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

Class MTDLineParser

java.lang.Object

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

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

public class MTDLineParser
extends MZTabLineParser

Parse a metadata line into a element. Metadata Element start with MTD, its structure like: MTD MetadataElement([id])(-MetadataProperty) {Element Value}

Since:

08/02/13

Author:

qingwei, nilshoffmann

See Also:

MetadataElement, MetadataProperty

Field Summary

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

context, errorList, items, line, lineNumber, section

Constructor Summary

Constructors

Constructor	Description
MTDLineParser(MZTabParserContext context)	Constructor for MTDLineParser.

Method Summary

Modifier and Type	Method	Description
de.isas.mztab2.model.Metadata	getMetadata()	Getter for the field metadata.
protected void	handleAssay(Matcher matcher, String defineLabel, MetadataElement element, String valueLabel)
protected void	handleColunit(String defineLabel, String valueLabel)
protected void	handleContact(String defineLabel, Matcher matcher, MetadataElement element, String valueLabel)
protected void	handleCustom(String defineLabel, Matcher matcher, String valueLabel)
protected void	handleCv(String defineLabel, Matcher matcher, MetadataElement element, String valueLabel)
protected void	handleDatabase(String defineLabel, Matcher matcher, MetadataElement element, String valueLabel)
protected void	handleDerivatizationAgent(String defineLabel, Matcher matcher, String valueLabel)
protected void	handleDescription(String defineLabel, String valueLabel)
protected void	handleExternalStudyUri(String defineLabel, Matcher matcher, String valueLabel)
protected void	handleIdConfidenceMeasure(String defineLabel, Matcher matcher, String valueLabel)
protected void	handleInstrument(String defineLabel, Matcher matcher, MetadataElement element, String valueLabel)
protected void	handleMsRun(String defineLabel, Matcher matcher, MetadataElement element, String valueLabel)
protected void	handleMzTab(MetadataElement element, Matcher matcher, String defineLabel, String valueLabel)
void	handleParam(String defineLabel, String valueLabel, uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorType errorType, int lineNumber, Consumer<de.isas.mztab2.model.Parameter> consumer)	handleParam.
protected void	handlePublication(String defineLabel, Matcher matcher, String valueLabel)
protected void	handleQuantificationMethod(String defineLabel, String valueLabel)
protected void	handleSample(String defineLabel, Matcher matcher, MetadataElement element, String valueLabel)
protected void	handleSampleProcessing(String defineLabel, Matcher matcher, String valueLabel)
protected void	handleSmallMolecule(MetadataElement element, Matcher matcher, String defineLabel, String valueLabel)
protected void	handleSmallMoleculeFeature(MetadataElement element, Matcher matcher, String defineLabel, String valueLabel)
protected void	handleSoftware(String defineLabel, Matcher matcher, MetadataElement element, String valueLabel)
protected void	handleStudyVariable(String defineLabel, Matcher matcher, MetadataElement element, String valueLabel)
protected void	handleTitle(String defineLabel, String valueLabel)
protected void	handleUri(String defineLabel, Matcher matcher, String valueLabel, boolean mandatory)
void	parse(int lineNumber, String mtdLine, uk.ac.ebi.pride.jmztab2.utils.errors.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	refineNormalMetadata()	Refine the metadata, and check whether missing some important information. fixed_mode, variable_mode must provide in the Complete file.

Methods inherited from class java.lang.Object

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

Constructor Detail

MTDLineParser

public MTDLineParser(MZTabParserContext context)

Constructor for MTDLineParser.

Parameters:

context - a MZTabParserContext object.

Method Detail

parse

public void parse(int lineNumber,
                  String mtdLine,
                  uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorList errorList)
           throws uk.ac.ebi.pride.jmztab2.utils.errors.MZTabException

We assume that user before call this method, have parse the raw line is not empty line and start with section prefix. Most of e, we use parseNormalMetadata(String, String) to parse defineLabel into Metadata Element.

Overrides:

parse in class MZTabLineParser

Parameters:

lineNumber - a int.

mtdLine - a String object.

errorList - a MZTabErrorList object.

