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

Class SMLLineParser

java.lang.Object

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

uk.ac.ebi.pride.jmztab2.utils.parser.MZTabDataLineParser<SmallMoleculeSummary>

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

public class SMLLineParser
extends MZTabDataLineParser<SmallMoleculeSummary>

SMLLineParser class.

Since:

10/02/13

Author:

qingwei, 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
SMLLineParser(MZTabParserContext context, MZTabColumnFactory factory, PositionMapping positionMapping, Metadata metadata, MZTabErrorList errorList)	Constructor for SMLLineParser.

Method Summary

Modifier and Type	Method	Description
protected int	checkData()	Check and translate the columns into mzTab elements.
protected void	checkItemNumbers(MZTabErrorList errorList, int lineNumber, List<?> reference, SmallMoleculeSummary.Properties referenceProperty, List<?> toCheck, SmallMoleculeSummary.Properties toCheckProperty)
protected void	checkRegexMatches(MZTabErrorList errorList, int lineNumber, SmallMoleculeSummary.Properties elementProperty, String regularExpression, List<String> elements)
SmallMoleculeSummary	getRecord()	getRecord.

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, 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

SMLLineParser

public SMLLineParser(MZTabParserContext context,
                     MZTabColumnFactory factory,
                     PositionMapping positionMapping,
                     Metadata metadata,
                     MZTabErrorList errorList)

Constructor for SMLLineParser.

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<SmallMoleculeSummary>

Returns:

a int.

checkRegexMatches

protected void checkRegexMatches(MZTabErrorList errorList,
                                 int lineNumber,
                                 SmallMoleculeSummary.Properties elementProperty,
                                 String regularExpression,
                                 List<String> elements)

checkItemNumbers

protected void checkItemNumbers(MZTabErrorList errorList,
                                int lineNumber,
                                List<?> reference,
                                SmallMoleculeSummary.Properties referenceProperty,
                                List<?> toCheck,
                                SmallMoleculeSummary.Properties toCheckProperty)
                         throws MZTabErrorOverflowException

Throws:

MZTabErrorOverflowException

getRecord

public SmallMoleculeSummary getRecord()

getRecord.

Specified by:

getRecord in class MZTabDataLineParser<SmallMoleculeSummary>

Returns:

a SmallMoleculeSummary object.