Modifier and Type | Method and Description |
---|---|
ArrayList<String> |
ModificationFactory.getExpectedVariableModifications(SearchParameters searchParameters)
Returns the expected variable modifications given the search parameters.
|
ArrayList<String> |
ModificationFactory.getSameMassNotFixedModifications(double modificationMass,
SearchParameters searchParameters)
Returns a list containing all not fixed modifications with the same
mass.
|
ArrayList<String> |
ModificationFactory.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.
|
boolean |
PeptideAssumptionFilter.validatePrecursor(PeptideAssumption assumption,
String spectrumFile,
String spectrumTitle,
SpectrumProvider spectrumProvider,
SearchParameters searchParameters)
Validates the mass deviation of a peptide assumption.
|
Modifier and Type | Method and Description |
---|---|
static double |
ModificationMassMapper.getMass(String searchEngineModificationName,
IdfileReader idfileReader,
SearchParameters searchParameters,
ModificationProvider modificationProvider)
Returns the mass indicated by the identification algorithm for the given
modification.
|
static double |
ModificationMassMapper.getMassAndromeda(String searchEngineModificationName,
ModificationProvider modificationProvider,
SearchParameters searchParameters)
Returns the mass indicated by the Andromeda for the given modification.
|
static double |
ModificationMassMapper.getMassOmssa(String searchEngineModificationName,
ModificationProvider modificationProvider,
SearchParameters searchParameters)
Returns the mass indicated by the OMSSA for the given modification.
|
static HashMap<Integer,HashSet<String>> |
ModificationNameMapper.getPossibleModificationNames(Peptide peptide,
ModificationMatch modificationMatch,
IdfileReader idfileReader,
SearchParameters searchParameters,
SequenceMatchingParameters sequenceMatchingParameters,
SequenceProvider sequenceProvider,
ModificationProvider modificationProvider)
Returns the possible modification names.
|
static HashMap<Integer,HashSet<String>> |
ModificationNameMapper.getPossibleModificationNamesAndromeda(Peptide peptide,
ModificationMatch modificationMatch,
SearchParameters searchParameters,
SequenceMatchingParameters sequenceMatchingParameters,
SequenceProvider sequenceProvider,
ModificationProvider modificationProvider)
Returns the possible Andromeda modification names.
|
static HashMap<Integer,HashSet<String>> |
ModificationNameMapper.getPossibleModificationNamesByMass(Peptide peptide,
ModificationMatch modificationMatch,
SearchParameters searchParameters,
SequenceMatchingParameters sequenceMatchingParameters,
SequenceProvider sequenceProvider,
ModificationProvider modificationProvider)
Returns the possible modifications names by mass.
|
static HashMap<Integer,HashSet<String>> |
ModificationNameMapper.getPossibleModificationNamesByName(Peptide peptide,
ModificationMatch modificationMatch,
SearchParameters searchParameters,
SequenceMatchingParameters sequenceMatchingParameters,
SequenceProvider sequenceProvider,
ModificationProvider modificationProvider)
Returns the possible modifications by name.
|
static HashMap<Integer,HashSet<String>> |
ModificationNameMapper.getPossibleModificationNamesOmssa(Peptide peptide,
ModificationMatch modificationMatch,
SearchParameters searchParameters,
SequenceMatchingParameters sequenceMatchingParameters,
SequenceProvider sequenceProvider,
ModificationProvider modificationProvider)
Returns the possible OMSSA modification names.
|
Constructor and Description |
---|
FMIndex(File fastaFile,
FastaParameters fastaParameters,
WaitingHandler waitingHandler,
boolean displayProgress,
PeptideVariantsParameters peptideVariantsPreferences,
SearchParameters searchParameters)
Constructor.
|
Modifier and Type | Method and Description |
---|---|
void |
AnnotationParameters.setParametersFromSearchParameters(SearchParameters searchParameters)
Updates the annotation parameters based on search parameters.
|
Constructor and Description |
---|
AnnotationParameters(SearchParameters searchParameters)
Constructor setting preferences from search parameters.
|
Modifier and Type | Method and Description |
---|---|
static HashMap<Integer,HashSet<String>> |
ModificationUtils.getExpectedModifications(double modMass,
ModificationParameters modificationParameters,
Peptide peptide,
double massTolerance,
SequenceProvider sequenceProvider,
SequenceMatchingParameters sequenceMatchingParameters,
SearchParameters searchParameters)
Returns the expected modifications for a given modification mass indexed
by site.
|
Modifier and Type | Method and Description |
---|---|
ArrayList<SpectrumMatch> |
IdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider,
WaitingHandler waitingHandler,
SearchParameters searchParameters)
Retrieves all the spectrum matches from an identification file as a list
of spectrum matches, one spectrum match per spectrum.
