Uses of Class
uk.ac.ebi.pride.jmztab2.utils.errors.MZTabException

Packages that use MZTabException

Package	Description
de.isas.mztab2.io	This package contains implementations for reading and writing of mzTab-M files.
uk.ac.ebi.pride.jmztab2.model	This package contains model classes for mzTab-M structural features like mandatory and optional columns.
uk.ac.ebi.pride.jmztab2.utils.parser	This package contains text file line parser implementations for the mzTab-M document sections.

Uses of MZTabException in de.isas.mztab2.io

Methods in de.isas.mztab2.io that throw MZTabException

Modifier and Type	Method	Description
com.fasterxml.jackson.dataformat.csv.CsvSchema	MzTabWriterDefaults.smallMoleculeEvidenceSchema(com.fasterxml.jackson.dataformat.csv.CsvMapper mapper, MzTab mzTabFile)	Creates the csv schema (column names and types) for the small molecule feature section.
com.fasterxml.jackson.dataformat.csv.CsvSchema	MzTabWriterDefaults.smallMoleculeFeatureSchema(com.fasterxml.jackson.dataformat.csv.CsvMapper mapper, MzTab mzTabFile)	Creates the csv schema (column names and types) for the small molecule feature section.
com.fasterxml.jackson.dataformat.csv.CsvSchema	MzTabWriterDefaults.smallMoleculeSummarySchema(com.fasterxml.jackson.dataformat.csv.CsvMapper mapper, MzTab mzTabFile)	Creates the csv schema (column names and types) for the small molecule summary section.

Uses of MZTabException in uk.ac.ebi.pride.jmztab2.model

Methods in uk.ac.ebi.pride.jmztab2.model that throw MZTabException

Modifier and Type	Method	Description
static Publication	MZTabUtils.parsePublicationItems(Publication publication, int lineNumber, String target)	A publication on this unit.

Uses of MZTabException in uk.ac.ebi.pride.jmztab2.utils.parser

Methods in uk.ac.ebi.pride.jmztab2.utils.parser that throw MZTabException

Modifier and Type	Method	Description
protected int	MZTabHeaderLineParser.checkAbundanceColumns(int offset, String order)	checkAbundanceColumns.
protected boolean	MZTabHeaderLineParser.checkOptColumnName(String nameLabel)	Additional columns can be added to the end of the protein table.
protected void	MTDLineParser.handleAssay(Matcher matcher, String defineLabel, MetadataElement element, String valueLabel)
protected void	MTDLineParser.handleContact(String defineLabel, Matcher matcher, MetadataElement element, String valueLabel)
protected void	MTDLineParser.handleCustom(String defineLabel, Matcher matcher, String valueLabel)
protected void	MTDLineParser.handleCv(String defineLabel, Matcher matcher, MetadataElement element, String valueLabel)
protected void	MTDLineParser.handleDatabase(String defineLabel, Matcher matcher, MetadataElement element, String valueLabel)
protected void	MTDLineParser.handleDerivatizationAgent(String defineLabel, Matcher matcher, String valueLabel)
protected void	MTDLineParser.handleDescription(String defineLabel, String valueLabel)
protected void	MTDLineParser.handleExternalStudyUri(String defineLabel, Matcher matcher, String valueLabel)
protected void	MTDLineParser.handleIdConfidenceMeasure(String defineLabel, Matcher matcher, String valueLabel)
protected void	MTDLineParser.handleInstrument(String defineLabel, Matcher matcher, MetadataElement element, String valueLabel)
protected void	MTDLineParser.handleMsRun(String defineLabel, Matcher matcher, MetadataElement element, String valueLabel)
protected void	MTDLineParser.handleMzTab(MetadataElement element, Matcher matcher, String defineLabel, String valueLabel)
protected void	MTDLineParser.handlePublication(String defineLabel, Matcher matcher, String valueLabel)
protected void	MTDLineParser.handleQuantificationMethod(String defineLabel, String valueLabel)
protected void	MTDLineParser.handleSample(String defineLabel, Matcher matcher, MetadataElement element, String valueLabel)
protected void	MTDLineParser.handleSampleProcessing(String defineLabel, Matcher matcher, String valueLabel)
protected void	MTDLineParser.handleSmallMolecule(MetadataElement element, Matcher matcher, String defineLabel, String valueLabel)
protected void	MTDLineParser.handleSmallMoleculeFeature(MetadataElement element, Matcher matcher, String defineLabel, String valueLabel)
protected void	MTDLineParser.handleSoftware(String defineLabel, Matcher matcher, MetadataElement element, String valueLabel)
protected void	MTDLineParser.handleStudyVariable(String defineLabel, Matcher matcher, MetadataElement element, String valueLabel)
protected void	MTDLineParser.handleTitle(String defineLabel, String valueLabel)
protected void	MTDLineParser.handleUri(String defineLabel, Matcher matcher, String valueLabel, boolean mandatory)
void	COMLineParser.parse(int lineNumber, String line, MZTabErrorList errorList)	We assume that user before call this method, have parse the raw line is not empty line and start with section prefix.
void	MTDLineParser.parse(int lineNumber, String mtdLine, MZTabErrorList errorList)	We assume that user before call this method, have parse the raw line is not empty line and start with section prefix.
void	MZTabDataLineParser.parse(int lineNumber, String line, MZTabErrorList errorList)	We assume that user before call this method, have parse the raw line is not empty line and start with section prefix.
void	MZTabHeaderLineParser.parse(int lineNumber, String line, MZTabErrorList errorList)	We assume that user before call this method, have parse the raw line is not empty line and start with section prefix.
protected void	MZTabLineParser.parse(int lineNumber, String line, MZTabErrorList errorList)	We assume that user before call this method, have parse the raw line is not empty line and start with section prefix.
protected abstract int	MZTabHeaderLineParser.parseColumns()	This methods delegates to the subclasses the parsing of the columns.
protected int	SEHLineParser.parseColumns()	This methods delegates to the subclasses the parsing of the columns.
protected int	SFHLineParser.parseColumns()	This methods delegates to the subclasses the parsing of the columns.
protected int	SMHLineParser.parseColumns()	This methods delegates to the subclasses the parsing of the columns.
protected int	MZTabHeaderLineParser.parseIndex(String header, String id)	Parse header to a index id number.
protected abstract void	MZTabHeaderLineParser.refine()	Some validate operation need to be done after the whole MZTabColumnFactory created.
protected void	SEHLineParser.refine()	Some validate operation need to be done after the whole MZTabColumnFactory created.
protected void	SFHLineParser.refine()	Some validate operation need to be done after the whole MZTabColumnFactory created.
protected void	SMHLineParser.refine()	Some validate operation need to be done after the whole MZTabColumnFactory created.
void	MTDLineParser.refineNormalMetadata()	Refine the metadata, and check whether missing some important information. fixed_mode, variable_mode must provide in the Complete file.
protected void	MZTabHeaderLineParser.refineOptionalColumn(Section section, String columnHeader)	Refine optional columns and check, whether they were properly defined.