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
All Methods Instance Methods Concrete Methods 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
-
-
-
-
Constructor Detail
-
SMLLineParser
public SMLLineParser(MZTabParserContext context, MZTabColumnFactory factory, PositionMapping positionMapping, Metadata metadata, MZTabErrorList errorList)
Constructor for SMLLineParser.
- Parameters:
context
- aMZTabParserContext
object.factory
- aMZTabColumnFactory
object.positionMapping
- aPositionMapping
object.metadata
- aMetadata
object.errorList
- aMZTabErrorList
object.
-
-
Method Detail
-
checkData
protected int checkData()
Check and translate the columns into mzTab elements.- Specified by:
checkData
in classMZTabDataLineParser<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 classMZTabDataLineParser<SmallMoleculeSummary>
- Returns:
- a
SmallMoleculeSummary
object.
-
-