|
ArrayList<SpectrumMatch> |
IdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider,
WaitingHandler waitingHandler,
SearchParameters searchParameters,
SequenceMatchingParameters sequenceMatchingPreferences,
boolean expandAaCombinations)
Retrieves all the spectrum matches from an identification file as a list
of spectrum matches, one spectrum match per spectrum.It is very important
to close the file reader after creation.
|
Constructor and Description |
---|
MzIdentMLIdfileSearchParametersConverter(File mzIdentMLFile,
SearchParameters searchParameters,
String species,
WaitingHandler waitingHandler)
Constructor.
|
Modifier and Type | Method and Description |
---|---|
ArrayList<SpectrumMatch> |
XTandemIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider,
WaitingHandler waitingHandler,
SearchParameters searchParameters) |
ArrayList<SpectrumMatch> |
TideIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider,
WaitingHandler waitingHandler,
SearchParameters searchParameters) |
ArrayList<SpectrumMatch> |
PNovoIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider,
WaitingHandler waitingHandler,
SearchParameters searchParameters) |
ArrayList<SpectrumMatch> |
PepxmlIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider,
WaitingHandler waitingHandler,
SearchParameters searchParameters) |
ArrayList<SpectrumMatch> |
PepNovoIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider,
WaitingHandler waitingHandler,
SearchParameters searchParameters) |
ArrayList<SpectrumMatch> |
OnyaseIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider,
WaitingHandler waitingHandler,
SearchParameters searchParameters) |
ArrayList<SpectrumMatch> |
NovorIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider,
WaitingHandler waitingHandler,
SearchParameters searchParameters) |
ArrayList<SpectrumMatch> |
MzIdentMLIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider,
WaitingHandler waitingHandler,
SearchParameters searchParameters) |
ArrayList<SpectrumMatch> |
MsAmandaIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider,
WaitingHandler waitingHandler,
SearchParameters searchParameters) |
ArrayList<SpectrumMatch> |
MascotIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider,
WaitingHandler waitingHandler,
SearchParameters searchParameters) |
ArrayList<SpectrumMatch> |
DirecTagIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider,
WaitingHandler waitingHandler,
SearchParameters searchParameters) |
ArrayList<SpectrumMatch> |
CossIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider,
WaitingHandler waitingHandler,
SearchParameters searchParameters) |
ArrayList<SpectrumMatch> |
AndromedaIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider,
WaitingHandler waitingHandler,
SearchParameters searchParameters) |
ArrayList<SpectrumMatch> |
XTandemIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider,
WaitingHandler waitingHandler,
SearchParameters searchParameters,
SequenceMatchingParameters sequenceMatchingPreferences,
boolean expandAaCombinations) |
ArrayList<SpectrumMatch> |
TideIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider,
WaitingHandler waitingHandler,
SearchParameters searchParameters,
SequenceMatchingParameters sequenceMatchingPreferences,
boolean expandAaCombinations) |
ArrayList<SpectrumMatch> |
PNovoIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider,
WaitingHandler waitingHandler,
SearchParameters searchParameters,
SequenceMatchingParameters sequenceMatchingPreferences,
boolean expandAaCombinations) |
ArrayList<SpectrumMatch> |
PepxmlIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider,
WaitingHandler waitingHandler,
SearchParameters searchParameters,
SequenceMatchingParameters sequenceMatchingPreferences,
boolean expandAaCombinations) |
ArrayList<SpectrumMatch> |
PepNovoIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider,
WaitingHandler waitingHandler,
SearchParameters searchParameters,
SequenceMatchingParameters sequenceMatchingPreferences,
boolean expandAaCombinations) |
ArrayList<SpectrumMatch> |
OnyaseIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider,
WaitingHandler waitingHandler,
SearchParameters searchParameters,
SequenceMatchingParameters sequenceMatchingPreferences,
boolean expandAaCombinations) |
ArrayList<SpectrumMatch> |
NovorIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider,
WaitingHandler waitingHandler,
SearchParameters searchParameters,
SequenceMatchingParameters sequenceMatchingPreferences,
boolean expandAaCombinations) |
ArrayList<SpectrumMatch> |
MzIdentMLIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider,
WaitingHandler waitingHandler,
SearchParameters searchParameters,
SequenceMatchingParameters sequenceMatchingPreferences,
boolean expandAaCombinations) |
ArrayList<SpectrumMatch> |
MsAmandaIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider,
WaitingHandler waitingHandler,
SearchParameters searchParameters,
SequenceMatchingParameters sequenceMatchingPreferences,
boolean expandAaCombinations) |
ArrayList<SpectrumMatch> |
MascotIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider,
WaitingHandler waitingHandler,
SearchParameters searchParameters,
SequenceMatchingParameters sequenceMatchingPreferences,
boolean expandAaCombinations) |
ArrayList<SpectrumMatch> |
DirecTagIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider,
WaitingHandler waitingHandler,
SearchParameters searchParameters,
SequenceMatchingParameters sequenceMatchingPreferences,
boolean expandAaCombinations) |
ArrayList<SpectrumMatch> |
CossIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider,
WaitingHandler waitingHandler,
SearchParameters searchParameters,
SequenceMatchingParameters sequenceMatchingPreferences,
boolean expandAaCombinations) |
ArrayList<SpectrumMatch> |
AndromedaIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider,
WaitingHandler waitingHandler,
SearchParameters searchParameters,
SequenceMatchingParameters sequenceMatchingPreferences,
boolean expandAaCombinations) |
Modifier and Type | Method and Description |
---|---|
static void |
MsFileExporter.writeAplFile(SpectrumProvider spectrumProvider,
String fileNameWithoutExtension,
File destinationFile,
SearchParameters searchParameters,
WaitingHandler waitingHandler)
Writes the spectra of a file in the Andromeda peak list (apl) format.
