public class MzIdentMLUnmarshallerAdaptor
extends uk.ac.ebi.jmzidml.xml.io.MzIdentMLUnmarshaller
Constructor and Description |
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MzIdentMLUnmarshallerAdaptor(File mzIdentMLFile,
boolean inMemory) |
MzIdentMLUnmarshallerAdaptor(File mzIdentMLFile,
boolean inMemory,
boolean avoidProteinInference) |
Modifier and Type | Method and Description |
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Date |
getCreationDate() |
List<uk.ac.ebi.jmzidml.model.mzidml.Cv> |
getCvList() |
uk.ac.ebi.jmzidml.model.mzidml.DBSequence |
getDBSequenceById(Comparable id) |
uk.ac.ebi.jmzidml.model.mzidml.FragmentationTable |
getFragmentationTable() |
uk.ac.ebi.jmzidml.model.mzidml.ProteinDetectionHypothesis |
getIdentificationById(Comparable identId) |
Comparable |
getMGFTitleReference(String spectrumIdentResultId) |
String |
getMzIdentMLName() |
int |
getNumIdentifiedPeptides() |
List<uk.ac.ebi.jmzidml.model.mzidml.Organization> |
getOrganizationContacts() |
Set<String> |
getPeptideEvidenceReferences(String spectrumIdentResultId,
String spectrumIdentItemId) |
List<uk.ac.ebi.jmzidml.model.mzidml.Person> |
getPersonContacts() |
uk.ac.ebi.jmzidml.model.mzidml.ProteinAmbiguityGroup |
getProteinAmbiguityGroup(Comparable id) |
uk.ac.ebi.jmzidml.model.mzidml.ProteinDetectionProtocol |
getProteinDetectionProtocol() |
uk.ac.ebi.jmzidml.model.mzidml.Provider |
getProvider() |
Iterator<uk.ac.ebi.jmzidml.model.mzidml.BibliographicReference> |
getReferences() |
List<uk.ac.ebi.jmzidml.model.mzidml.Sample> |
getSampleList() |
List<uk.ac.ebi.jmzidml.model.mzidml.SearchDatabase> |
getSearchDatabases() |
List<uk.ac.ebi.jmzidml.model.mzidml.AnalysisSoftware> |
getSoftwares() |
List<uk.ac.ebi.jmzidml.model.mzidml.SourceFile> |
getSourceFiles() |
List<uk.ac.ebi.jmzidml.model.mzidml.SpectraData> |
getSpectraData() |
Map<Comparable,uk.ac.ebi.jmzidml.model.mzidml.SpectraData> |
getSpectraDataMap() |
Set<String> |
getSpectrumIdentificationItemIds(String spectrumIdentResultId) |
List<uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationProtocol> |
getSpectrumIdentificationProtocol() |
List<uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationItem> |
getSpectrumIdentificationsByIds(List<Comparable> spectrumIdentIds) |
List<Comparable> |
getTitleReferenceFile(Map<Comparable,uk.ac.ebi.jmzidml.model.mzidml.SpectraData> spectraDataMap)
Check for all the SpectraData if they are referenced by title instead of using the normal index.
|
boolean |
hasDecoyInformation() |
boolean |
hasProteinGroup() |
boolean |
hasProteinSequence() |
public MzIdentMLUnmarshallerAdaptor(File mzIdentMLFile, boolean inMemory) throws ConfigurationException
ConfigurationException
public MzIdentMLUnmarshallerAdaptor(File mzIdentMLFile, boolean inMemory, boolean avoidProteinInference) throws ConfigurationException
ConfigurationException
public List<uk.ac.ebi.jmzidml.model.mzidml.Sample> getSampleList()
public List<uk.ac.ebi.jmzidml.model.mzidml.SourceFile> getSourceFiles()
public List<uk.ac.ebi.jmzidml.model.mzidml.AnalysisSoftware> getSoftwares()
public List<uk.ac.ebi.jmzidml.model.mzidml.Person> getPersonContacts()
public List<uk.ac.ebi.jmzidml.model.mzidml.Organization> getOrganizationContacts()
public Iterator<uk.ac.ebi.jmzidml.model.mzidml.BibliographicReference> getReferences()
public uk.ac.ebi.jmzidml.model.mzidml.ProteinDetectionHypothesis getIdentificationById(Comparable identId) throws JAXBException
JAXBException
public int getNumIdentifiedPeptides() throws ConfigurationException
ConfigurationException
public uk.ac.ebi.jmzidml.model.mzidml.FragmentationTable getFragmentationTable()
public List<uk.ac.ebi.jmzidml.model.mzidml.Cv> getCvList()
public String getMzIdentMLName()
getMzIdentMLName
in class uk.ac.ebi.jmzidml.xml.io.MzIdentMLUnmarshaller
public Date getCreationDate()
public uk.ac.ebi.jmzidml.model.mzidml.Provider getProvider()
public List<uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationProtocol> getSpectrumIdentificationProtocol()
public uk.ac.ebi.jmzidml.model.mzidml.ProteinDetectionProtocol getProteinDetectionProtocol()
public List<uk.ac.ebi.jmzidml.model.mzidml.SearchDatabase> getSearchDatabases()
public List<uk.ac.ebi.jmzidml.model.mzidml.SpectraData> getSpectraData()
public Map<Comparable,uk.ac.ebi.jmzidml.model.mzidml.SpectraData> getSpectraDataMap()
public uk.ac.ebi.jmzidml.model.mzidml.ProteinAmbiguityGroup getProteinAmbiguityGroup(Comparable id) throws JAXBException
JAXBException
public uk.ac.ebi.jmzidml.model.mzidml.DBSequence getDBSequenceById(Comparable id) throws JAXBException
JAXBException
public boolean hasProteinGroup() throws ConfigurationException
ConfigurationException
public List<uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationItem> getSpectrumIdentificationsByIds(List<Comparable> spectrumIdentIds) throws JAXBException
JAXBException
public Set<String> getSpectrumIdentificationItemIds(String spectrumIdentResultId) throws JAXBException
JAXBException
public Set<String> getPeptideEvidenceReferences(String spectrumIdentResultId, String spectrumIdentItemId)
public boolean hasProteinSequence() throws ConfigurationException
ConfigurationException
public boolean hasDecoyInformation() throws ConfigurationException
ConfigurationException
public List<Comparable> getTitleReferenceFile(Map<Comparable,uk.ac.ebi.jmzidml.model.mzidml.SpectraData> spectraDataMap) throws JAXBException
spectraDataMap
- Map of all the SpectraDataJAXBException
public Comparable getMGFTitleReference(String spectrumIdentResultId) throws JAXBException
JAXBException
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