Uses of Interface
com.compomics.util.experiment.mass_spectrometry.SpectrumProvider
Package | Description |
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com.compomics.util.experiment.identification.features |
Classes for the generation of identification features.
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com.compomics.util.experiment.identification.filtering |
Classes for the filtering of identification objects.
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com.compomics.util.experiment.io.identification |
Experiment identification classes.
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com.compomics.util.experiment.io.identification.idfilereaders |
Experiment classes related to reading search engine files.
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com.compomics.util.experiment.io.identification.writers |
Writer for identification results.
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com.compomics.util.experiment.io.mass_spectrometry |
Classes for the handling of mass spectrometry files.
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com.compomics.util.experiment.io.mass_spectrometry.cms |
Classes for the handling of Compomics mass spectrometry (cms) files.
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com.compomics.util.gui.modification |
PTM GUI dialogs.
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Uses of SpectrumProvider in com.compomics.util.experiment.identification.features
Constructors in com.compomics.util.experiment.identification.features with parameters of type SpectrumProvider Constructor Description IdentificationFeaturesGenerator(Identification identification, IdentificationParameters identificationParameters, SequenceProvider sequenceProvider, SpectrumProvider spectrumProvider, Metrics metrics, SpectrumCountingParameters spectrumCountingPreferences)
Constructor. -
Uses of SpectrumProvider in com.compomics.util.experiment.identification.filtering
Methods in com.compomics.util.experiment.identification.filtering with parameters of type SpectrumProvider Modifier and Type Method Description boolean
AssumptionFilter. isValidated(long spectrumMatchKey, String spectrumFile, String spectrumTitle, PeptideAssumption peptideAssumption, Identification identification, SequenceProvider sequenceProvider, SpectrumProvider spectrumProvider, IdentificationFeaturesGenerator identificationFeaturesGenerator, IdentificationParameters identificationParameters)
Tests whether a match is validated by this filter.boolean
AssumptionFilter. isValidated(String itemName, FilterItemComparator filterItemComparator, Object value, long spectrumMatchKey, Identification identification, GeneMaps geneMaps, IdentificationFeaturesGenerator identificationFeaturesGenerator, IdentificationParameters identificationParameters, SequenceProvider sequenceProvider, ProteinDetailsProvider proteinDetailsProvider, SpectrumProvider spectrumProvider)
boolean
AssumptionFilter. isValidated(String itemName, FilterItemComparator filterItemComparator, Object value, long spectrumMatchKey, String spectrumFile, String spectrumTitle, PeptideAssumption peptideAssumption, Identification identification, SequenceProvider sequenceProvider, SpectrumProvider spectrumProvider, IdentificationFeaturesGenerator identificationFeaturesGenerator, IdentificationParameters identificationParameters)
Indicates whether the match designated by the match key validates the given item using the given comparator and value threshold.boolean
MatchFilter. isValidated(long matchKey, Identification identification, GeneMaps geneMaps, IdentificationFeaturesGenerator identificationFeaturesGenerator, IdentificationParameters identificationParameters, SequenceProvider sequenceProvider, ProteinDetailsProvider proteinDetailsProvider, SpectrumProvider spectrumProvider)
Tests whether a match is validated by this filter.abstract boolean
MatchFilter. isValidated(String itemName, FilterItemComparator filterItemComparator, Object value, long matchKey, Identification identification, GeneMaps geneMaps, IdentificationFeaturesGenerator identificationFeaturesGenerator, IdentificationParameters identificationParameters, SequenceProvider sequenceProvider, ProteinDetailsProvider proteinDetailsProvider, SpectrumProvider spectrumProvider)
Indicates whether the match designated by the match key validates the given item using the given comparator and value threshold.boolean