|
static void |
MsFileExporter.writeMsFile(SpectrumProvider spectrumProvider,
String fileNameWithoutExtension,
File destinationFile,
MsFileExporter.Format format,
SearchParameters searchParameters,
WaitingHandler waitingHandler)
Writes the spectra of a file in the given format.
|
Constructor and Description |
---|
GeneParametersDialog(JDialog owner,
Frame parentFrame,
GeneParameters genePreferences,
SearchParameters searchParameters,
boolean editable)
Creates a new GenePreferencesDialog with a dialog as owner.
|
GeneParametersDialog(JFrame parentFrame,
GeneParameters genePreferences,
SearchParameters searchParameters,
boolean editable)
Creates a new GenePreferencesDialog with a frame as owner.
|
Modifier and Type | Method and Description |
---|---|
SearchParameters |
SearchParametersDialog.getSearchParameters()
Returns a SearchParameters instance based on the user input in the GUI.
|
Constructor and Description |
---|
SearchParametersDialog(Dialog owner,
Frame parentFrame,
SearchParameters searchParameters,
Image normalIcon,
Image waitingIcon,
boolean setVisible,
boolean modal,
LastSelectedFolder lastSelectedFolder,
String settingsName,
boolean editable)
Creates a new SearchSettingsDialog with a dialog as owner.
|
SearchParametersDialog(Frame parentFrame,
SearchParameters searchParameters,
Image normalIcon,
Image waitingIcon,
boolean setVisible,
boolean modal,
LastSelectedFolder lastSelectedFolder,
String settingsName,
boolean editable)
Creates a new SearchSettingsDialog with a frame as owner.
|
Modifier and Type | Method and Description |
---|---|
SearchParameters |
IdentificationParameters.getSearchParameters()
Returns the parameters used for the spectrum matching.
|
Modifier and Type | Method and Description |
---|---|
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.
|
Constructor and Description |
---|
IdentificationParameters(SearchParameters searchParameters)
Creates default identification parameters from the given search
parameters.
|
IdentificationParameters(String name,
String description,
SearchParameters searchParameters,
AnnotationParameters annotationParameters,
SequenceMatchingParameters sequenceMatchingParameters,
PeptideVariantsParameters peptideVariantsParameters,
GeneParameters geneParameters,
PsmScoringParameters psmScoringParameters,
PeptideAssumptionFilter peptideAssumptionFilter,
ModificationLocalizationParameters ModificationLocalizationParameters,
ProteinInferenceParameters proteinInferenceParameters,
IdMatchValidationParameters idValidationParameters,
FractionParameters fractionParameters,
FastaParameters fastaParameters)
Constructor.
|
Modifier and Type | Method and Description |
---|---|
static SearchParameters |
SearchParameters.getIdentificationParameters(File searchParametersFile)
Loads the identification parameters from a file.
|
Modifier and Type | Method and Description |
---|---|
boolean |
SearchParameters.equals(SearchParameters otherSearchParameters)
Returns true if the search parameter objects have identical settings.
|
static void |
SearchParameters.saveIdentificationParameters(SearchParameters searchParameters,
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 |
---|---|
static PtmToPrideMap |
PtmToPrideMap.loadPtmToPrideMap(SearchParameters searchParameters)
Deprecated.
the CV term is now part of the PTM object
|
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