
|
void |
IdentificationParameters.setSearchParameters(SearchParameters searchParameters)
Sets the parameters used for the spectrum matching.
|
Modifier and Type | Method and Description |
---|---|
static PtmToPrideMap |
PtmToPrideMap.loadPtmToPrideMap(SearchParameters searchParameters)
Deprecated.
the CV term is now part of the PTM object
|
Copyright © 2015. All rights reserved.