public class PRIDEMzTabConverter extends AbstractMzTabConverter
Modifier and Type | Field and Description |
---|---|
static String |
EMPAI |
static String |
GEL_COORDINATES |
static String |
GEL_IDENTIFIER |
static String |
GEL_SPOTIDENTIFIER |
logger, metadata, proteinColumnFactory, proteinScoreToScoreIndex, psmColumnFactory, psmScoreToScoreIndex
Constructor and Description |
---|
PRIDEMzTabConverter(DataAccessController controller) |
Modifier and Type | Method and Description |
---|---|
protected uk.ac.ebi.pride.jmztab.model.MZTabColumnFactory |
convertProteinColumnFactory()
Generate
MZTabColumnFactory which maintain a couple of ProteinColumn |
protected void |
fillData()
Fill the data from the file, proteins and PSMs
|
protected void |
loadExperimentParams()
Processes the experiment additional params: (f.e.
|
protected void |
loadGelData()
Load Gel Data
|
protected void |
loadInstrument()
Retrieve the data for instrument in and Instrument Processing (Analyzer, Source and Detector)
|
protected void |
loadMsRun()
Load all the files related with the original Identification file
|
protected void |
loadSampleProcessing()
Load Sample Processing should be implemented by different controllers
|
protected void |
loadSamples()
Adds the sample parameters (species, tissue, cell type, disease) to the unit and the various sub-samples.
|
protected void |
loadSoftware()
Load software information
|
convertMetadata, convertPSMColumnFactory, generateAccession, generateAccession, init, isIdentification, isSupported, loadContacts, loadReferences, loadSearchEngineScores
public static final String GEL_IDENTIFIER
public static final String GEL_SPOTIDENTIFIER
public static final String EMPAI
public static final String GEL_COORDINATES
public PRIDEMzTabConverter(DataAccessController controller)
protected void loadGelData()
AbstractMzTabConverter
loadGelData
in class AbstractMzTabConverter
protected void loadExperimentParams()
AbstractMzTabConverter
loadExperimentParams
in class AbstractMzTabConverter
protected void loadSoftware()
AbstractMzTabConverter
loadSoftware
in class AbstractMzTabConverter
protected void loadSamples()
AbstractMzTabConverter
loadSamples
in class AbstractMzTabConverter
protected void loadSampleProcessing()
AbstractMzTabConverter
loadSampleProcessing
in class AbstractMzTabConverter
protected void loadInstrument()
loadInstrument
in class AbstractMzTabConverter
protected void loadMsRun()
AbstractMzTabConverter
loadMsRun
in class AbstractMzTabConverter
protected uk.ac.ebi.pride.jmztab.model.MZTabColumnFactory convertProteinColumnFactory()
MZTabColumnFactory
which maintain a couple of ProteinColumn
convertProteinColumnFactory
in class AbstractMzTabConverter
protected void fillData()
fillData
in class AbstractMzTabConverter
Copyright © 2015 European Bioinformatics Institute. All Rights Reserved.