Package uk.ac.ebi.pride.jmztab2.utils.parser

Class SMELineParser

java.lang.Object

uk.ac.ebi.pride.jmztab2.utils.parser.MZTabLineParser

uk.ac.ebi.pride.jmztab2.utils.parser.MZTabDataLineParser<de.isas.mztab2.model.SmallMoleculeEvidence>

uk.ac.ebi.pride.jmztab2.utils.parser.SMELineParser

public class SMELineParser
extends MZTabDataLineParser<de.isas.mztab2.model.SmallMoleculeEvidence>

SMELineParser class.

Since:

11/09/17

Author:

nilshoffmann

Field Summary

Fields inherited from class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabDataLineParser

exchangeMapping, factory, mapping, metadata, positionMapping

Fields inherited from class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabLineParser

context, errorList, items, line, lineNumber, section

Constructor Summary

Constructors

Constructor	Description
SMELineParser(MZTabParserContext context, MZTabColumnFactory factory, PositionMapping positionMapping, de.isas.mztab2.model.Metadata metadata, uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorList errorList)	Constructor for SMELineParser.

Method Summary

Modifier and Type	Method	Description
protected int	checkData()	Check and translate the columns into mzTab elements.
de.isas.mztab2.model.SmallMoleculeEvidence	getRecord()	Retrieve the data line to a type mzTab domain object.

Methods inherited from class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabDataLineParser

checkAmbiguityMembers, checkBestSearchEngineScore, checkCalcMassToCharge, checkCharge, checkChemicalFormula, checkData, checkDatabase, checkDatabaseVersion, checkDescription, checkDouble, checkDouble, checkDoubleList, checkEnd, checkExpMassToCharge, checkGOTerms, checkIdentifier, checkInchiKey, checkInteger, checkInteger, checkIntegerList, checkIntegerList, checkMassToCharge, checkMZBoolean, checkNumPeptidesDistinct, checkNumPeptidesUnique, checkNumPSMs, checkParameter, checkParamList, checkPost, checkPre, checkProteinCoverage, checkPSMID, checkRetentionTime, checkRetentionTimeWindow, checkSearchEngine, checkSearchEngineScore, checkSequence, checkSmiles, checkSpecies, checkSpectraRef, checkSpectraRef, checkStart, checkString, checkString, checkStringList, checkTaxid, checkUnique, checkURI, loadBestSearchEngineScoreId, loadSearchEngineScoreId, parse

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

SMELineParser

public SMELineParser(MZTabParserContext context,
                     MZTabColumnFactory factory,
                     PositionMapping positionMapping,
                     de.isas.mztab2.model.Metadata metadata,
                     uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorList errorList)

Constructor for SMELineParser.

Parameters:

context - a MZTabParserContext object.

factory - a MZTabColumnFactory object.

positionMapping - a PositionMapping object.

metadata - a Metadata object.

errorList - a MZTabErrorList object.

Method Detail

checkData

protected int checkData()

Check and translate the columns into mzTab elements.

Specified by:

checkData in class MZTabDataLineParser<de.isas.mztab2.model.SmallMoleculeEvidence>

Returns:

a int.

getRecord

public de.isas.mztab2.model.SmallMoleculeEvidence getRecord()

Retrieve the data line to a type mzTab domain object.

Specified by:

getRecord in class MZTabDataLineParser<de.isas.mztab2.model.SmallMoleculeEvidence>

Returns:

a typed mzTab domain object.