Package | Description |
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com.compomics.util.experiment |
Gene factory classes.
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com.compomics.util.experiment.biology |
Experiment classes related to biological entities.
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com.compomics.util.experiment.identification |
Experiment classes related to identifications.
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com.compomics.util.experiment.identification.search_parameters_cli |
Identification search parameters.
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com.compomics.util.experiment.io.identifications |
Experiment identification classes.
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com.compomics.util.experiment.io.identifications.idfilereaders |
Experiment classes related to reading search engine files.
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com.compomics.util.gui.searchsettings |
Search settings dialog.
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com.compomics.util.preferences |
Utilities preferences classes.
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com.compomics.util.pride |
Objects related to mapping to PRIDE.
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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.
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Modifier and Type | Method and Description |
---|---|
static SearchParameters |
SearchParameters.getIdentificationParameters(File file)
Loads the identification parameters from a serialized file.
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Modifier and Type | Method and Description |
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boolean |
SearchParameters.equals(SearchParameters otherSearchParameters)
Returns true of the search parameter objects have identical settings.
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static void |
SearchParameters.saveIdentificationParameters(SearchParameters identificationParameters,
File file)
Saves the identification parameters to a serialized file.
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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 |
---|---|
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> |
PNovoIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler,
SearchParameters searchParameters) |
LinkedList<SpectrumMatch> |
PepxmlIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler,
SearchParameters searchParameters) |
LinkedList<SpectrumMatch> |
PepNovoIdfileReader.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> |
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> |
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.
|
Constructor and Description |
---|
SearchSettingsDialog(JFrame parentFrame,
SearchParameters searchParameters,
Image normalIcon,
Image waitingIcon,
boolean setVisible,
boolean modal,
ConfigurationFile configurationFile,
LastSelectedFolder lastSelectedFolder)
Creates a new SearchSettingsDialog.
|
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.
|
static SequenceMatchingPreferences |
SequenceMatchingPreferences.getDefaultSequenceMatching(SearchParameters searchParameters)
Returns default preferences from amino acid matching.
|
void |
IdFilter.setFilterFromSearchParameters(SearchParameters searchParameters)
Updates the filter based on the search parameters.
|
void |
IdentificationParameters.setParametersFromSearch(SearchParameters searchParameters)
Sets identification parameters based on given search parameters.
|
void |
AnnotationPreferences.setPreferencesFromSearchParameters(SearchParameters searchParameters)
Updates the annotation parameters based on search parameters.
|
void |
IdentificationParameters.setSearchParameters(SearchParameters searchParameters)
Sets the parameters used for the spectrum matching.
|
Constructor and Description |
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AnnotationPreferences(SearchParameters searchParameters)
Constructor setting preferences from 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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