Uses of Class
com.compomics.util.experiment.identification.matches.SpectrumMatch

Packages that use SpectrumMatch

Package	Description
com.compomics.util.experiment.identification	Experiment classes related to identifications.
com.compomics.util.experiment.identification.matches_iterators	Identification match iterators.
com.compomics.util.experiment.identification.protein_inference	Classes related to protein inference.
com.compomics.util.experiment.io.identification	Experiment identification classes.
com.compomics.util.experiment.io.identification.idfilereaders	Experiment classes related to reading search engine files.

Uses of SpectrumMatch in com.compomics.util.experiment.identification

Methods in com.compomics.util.experiment.identification that return SpectrumMatch

Modifier and Type	Method	Description
SpectrumMatch	Identification.getSpectrumMatch(long key)	Returns the spectrum match with the given key.

Uses of SpectrumMatch in com.compomics.util.experiment.identification.matches_iterators

Methods in com.compomics.util.experiment.identification.matches_iterators that return SpectrumMatch

Modifier and Type	Method	Description
SpectrumMatch	SpectrumMatchesIterator.next()	Returns the next match and updates the buffer.

Uses of SpectrumMatch in com.compomics.util.experiment.identification.protein_inference

Methods in com.compomics.util.experiment.identification.protein_inference with parameters of type SpectrumMatch

Modifier and Type	Method	Description
void	PeptideAndProteinBuilder.buildPeptidesAndProteins(SpectrumMatch spectrumMatch, SequenceMatchingParameters sequenceMatchingPreferences, SequenceProvider sequenceProvider, boolean protein)	Creates the peptides and protein instances based on the given spectrum match.

Uses of SpectrumMatch in com.compomics.util.experiment.io.identification

Methods in com.compomics.util.experiment.io.identification that return types with arguments of type SpectrumMatch

Modifier and Type	Method	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.

Uses of SpectrumMatch in com.compomics.util.experiment.io.identification.idfilereaders

Methods in com.compomics.util.experiment.io.identification.idfilereaders that return types with arguments of type SpectrumMatch

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)
ArrayList<SpectrumMatch>	CossIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider, WaitingHandler waitingHandler, SearchParameters searchParameters)
ArrayList<SpectrumMatch>	CossIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider, WaitingHandler waitingHandler, SearchParameters searchParameters, SequenceMatchingParameters sequenceMatchingPreferences, boolean expandAaCombinations)
ArrayList<SpectrumMatch>	DirecTagIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider, WaitingHandler waitingHandler, SearchParameters searchParameters)
ArrayList<SpectrumMatch>	DirecTagIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider, WaitingHandler waitingHandler, SearchParameters searchParameters, SequenceMatchingParameters sequenceMatchingPreferences, boolean expandAaCombinations)
ArrayList<SpectrumMatch>	MascotIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider, WaitingHandler waitingHandler, SearchParameters searchParameters)
ArrayList<SpectrumMatch>	MascotIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider, WaitingHandler waitingHandler, SearchParameters searchParameters, SequenceMatchingParameters sequenceMatchingPreferences, boolean expandAaCombinations)
ArrayList<SpectrumMatch>	MsAmandaIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider, WaitingHandler waitingHandler, SearchParameters searchParameters)
ArrayList<SpectrumMatch>	MsAmandaIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider, WaitingHandler waitingHandler, SearchParameters searchParameters, SequenceMatchingParameters sequenceMatchingPreferences, boolean expandAaCombinations)
ArrayList<SpectrumMatch>	MzIdentMLIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider, WaitingHandler waitingHandler, SearchParameters searchParameters)
ArrayList<SpectrumMatch>	MzIdentMLIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider, WaitingHandler waitingHandler, SearchParameters searchParameters, SequenceMatchingParameters sequenceMatchingPreferences, boolean expandAaCombinations)
ArrayList<SpectrumMatch>	NovorIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider, WaitingHandler waitingHandler, SearchParameters searchParameters)
ArrayList<SpectrumMatch>	NovorIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider, WaitingHandler waitingHandler, SearchParameters searchParameters, SequenceMatchingParameters sequenceMatchingPreferences, boolean expandAaCombinations)
ArrayList<SpectrumMatch>	OnyaseIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider, WaitingHandler waitingHandler, SearchParameters searchParameters)
ArrayList<SpectrumMatch>	OnyaseIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider, WaitingHandler waitingHandler, SearchParameters searchParameters, SequenceMatchingParameters sequenceMatchingPreferences, boolean expandAaCombinations)
ArrayList<SpectrumMatch>	PepNovoIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider, WaitingHandler waitingHandler, SearchParameters searchParameters)
ArrayList<SpectrumMatch>	PepNovoIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider, WaitingHandler waitingHandler, SearchParameters searchParameters, SequenceMatchingParameters sequenceMatchingPreferences, boolean expandAaCombinations)
ArrayList<SpectrumMatch>	PepxmlIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider, WaitingHandler waitingHandler, SearchParameters searchParameters)
ArrayList<SpectrumMatch>	PepxmlIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider, WaitingHandler waitingHandler, SearchParameters searchParameters, SequenceMatchingParameters sequenceMatchingPreferences, boolean expandAaCombinations)
ArrayList<SpectrumMatch>	PNovoIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider, WaitingHandler waitingHandler, SearchParameters searchParameters)
ArrayList<SpectrumMatch>	PNovoIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider, WaitingHandler waitingHandler, SearchParameters searchParameters, SequenceMatchingParameters sequenceMatchingPreferences, boolean expandAaCombinations)
ArrayList<SpectrumMatch>	SageIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider, WaitingHandler waitingHandler, SearchParameters searchParameters)
ArrayList<SpectrumMatch>	SageIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider, WaitingHandler waitingHandler, SearchParameters searchParameters, SequenceMatchingParameters sequenceMatchingPreferences, boolean expandAaCombinations)
ArrayList<SpectrumMatch>	TideIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider, WaitingHandler waitingHandler, SearchParameters searchParameters)
ArrayList<SpectrumMatch>	TideIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider, WaitingHandler waitingHandler, SearchParameters searchParameters, SequenceMatchingParameters sequenceMatchingPreferences, boolean expandAaCombinations)
ArrayList<SpectrumMatch>	XTandemIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider, WaitingHandler waitingHandler, SearchParameters searchParameters)
ArrayList<SpectrumMatch>	XTandemIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider, WaitingHandler waitingHandler, SearchParameters searchParameters, SequenceMatchingParameters sequenceMatchingPreferences, boolean expandAaCombinations)