Throws:

uk.ac.ebi.pride.jmztab2.utils.errors.MZTabException - if any.

handleIdConfidenceMeasure

protected void handleIdConfidenceMeasure(String defineLabel,
                                         Matcher matcher,
                                         String valueLabel)
                                  throws uk.ac.ebi.pride.jmztab2.utils.errors.MZTabException

Throws:

uk.ac.ebi.pride.jmztab2.utils.errors.MZTabException

handleColunit

protected void handleColunit(String defineLabel,
                             String valueLabel)
                      throws uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorOverflowException

Throws:

uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorOverflowException

handleDatabase

protected void handleDatabase(String defineLabel,
                              Matcher matcher,
                              MetadataElement element,
                              String valueLabel)
                       throws uk.ac.ebi.pride.jmztab2.utils.errors.MZTabException

Throws:

uk.ac.ebi.pride.jmztab2.utils.errors.MZTabException

handleCv

protected void handleCv(String defineLabel,
                        Matcher matcher,
                        MetadataElement element,
                        String valueLabel)
                 throws uk.ac.ebi.pride.jmztab2.utils.errors.MZTabException

Throws:

uk.ac.ebi.pride.jmztab2.utils.errors.MZTabException

handleStudyVariable

protected void handleStudyVariable(String defineLabel,
                                   Matcher matcher,
                                   MetadataElement element,
                                   String valueLabel)
                            throws uk.ac.ebi.pride.jmztab2.utils.errors.MZTabException,
                                   uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorOverflowException

Throws:

uk.ac.ebi.pride.jmztab2.utils.errors.MZTabException

uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorOverflowException

handleAssay

protected void handleAssay(Matcher matcher,
                           String defineLabel,
                           MetadataElement element,
                           String valueLabel)
                    throws uk.ac.ebi.pride.jmztab2.utils.errors.MZTabException

Throws:

uk.ac.ebi.pride.jmztab2.utils.errors.MZTabException

handleSample

protected void handleSample(String defineLabel,
                            Matcher matcher,
                            MetadataElement element,
                            String valueLabel)
                     throws uk.ac.ebi.pride.jmztab2.utils.errors.MZTabException

Throws:

uk.ac.ebi.pride.jmztab2.utils.errors.MZTabException

handleCustom

protected void handleCustom(String defineLabel,
                            Matcher matcher,
                            String valueLabel)
                     throws uk.ac.ebi.pride.jmztab2.utils.errors.MZTabException

Throws:

uk.ac.ebi.pride.jmztab2.utils.errors.MZTabException

handleDerivatizationAgent

protected void handleDerivatizationAgent(String defineLabel,
                                         Matcher matcher,
                                         String valueLabel)
                                  throws uk.ac.ebi.pride.jmztab2.utils.errors.MZTabException

Throws:

uk.ac.ebi.pride.jmztab2.utils.errors.MZTabException

handleMsRun

protected void handleMsRun(String defineLabel,
                           Matcher matcher,
                           MetadataElement element,
                           String valueLabel)
                    throws uk.ac.ebi.pride.jmztab2.utils.errors.MZTabException

Throws:

uk.ac.ebi.pride.jmztab2.utils.errors.MZTabException

handleSmallMoleculeFeature

protected void handleSmallMoleculeFeature(MetadataElement element,
                                          Matcher matcher,
                                          String defineLabel,
                                          String valueLabel)
                                   throws uk.ac.ebi.pride.jmztab2.utils.errors.MZTabException

Throws:

uk.ac.ebi.pride.jmztab2.utils.errors.MZTabException

handleSmallMolecule

protected void handleSmallMolecule(MetadataElement element,
                                   Matcher matcher,
                                   String defineLabel,
                                   String valueLabel)
                            throws uk.ac.ebi.pride.jmztab2.utils.errors.MZTabException

Throws:

uk.ac.ebi.pride.jmztab2.utils.errors.MZTabException

handleQuantificationMethod

protected void handleQuantificationMethod(String defineLabel,
                                          String valueLabel)
                                   throws uk.ac.ebi.pride.jmztab2.utils.errors.MZTabException

