public class MzIdentMLMzTabConverter extends AbstractMzTabConverter
Modifier and Type | Field and Description |
---|---|
static String |
CHEMMOD |
protected static org.apache.log4j.Logger |
logger |
static String |
PEPTIDE_C_TERM |
static String |
PEPTIDE_N_TERM |
static String |
PROTEIN_C_TERM |
static String |
PROTEIN_N_TERM |
protected Set<Comparable> |
proteinIds |
protected Map<Comparable,Integer> |
spectraToRun |
static String |
UNKNOWN_MODIFICATION |
protected Map<uk.ac.ebi.pride.jmztab.model.Param,Set<String>> |
variableModifications |
metadata, proteinColumnFactory, proteinScoreToScoreIndex, psmColumnFactory, psmScoreToScoreIndex
Constructor and Description |
---|
MzIdentMLMzTabConverter(MzIdentMLControllerImpl controller)
Default constructor
|
Modifier and Type | Method and Description |
---|---|
protected uk.ac.ebi.pride.jmztab.model.Metadata |
convertMetadata()
Returns the converted metadata, now including a check for chromosome information present, and if so,
is set as a user param entry.
|
protected uk.ac.ebi.pride.jmztab.model.MZTabColumnFactory |
convertProteinColumnFactory()
Generate
MZTabColumnFactory which maintain a couple of ProteinColumn |
protected uk.ac.ebi.pride.jmztab.model.MZTabColumnFactory |
convertPSMColumnFactory()
Generate
MZTabColumnFactory which maintain a couple of PSMColumn |
protected void |
fillData()
Fill records into model.
|
protected String |
getDatabaseName(List<CvParam> databaseName,
List<UserParam> userParam) |
protected String |
getDescriptionFromCVParams(List<CvParam> cvParams) |
protected boolean |
isIdentification()
MzIdentML is always an Identification File
|
static boolean |
isSupported(DataAccessController controller) |
protected void |
loadExperimentParams()
Processes the experiment additional params: (f.e.
|
protected void |
loadGelData()
Load Gel Data
|
protected void |
loadInstrument()
Load Instrument should be implemented by different controllers
|
protected void |
loadMetadataModifications() |
protected void |
loadModifications(uk.ac.ebi.pride.jmztab.model.Protein protein,
List<Peptide> items) |
protected void |
loadMsRun()
Load all the files related with the original Identification file
|
protected uk.ac.ebi.pride.jmztab.model.Protein |
loadProtein(Protein msProtein,
List<Peptide> peptides) |
protected List<uk.ac.ebi.pride.jmztab.model.PSM> |
loadPSMs(List<Comparable> ids) |
protected List<uk.ac.ebi.pride.jmztab.model.PSM> |
loadPSMs(Protein protein,
List<Peptide> peptides)
Converts the passed Identification object into an MzTab PSM.
|
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
|
generateAccession, generateAccession, init, loadContacts, loadReferences, loadSearchEngineScores
public static final String PEPTIDE_N_TERM
public static final String PROTEIN_N_TERM
public static final String PEPTIDE_C_TERM
public static final String PROTEIN_C_TERM
public static final String CHEMMOD
public static final String UNKNOWN_MODIFICATION
protected static org.apache.log4j.Logger logger
protected Map<Comparable,Integer> spectraToRun
protected Map<uk.ac.ebi.pride.jmztab.model.Param,Set<String>> variableModifications
protected Set<Comparable> proteinIds
public MzIdentMLMzTabConverter(MzIdentMLControllerImpl controller)
controller
- The DataAccessController to be Converted to MzTabprotected boolean isIdentification()
isIdentification
in class AbstractMzTabConverter
protected void loadInstrument()
AbstractMzTabConverter
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 uk.ac.ebi.pride.jmztab.model.MZTabColumnFactory convertPSMColumnFactory()
MZTabColumnFactory
which maintain a couple of PSMColumn
convertPSMColumnFactory
in class AbstractMzTabConverter
protected void fillData()
ConvertProvider.getMZTabFile()
method.fillData
in class AbstractMzTabConverter
protected void loadMetadataModifications()
protected void loadSoftware()
AbstractMzTabConverter
loadSoftware
in class AbstractMzTabConverter
protected void loadExperimentParams()
loadExperimentParams
in class AbstractMzTabConverter
protected void loadSampleProcessing()
AbstractMzTabConverter
loadSampleProcessing
in class AbstractMzTabConverter
protected void loadSamples()
loadSamples
in class AbstractMzTabConverter
protected void loadGelData()
AbstractMzTabConverter
loadGelData
in class AbstractMzTabConverter
protected List<uk.ac.ebi.pride.jmztab.model.PSM> loadPSMs(List<Comparable> ids)
protected List<uk.ac.ebi.pride.jmztab.model.PSM> loadPSMs(Protein protein, List<Peptide> peptides)
protected uk.ac.ebi.pride.jmztab.model.Protein loadProtein(Protein msProtein, List<Peptide> peptides)
protected void loadModifications(uk.ac.ebi.pride.jmztab.model.Protein protein, List<Peptide> items)
protected String getDatabaseName(List<CvParam> databaseName, List<UserParam> userParam)
public static boolean isSupported(DataAccessController controller)
protected uk.ac.ebi.pride.jmztab.model.Metadata convertMetadata()
convertMetadata
in class AbstractMzTabConverter
Copyright © 2015 European Bioinformatics Institute. All Rights Reserved.