public abstract class AbstractMzTabConverter extends uk.ac.ebi.pride.jmztab.utils.convert.ConvertProvider<DataAccessController,Void>
Modifier and Type | Field and Description |
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protected static org.apache.log4j.Logger |
logger |
protected uk.ac.ebi.pride.jmztab.model.Metadata |
metadata |
protected uk.ac.ebi.pride.jmztab.model.MZTabColumnFactory |
proteinColumnFactory |
protected Map<String,Integer> |
proteinScoreToScoreIndex |
protected uk.ac.ebi.pride.jmztab.model.MZTabColumnFactory |
psmColumnFactory |
protected Map<String,Integer> |
psmScoreToScoreIndex |
Constructor and Description |
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AbstractMzTabConverter(DataAccessController controller) |
Modifier and Type | Method and Description |
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protected uk.ac.ebi.pride.jmztab.model.Metadata |
convertMetadata()
Generate
Metadata |
protected abstract 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 abstract void |
fillData()
Fill records into model.
|
protected static String |
generateAccession(Peptide identification) |
protected static String |
generateAccession(Protein identification) |
protected void |
init() |
protected boolean |
isIdentification()
Only one sample means this file is Identification and Complete.
|
protected static boolean |
isSupported(DataAccessController controller)
This function validate if the file is supported in this case it only supports MZIdentML, PRIDE XML and MzTab
|
protected void |
loadContacts()
Converts a list of Contacts into an ArrayList of mzTab Contacts.
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protected abstract void |
loadExperimentParams()
Processes the experiment additional params: (f.e.
|
protected abstract void |
loadGelData()
Load Gel Data
|
protected abstract void |
loadInstrument()
Load Instrument should be implemented by different controllers
|
protected abstract void |
loadMsRun()
Load all the files related with the original Identification file
|
protected void |
loadReferences()
Converts the experiment's references into a couple of
PublicationItem (including DOIs and PubMed ids) |
protected abstract void |
loadSampleProcessing()
Load Sample Processing should be implemented by different controllers
|
protected abstract void |
loadSamples()
Adds the sample parameters (species, tissue, cell type, disease) to the unit and the various sub-samples.
|
protected void |
loadSearchEngineScores() |
protected abstract void |
loadSoftware()
Load software information
|
protected static final org.apache.log4j.Logger logger
protected uk.ac.ebi.pride.jmztab.model.Metadata metadata
protected uk.ac.ebi.pride.jmztab.model.MZTabColumnFactory proteinColumnFactory
protected uk.ac.ebi.pride.jmztab.model.MZTabColumnFactory psmColumnFactory
public AbstractMzTabConverter(DataAccessController controller)
protected void init()
init
in class uk.ac.ebi.pride.jmztab.utils.convert.ConvertProvider<DataAccessController,Void>
protected uk.ac.ebi.pride.jmztab.model.Metadata convertMetadata()
Metadata
convertMetadata
in class uk.ac.ebi.pride.jmztab.utils.convert.ConvertProvider<DataAccessController,Void>
protected abstract void loadSoftware()
protected void loadReferences()
PublicationItem
(including DOIs and PubMed ids)protected void loadContacts()
protected abstract void loadExperimentParams()
protected abstract void loadSampleProcessing()
protected abstract void loadInstrument()
protected void loadSearchEngineScores()
protected abstract void loadMsRun()
protected abstract void loadSamples()
protected abstract void loadGelData()
protected abstract uk.ac.ebi.pride.jmztab.model.MZTabColumnFactory convertProteinColumnFactory()
MZTabColumnFactory
which maintain a couple of ProteinColumn
convertProteinColumnFactory
in class uk.ac.ebi.pride.jmztab.utils.convert.ConvertProvider<DataAccessController,Void>
protected uk.ac.ebi.pride.jmztab.model.MZTabColumnFactory convertPSMColumnFactory()
MZTabColumnFactory
which maintain a couple of PSMColumn
convertPSMColumnFactory
in class uk.ac.ebi.pride.jmztab.utils.convert.ConvertProvider<DataAccessController,Void>
protected abstract void fillData()
ConvertProvider.getMZTabFile()
method.fillData
in class uk.ac.ebi.pride.jmztab.utils.convert.ConvertProvider<DataAccessController,Void>
protected boolean isIdentification()
protected static boolean isSupported(DataAccessController controller)
controller
- DataAccessControllerCopyright © 2015 European Bioinformatics Institute. All Rights Reserved.