Throws:

uk.ac.ebi.pride.jmztab2.utils.errors.MZTabException

handleExternalStudyUri

protected void handleExternalStudyUri(String defineLabel,
                                      Matcher matcher,
                                      String valueLabel)
                               throws uk.ac.ebi.pride.jmztab2.utils.errors.MZTabException

Throws:

uk.ac.ebi.pride.jmztab2.utils.errors.MZTabException

handleUri

protected void handleUri(String defineLabel,
                         Matcher matcher,
                         String valueLabel,
                         boolean mandatory)
                  throws uk.ac.ebi.pride.jmztab2.utils.errors.MZTabException

Throws:

uk.ac.ebi.pride.jmztab2.utils.errors.MZTabException

handleContact

protected void handleContact(String defineLabel,
                             Matcher matcher,
                             MetadataElement element,
                             String valueLabel)
                      throws uk.ac.ebi.pride.jmztab2.utils.errors.MZTabException

Throws:

uk.ac.ebi.pride.jmztab2.utils.errors.MZTabException

handlePublication

protected void handlePublication(String defineLabel,
                                 Matcher matcher,
                                 String valueLabel)
                          throws uk.ac.ebi.pride.jmztab2.utils.errors.MZTabException

Throws:

uk.ac.ebi.pride.jmztab2.utils.errors.MZTabException

handleSoftware

protected void handleSoftware(String defineLabel,
                              Matcher matcher,
                              MetadataElement element,
                              String valueLabel)
                       throws uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorOverflowException,
                              uk.ac.ebi.pride.jmztab2.utils.errors.MZTabException

Throws:

uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorOverflowException

uk.ac.ebi.pride.jmztab2.utils.errors.MZTabException

handleInstrument

protected void handleInstrument(String defineLabel,
                                Matcher matcher,
                                MetadataElement element,
                                String valueLabel)
                         throws uk.ac.ebi.pride.jmztab2.utils.errors.MZTabException

Throws:

uk.ac.ebi.pride.jmztab2.utils.errors.MZTabException

handleSampleProcessing

protected void handleSampleProcessing(String defineLabel,
                                      Matcher matcher,
                                      String valueLabel)
                               throws uk.ac.ebi.pride.jmztab2.utils.errors.MZTabException

Throws:

uk.ac.ebi.pride.jmztab2.utils.errors.MZTabException

handleDescription

protected void handleDescription(String defineLabel,
                                 String valueLabel)
                          throws uk.ac.ebi.pride.jmztab2.utils.errors.MZTabException

Throws:

uk.ac.ebi.pride.jmztab2.utils.errors.MZTabException

handleTitle

protected void handleTitle(String defineLabel,
                           String valueLabel)
                    throws uk.ac.ebi.pride.jmztab2.utils.errors.MZTabException

Throws:

uk.ac.ebi.pride.jmztab2.utils.errors.MZTabException

handleMzTab

protected void handleMzTab(MetadataElement element,
                           Matcher matcher,
                           String defineLabel,
                           String valueLabel)
                    throws uk.ac.ebi.pride.jmztab2.utils.errors.MZTabException

Throws:

uk.ac.ebi.pride.jmztab2.utils.errors.MZTabException

refineNormalMetadata

public void refineNormalMetadata()
                          throws uk.ac.ebi.pride.jmztab2.utils.errors.MZTabException

Refine the metadata, and check whether missing some important information. fixed_mode, variable_mode must provide in the Complete file. Detail information see specification 5.5

Throws:

uk.ac.ebi.pride.jmztab2.utils.errors.MZTabException - if any.

getMetadata

public de.isas.mztab2.model.Metadata getMetadata()

Getter for the field metadata.

Returns:

a Metadata object.

handleParam

public void handleParam(String defineLabel,
                        String valueLabel,
                        uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorType errorType,
                        int lineNumber,
                        Consumer<de.isas.mztab2.model.Parameter> consumer)
                 throws uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorOverflowException

handleParam.

Parameters:

defineLabel - a String object.

valueLabel - a String object.

errorType - a MZTabErrorType object.

lineNumber - a int.

consumer - a Consumer object.

Throws:

uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorOverflowException - if any.