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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Constructor and Description |
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IdentificationFeaturesGenerator(Identification identification,
IdentificationParameters identificationParameters,
SequenceProvider sequenceProvider,
SpectrumProvider spectrumProvider,
Metrics metrics,
SpectrumCountingParameters spectrumCountingPreferences)
Constructor.
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Modifier and Type | Method and Description |
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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.
|
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 |
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 |
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 |
PeptideFilter.isValidated(String itemName,
FilterItemComparator filterItemComparator,
Object value,
long matchKey,
Identification identification,
GeneMaps geneMaps,
IdentificationFeaturesGenerator identificationFeaturesGenerator,
IdentificationParameters identificationParameters,
SequenceProvider sequenceProvider,
ProteinDetailsProvider proteinDetailsProvider,
SpectrumProvider spectrumProvider) |
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 |
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.
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boolean |
PeptideAssumptionFilter.validatePrecursor(PeptideAssumption assumption,
String spectrumFile,
String spectrumTitle,
SpectrumProvider spectrumProvider,
SearchParameters searchParameters)
Validates the mass deviation of a peptide assumption.
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Modifier and Type | Method and Description |
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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.
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Modifier and Type | Method and Description |
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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) |
Constructor and Description |
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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.
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Modifier and Type | Class and Description |
---|---|
class |
MsFileHandler
A spectrum provider for mass spectrometry files based on Compomics Mass
Spectrometry (cms) files.
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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.writeMgfFile(SpectrumProvider spectrumProvider,
String fileNameWithoutExtension,
File destinationFile,
WaitingHandler waitingHandler)
Writes the spectra of a file in the Mascot Generic File (mgf) format.
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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.
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Modifier and Type | Class and Description |
---|---|
class |
CmsFileReader
Reader for Compomics Mass Spectrometry (cms) files.
|
Constructor and Description |
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ModificationTable(Identification identification,
AnnotationParameters annotationParameters,
PeptideMatch peptideMatch,
Modification modification,
boolean areaChart,
ModificationParameters modificationParameters,
SequenceProvider sequenceProvider,
SpectrumProvider spectrumProvider,
SequenceMatchingParameters modificationSequenceMatchingParameters)
Constructor.
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