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

Class SMFLineParser

java.lang.Object

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

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

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

public class SMFLineParser
extends MZTabDataLineParser<de.isas.mztab2.model.SmallMoleculeFeature>

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

Method Summary

Modifier and Type	Method	Description
protected int	checkData()	Check and translate the columns into mzTab elements.
protected void	checkRegexMatches(uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorList errorList, int lineNumber, de.isas.mztab2.model.SmallMoleculeFeature.Properties elementProperty, String regularExpression, List<String> elements)
de.isas.mztab2.model.SmallMoleculeFeature	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

SMFLineParser

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

Constructor for SMFLineParser.

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.SmallMoleculeFeature>

Returns:

a int.

checkRegexMatches

protected void checkRegexMatches(uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorList errorList,
                                 int lineNumber,
                                 de.isas.mztab2.model.SmallMoleculeFeature.Properties elementProperty,
                                 String regularExpression,
                                 List<String> elements)

getRecord

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

Retrieve the data line to a type mzTab domain object.

Specified by:

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

Returns:

a typed mzTab domain object.