PeptideFilter. isValidated(String itemName, FilterItemComparator filterItemComparator, Object value, long matchKey, Identification identification, GeneMaps geneMaps, IdentificationFeaturesGenerator identificationFeaturesGenerator, IdentificationParameters identificationParameters, SequenceProvider sequenceProvider, ProteinDetailsProvider proteinDetailsProvider, SpectrumProvider spectrumProvider)
boolean
ProteinFilter. isValidated(String itemName, FilterItemComparator filterItemComparator, Object value, long matchKey, Identification identification, GeneMaps geneMaps, IdentificationFeaturesGenerator identificationFeaturesGenerator, IdentificationParameters identificationParameters, SequenceProvider sequenceProvider, ProteinDetailsProvider proteinDetailsProvider, SpectrumProvider spectrumProvider)
boolean
PsmFilter. isValidated(String itemName, FilterItemComparator filterItemComparator, Object value, long matchKey, Identification identification, GeneMaps geneMaps, IdentificationFeaturesGenerator identificationFeaturesGenerator, IdentificationParameters identificationParameters, SequenceProvider sequenceProvider, ProteinDetailsProvider proteinDetailsProvider, SpectrumProvider spectrumProvider)
boolean
PeptideAssumptionFilter. validatePrecursor(PeptideAssumption assumption, String spectrumFile, String spectrumTitle, SpectrumProvider spectrumProvider, SearchParameters searchParameters)
Validates the mass deviation of a peptide assumption. -
Uses of SpectrumProvider in com.compomics.util.experiment.io.identification
Methods in com.compomics.util.experiment.io.identification with parameters of type SpectrumProvider 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 SpectrumProvider in com.compomics.util.experiment.io.identification.idfilereaders
Methods in com.compomics.util.experiment.io.identification.idfilereaders with parameters of type SpectrumProvider 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)
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Uses of SpectrumProvider in com.compomics.util.experiment.io.identification.writers
Constructors in com.compomics.util.experiment.io.identification.writers with parameters of type SpectrumProvider Constructor Description SimpleMzIdentMLExporter(String softwareName, String softwareVersion, String softwareUrl, File tempFolder, File destinationFile, ArrayList<File> spectrumFiles, File searchEngineFile, HashMap<String,ArrayList<String>> searchEngines, File fastaFile, IdentificationParameters identificationParameters, SequenceProvider sequenceProvider, ProteinDetailsProvider proteinDetailsProvider, SpectrumProvider spectrumProvider, ModificationProvider modificationProvider, FastaSummary fastaSummary, String contactFirstName, String contactLastName, String contactAddress, String contactEmail, String contactOrganizationName, String contactOrganizationAddress, String contactOrganizationEmail, boolean peptideInference)
Constructor. -
Uses of SpectrumProvider in com.compomics.util.experiment.io.mass_spectrometry
Classes in com.compomics.util.experiment.io.mass_spectrometry that implement SpectrumProvider Modifier and Type Class Description class
MsFileHandler
A spectrum provider for mass spectrometry files based on Compomics Mass Spectrometry (cms) files.Methods in com.compomics.util.experiment.io.mass_spectrometry with parameters of type SpectrumProvider Modifier and Type Method 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. writeMgfFile(SpectrumProvider spectrumProvider, String fileNameWithoutExtension, File destinationFile, WaitingHandler waitingHandler)
Writes the spectra of a file in the Mascot Generic File (mgf) format.static void
MsFileExporter. writeMs2File(SpectrumProvider spectrumProvider, String fileNameWithoutExtension, File destinationFile, WaitingHandler waitingHandler)
Writes the spectra of a file in the ms2 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. -
Uses of SpectrumProvider in com.compomics.util.experiment.io.mass_spectrometry.cms
Classes in com.compomics.util.experiment.io.mass_spectrometry.cms that implement SpectrumProvider Modifier and Type Class Description class
CmsFileReader
Reader for Compomics Mass Spectrometry (cms) files. -
Uses of SpectrumProvider in com.compomics.util.gui.modification
Constructors in com.compomics.util.gui.modification with parameters of type SpectrumProvider Constructor Description ModificationTable(Identification identification, AnnotationParameters annotationParameters, PeptideMatch peptideMatch, Modification modification, boolean areaChart, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SpectrumProvider spectrumProvider, SequenceMatchingParameters modificationSequenceMatchingParameters)
Constructor.