Class SMFLineParser
- java.lang.Object
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- uk.ac.ebi.pride.jmztab2.utils.parser.MZTabLineParser
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- uk.ac.ebi.pride.jmztab2.utils.parser.MZTabDataLineParser<SmallMoleculeFeature>
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- uk.ac.ebi.pride.jmztab2.utils.parser.SMFLineParser
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public class SMFLineParser extends MZTabDataLineParser<SmallMoleculeFeature>
SMFLineParser class.
- Since:
- 11/09/17
- Author:
- nilshoffmann
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Field Summary
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Fields inherited from class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabDataLineParser
exchangeMapping, factory, mapping, metadata, positionMapping
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Fields inherited from class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabLineParser
context, errorList, items, line, lineNumber, section
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Constructor Summary
Constructors Constructor Description SMFLineParser(MZTabParserContext context, MZTabColumnFactory factory, PositionMapping positionMapping, Metadata metadata, MZTabErrorList errorList)
Constructor for SMFLineParser.
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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
checkRegexMatches(MZTabErrorList errorList, int lineNumber, SmallMoleculeFeature.Properties elementProperty, String regularExpression, List<String> elements)
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, checkStart, checkString, checkString, checkStringList, checkTaxid, checkUnique, checkURI, loadBestSearchEngineScoreId, loadSearchEngineScoreId, parse
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Constructor Detail
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SMFLineParser
public SMFLineParser(MZTabParserContext context, MZTabColumnFactory factory, PositionMapping positionMapping, Metadata metadata, MZTabErrorList errorList)
Constructor for SMFLineParser.
- Parameters:
context
- aMZTabParserContext
object.factory
- aMZTabColumnFactory
object.positionMapping
- aPositionMapping
object.metadata
- aMetadata
object.errorList
- aMZTabErrorList
object.
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Method Detail
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checkData
protected int checkData()
Check and translate the columns into mzTab elements.- Specified by:
checkData
in classMZTabDataLineParser<SmallMoleculeFeature>
- Returns:
- a int.
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checkRegexMatches
protected void checkRegexMatches(MZTabErrorList errorList, int lineNumber, SmallMoleculeFeature.Properties elementProperty, String regularExpression, List<String> elements)
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getRecord
public SmallMoleculeFeature getRecord()
Retrieve the data line to a type mzTab domain object.- Specified by:
getRecord
in classMZTabDataLineParser<SmallMoleculeFeature>
- Returns:
- a typed mzTab domain object.
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