Uses of Class
com.compomics.util.experiment.identification.matches.SpectrumMatch
Package | Description |
---|---|
com.compomics.util.experiment.identification |
Experiment classes related to identifications.
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com.compomics.util.experiment.identification.matches_iterators |
Identification match iterators.
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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.
|
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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>
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)