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Methods in com.compomics.util.experiment.identification.modification.mapping with parameters of type SearchParameters
Modifier and Type |
Method |
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.
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static double |
ModificationMassMapper.getMassAndromeda(String searchEngineModificationName,
ModificationProvider modificationProvider,
SearchParameters searchParameters) |
Returns the mass indicated by the Andromeda for the given modification.
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static double |
ModificationMassMapper.getMassOmssa(String searchEngineModificationName,
ModificationProvider modificationProvider,
SearchParameters searchParameters) |
Returns the mass indicated by the OMSSA for the given modification.
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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.
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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.
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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.
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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.
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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.
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Methods in com.compomics.util.experiment.io.identification.idfilereaders with parameters of type SearchParameters
Modifier and Type |
Method |
Description |
ArrayList<SpectrumMatch> |
AndromedaIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider,
WaitingHandler waitingHandler,
SearchParameters searchParameters) |
|
ArrayList<SpectrumMatch> |
AndromedaIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider,
WaitingHandler waitingHandler,
SearchParameters searchParameters,
SequenceMatchingParameters sequenceMatchingPreferences,
boolean expandAaCombinations) |
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ArrayList<SpectrumMatch> |
CossIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider,
WaitingHandler waitingHandler,
SearchParameters searchParameters) |
|
ArrayList<SpectrumMatch> |
CossIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider,
WaitingHandler waitingHandler,
SearchParameters searchParameters,
SequenceMatchingParameters sequenceMatchingPreferences,
boolean expandAaCombinations) |
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ArrayList<SpectrumMatch> |
DirecTagIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider,
WaitingHandler waitingHandler,
SearchParameters searchParameters) |
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ArrayList<SpectrumMatch> |
DirecTagIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider,
WaitingHandler waitingHandler,
SearchParameters searchParameters,
SequenceMatchingParameters sequenceMatchingPreferences,
boolean expandAaCombinations) |
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ArrayList<SpectrumMatch> |
MascotIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider,
WaitingHandler waitingHandler,
SearchParameters searchParameters) |
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ArrayList<SpectrumMatch> |
MascotIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider,
WaitingHandler waitingHandler,
SearchParameters searchParameters,
SequenceMatchingParameters sequenceMatchingPreferences,
boolean expandAaCombinations) |
|
ArrayList<SpectrumMatch> |
MsAmandaIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider,
WaitingHandler waitingHandler,
SearchParameters searchParameters) |
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ArrayList<SpectrumMatch> |
MsAmandaIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider,
WaitingHandler waitingHandler,
SearchParameters searchParameters,
SequenceMatchingParameters sequenceMatchingPreferences,
boolean expandAaCombinations) |
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ArrayList<SpectrumMatch> |
MzIdentMLIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider,
WaitingHandler waitingHandler,
SearchParameters searchParameters) |
|
ArrayList<SpectrumMatch> |
MzIdentMLIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider,
WaitingHandler waitingHandler,
SearchParameters searchParameters,
SequenceMatchingParameters sequenceMatchingPreferences,
boolean expandAaCombinations) |
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ArrayList<SpectrumMatch> |
NovorIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider,
WaitingHandler waitingHandler,
SearchParameters searchParameters) |
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ArrayList<SpectrumMatch> |
NovorIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider,
WaitingHandler waitingHandler,
SearchParameters searchParameters,
SequenceMatchingParameters sequenceMatchingPreferences,
boolean expandAaCombinations) |
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ArrayList<SpectrumMatch> |
OnyaseIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider,
WaitingHandler waitingHandler,
SearchParameters searchParameters) |
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ArrayList<SpectrumMatch> |
OnyaseIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider,
WaitingHandler waitingHandler,
SearchParameters searchParameters,
SequenceMatchingParameters sequenceMatchingPreferences,
boolean expandAaCombinations) |
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ArrayList<SpectrumMatch> |
PepNovoIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider,
WaitingHandler waitingHandler,
SearchParameters searchParameters) |
|
ArrayList<SpectrumMatch> |
PepNovoIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider,
WaitingHandler waitingHandler,
SearchParameters searchParameters,
SequenceMatchingParameters sequenceMatchingPreferences,
boolean expandAaCombinations) |
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ArrayList<SpectrumMatch> |
PepxmlIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider,
WaitingHandler waitingHandler,
SearchParameters searchParameters) |
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ArrayList<SpectrumMatch> |
PepxmlIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider,
WaitingHandler waitingHandler,
SearchParameters searchParameters,
SequenceMatchingParameters sequenceMatchingPreferences,
boolean expandAaCombinations) |
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ArrayList<SpectrumMatch> |
PNovoIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider,
WaitingHandler waitingHandler,
SearchParameters searchParameters) |
|
ArrayList<SpectrumMatch> |
PNovoIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider,
WaitingHandler waitingHandler,
SearchParameters searchParameters,
SequenceMatchingParameters sequenceMatchingPreferences,
boolean expandAaCombinations) |
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ArrayList<SpectrumMatch> |
TideIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider,
WaitingHandler waitingHandler,
SearchParameters searchParameters) |
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ArrayList<SpectrumMatch> |
TideIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider,
WaitingHandler waitingHandler,
SearchParameters searchParameters,
SequenceMatchingParameters sequenceMatchingPreferences,
boolean expandAaCombinations) |
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ArrayList<SpectrumMatch> |
XTandemIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider,
WaitingHandler waitingHandler,
SearchParameters searchParameters) |
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ArrayList<SpectrumMatch> |
XTandemIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider,
WaitingHandler waitingHandler,
SearchParameters searchParameters,
SequenceMatchingParameters sequenceMatchingPreferences,
boolean expandAaCombinations) |
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Constructors in com.compomics.util.gui.parameters.identification.search with parameters of type SearchParameters
Constructor |
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.
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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.
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Constructors in com.compomics.util.parameters.identification with parameters of type SearchParameters
Constructor |
Description |
IdentificationParameters(SearchParameters searchParameters) |
Creates default identification parameters from the given search
parameters.
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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.
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