public class HQMzIdentMLMzTabConverter extends MzIdentMLMzTabConverter
Modifier and Type | Field and Description |
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protected static org.apache.log4j.Logger |
logger |
static String |
NO_THRESHOLD |
static String |
NO_THRESHOLD_MS_AC |
CHEMMOD, PEPTIDE_C_TERM, PEPTIDE_N_TERM, PROTEIN_C_TERM, PROTEIN_N_TERM, proteinIds, spectraToRun, UNKNOWN_MODIFICATION, variableModifications
metadata, proteinColumnFactory, proteinScoreToScoreIndex, psmColumnFactory, psmScoreToScoreIndex
Constructor and Description |
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HQMzIdentMLMzTabConverter(MzIdentMLControllerImpl controller)
Default constructor
|
Modifier and Type | Method and Description |
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protected uk.ac.ebi.pride.jmztab.model.MZTabColumnFactory |
convertProteinColumnFactory()
Generate
MZTabColumnFactory which maintain a couple of ProteinColumn |
protected void |
fillData()
Fill records into model.
|
protected List<uk.ac.ebi.pride.utilities.data.exporters.HQMzIdentMLMzTabConverter.AmbiguityGroup> |
getProteinGroupById(List<Protein> proteins,
ProteinFilter proteinFilter,
PeptideFilter peptidesFilter) |
convertMetadata, convertPSMColumnFactory, getDatabaseName, getDescriptionFromCVParams, isIdentification, isSupported, loadExperimentParams, loadGelData, loadInstrument, loadMetadataModifications, loadModifications, loadMsRun, loadProtein, loadPSMs, loadPSMs, loadSampleProcessing, loadSamples, loadSoftware
generateAccession, generateAccession, init, loadContacts, loadReferences, loadSearchEngineScores
protected static org.apache.log4j.Logger logger
public static final String NO_THRESHOLD_MS_AC
public static final String NO_THRESHOLD
public HQMzIdentMLMzTabConverter(MzIdentMLControllerImpl controller)
controller
- The DataAccessController to be Converted to MzTabprotected uk.ac.ebi.pride.jmztab.model.MZTabColumnFactory convertProteinColumnFactory()
MzIdentMLMzTabConverter
MZTabColumnFactory
which maintain a couple of ProteinColumn
convertProteinColumnFactory
in class MzIdentMLMzTabConverter
protected void fillData()
ConvertProvider.getMZTabFile()
method.fillData
in class MzIdentMLMzTabConverter
protected List<uk.ac.ebi.pride.utilities.data.exporters.HQMzIdentMLMzTabConverter.AmbiguityGroup> getProteinGroupById(List<Protein> proteins, ProteinFilter proteinFilter, PeptideFilter peptidesFilter)
Copyright © 2015 European Bioinformatics Institute. All Rights Reserved.