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

Class SMHLineParser

java.lang.Object

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

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

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

public class SMHLineParser
extends MZTabHeaderLineParser

Parse and validate Small Molecule header line into a MZTabColumnFactory.

Since:

10/02/13

Author:

qingwei, ntoro, nilshoffmann

Field Summary

Fields inherited from class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabHeaderLineParser

factory, metadata

Fields inherited from class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabLineParser

context, errorList, items, line, lineNumber, section

Constructor Summary

Constructors

Constructor	Description
SMHLineParser(MZTabParserContext context, de.isas.mztab2.model.Metadata metadata)	Constructor for SMHLineParser.

Method Summary

Modifier and Type	Method	Description
protected int	parseColumns()	This methods delegates to the subclasses the parsing of the columns.
protected void	refine()	Some validate operation need to be done after the whole MZTabColumnFactory created.

Methods inherited from class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabHeaderLineParser

checkAbundanceColumns, checkOptColumnName, fromIndexToOrder, getFactory, parse, parseIndex, refineOptionalColumn

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

SMHLineParser

public SMHLineParser(MZTabParserContext context,
                     de.isas.mztab2.model.Metadata metadata)

Constructor for SMHLineParser.

Parameters:

context - a MZTabParserContext object.

metadata - a Metadata object.

Method Detail

parseColumns

protected int parseColumns()
                    throws uk.ac.ebi.pride.jmztab2.utils.errors.MZTabException

This methods delegates to the subclasses the parsing of the columns. All of the columns are defined in SmallMoleculeColumn, SmallMoleculeFeatureColumn, or SmallMoleculeEvidenceColumn.

Specified by:

parseColumns in class MZTabHeaderLineParser

Returns:

the next physical index of column available after the parsing.

Throws:

uk.ac.ebi.pride.jmztab2.utils.errors.MZTabException - if any structural or logical errors are encountered that prohibit further processing.

refine

protected void refine()
               throws uk.ac.ebi.pride.jmztab2.utils.errors.MZTabException

Some validate operation need to be done after the whole MZTabColumnFactory created. Thus, user can add them, and called at the end of the MZTabHeaderLineParser.parse(int, String, MZTabErrorList) method. The following optional columns are mandatory: 1. abundance_assay[1-n] 2. abundance_study_variable[1-m] 3. abundance_variation_study_variable[1-m] NOTICE: this method will be called at end of parse() function.

Specified by:

refine in class MZTabHeaderLineParser

Throws:

uk.ac.ebi.pride.jmztab2.utils.errors.MZTabException - if any structural or logical errors are encountered that prohibit further processing.

See Also:

MZTabHeaderLineParser.parse(int, String, MZTabErrorList), MZTabHeaderLineParser.parse(int, String, MZTabErrorList)