public class MzTabUnmarshallerAdaptor
extends uk.ac.ebi.pride.jmztab.utils.MZTabFileParser
Constructor and Description |
---|
MzTabUnmarshallerAdaptor(File tabFile,
OutputStream out) |
Modifier and Type | Method and Description |
---|---|
List<uk.ac.ebi.pride.jmztab.model.Param> |
getAdditionalParams()
Retrieve a general description from the file
|
uk.ac.ebi.pride.utilities.util.Tuple<Map<String,List<String>>,Map<String,List<String>>> |
getAllProteinAccessions()
Retrieve the Map of proteins with the corresponding list of PSMs for each protein.
|
Map<Integer,uk.ac.ebi.pride.jmztab.model.Protein> |
getAllProteins() |
Map<Integer,uk.ac.ebi.pride.jmztab.model.Assay> |
getAssays() |
Map<Integer,uk.ac.ebi.pride.jmztab.model.Contact> |
getContacts() |
Set<uk.ac.ebi.pride.utilities.util.Tuple<String,String>> |
getDatabases() |
Map<Integer,uk.ac.ebi.pride.jmztab.model.Software> |
getDataSoftwares() |
String |
getExpAccession() |
String |
getExpTitle() |
Map<Integer,uk.ac.ebi.pride.jmztab.model.Instrument> |
getInstrument() |
uk.ac.ebi.pride.jmztab.model.Metadata |
getMetadata() |
Map<Integer,uk.ac.ebi.pride.jmztab.model.MsRun> |
getMRunMap() |
int |
getNumberOfPeptides(int rank) |
int |
getNumIdentifiedPeptides() |
Map<String,uk.ac.ebi.pride.jmztab.model.Peptide> |
getPeptideByIds(List<Comparable> peptideIds) |
Map<Integer,uk.ac.ebi.pride.jmztab.model.Peptide> |
getPeptides() |
uk.ac.ebi.pride.utilities.util.Tuple<Integer,uk.ac.ebi.pride.jmztab.model.Protein> |
getProteinById(Comparable proteinId)
It would look if the protein is in the file and retrieve the data, if the accession is not in the file with information
it would create an empty entry Protein for it.
|
List<String> |
getProteinGroupIds() |
SortedMap<Integer,uk.ac.ebi.pride.jmztab.model.SplitList<uk.ac.ebi.pride.jmztab.model.Param>> |
getProtocol() |
Map<Integer,uk.ac.ebi.pride.jmztab.model.PSM> |
getPSMs() |
Map<Integer,List<String>> |
getPSMtoMsRunMap() |
Map<Integer,uk.ac.ebi.pride.jmztab.model.Publication> |
getReferences()
Retrieve all publications from mzTab file
|
Map<Integer,uk.ac.ebi.pride.jmztab.model.Sample> |
getSamples() |
Map<Integer,uk.ac.ebi.pride.jmztab.model.MsRun> |
getSourceFiles() |
Map<String,uk.ac.ebi.pride.jmztab.model.PSM> |
getSpectrumIdentificationsByIds(List<Comparable> spectrumIdentIds) |
Map<Integer,uk.ac.ebi.pride.jmztab.model.StudyVariable> |
getStudyVariables() |
String |
getVersion() |
boolean |
hasProteinGroup() |
boolean |
hasProteinSequence() |
boolean |
hasQuantitationData() |
public MzTabUnmarshallerAdaptor(File tabFile, OutputStream out) throws IOException
IOException
public Map<Integer,uk.ac.ebi.pride.jmztab.model.StudyVariable> getStudyVariables()
public Map<Integer,uk.ac.ebi.pride.jmztab.model.Publication> getReferences()
public List<uk.ac.ebi.pride.jmztab.model.Param> getAdditionalParams()
public String getExpTitle()
public String getExpAccession()
public String getVersion()
public int getNumberOfPeptides(int rank)
public boolean hasProteinSequence()
public boolean hasProteinGroup()
public uk.ac.ebi.pride.utilities.util.Tuple<Map<String,List<String>>,Map<String,List<String>>> getAllProteinAccessions()
public SortedMap<Integer,uk.ac.ebi.pride.jmztab.model.SplitList<uk.ac.ebi.pride.jmztab.model.Param>> getProtocol()
public uk.ac.ebi.pride.utilities.util.Tuple<Integer,uk.ac.ebi.pride.jmztab.model.Protein> getProteinById(Comparable proteinId)
proteinId
- Protein Identifierpublic Map<String,uk.ac.ebi.pride.jmztab.model.PSM> getSpectrumIdentificationsByIds(List<Comparable> spectrumIdentIds)
public uk.ac.ebi.pride.jmztab.model.Metadata getMetadata()
public int getNumIdentifiedPeptides()
public boolean hasQuantitationData()
public Map<String,uk.ac.ebi.pride.jmztab.model.Peptide> getPeptideByIds(List<Comparable> peptideIds)
Copyright © 2015 European Bioinformatics Institute. All Rights Reserved.