Package de.isas.mztab2.io

Class MzTabFileParser

java.lang.Object

de.isas.mztab2.io.MzTabFileParser

public class MzTabFileParser
extends Object

MZTabFileParser provides reading functionality of the mzTab file. During the parsing process, minimal integrity checks are preformed.

Since:

21/02/13

Author:

qingwei, nilshoffmann

Constructor Summary

Constructors

Constructor	Description
MzTabFileParser(File tabFile)	Create a new MZTabFileParser for the given file.
MzTabFileParser(URI tabFileUri)	Create a new MZTabFileParser for the given file URI.

Method Summary

Modifier and Type	Method	Description
protected void	checkColunitMapping(MZTabColumnFactory columnFactory, Optional<Collection<de.isas.mztab2.model.ColumnParameterMapping>> columnParameterMapping, de.isas.mztab2.model.Metadata.Properties colUnitProperty, de.isas.mztab2.model.MzTab.Properties mzTabSection)
uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorList	getErrorList()	Getter for the field errorList.
de.isas.mztab2.model.MzTab	getMZTabFile()	getMZTabFile.
uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorList	parse(OutputStream out)	Create a new MZTabParserContext and MZTabErrorList for the given file URI.
uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorList	parse(OutputStream out, uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorType.Level level)	Create a new MZTabParserContext and MZTabErrorList for the given file URI.
uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorList	parse(OutputStream out, uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorType.Level level, int maxErrorCount)	Create a new MZTabParserContext and MZTabErrorList for the given file URI.

Methods inherited from class java.lang.Object

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

Constructor Detail

MzTabFileParser

public MzTabFileParser(File tabFile)
                throws IllegalArgumentException

Create a new MZTabFileParser for the given file.

Parameters:

tabFile - the MZTab file. The file SHOULD not be null and MUST exist

Throws:

IllegalArgumentException - if the provided argument in invalid.

MzTabFileParser

public MzTabFileParser(URI tabFileUri)
                throws IllegalArgumentException

Create a new MZTabFileParser for the given file URI.

Parameters:

tabFileUri - the MZTab file URI. The file SHOULD not be null and MUST exist MZTabErrorList return by getErrorList()

Throws:

IllegalArgumentException - if the provided argument in invalid.

Method Detail

parse

public uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorList parse(OutputStream out,
                                                                 uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorType.Level level,
                                                                 int maxErrorCount)
                                                          throws IOException

Create a new MZTabParserContext and MZTabErrorList for the given file URI. Parsing output and errors are written to the provided OutputStream.

Parameters:

out - the output stream for parsing messages

level - the minimum error level to report errors for

maxErrorCount - the maximum number of errors to report in the MZTabErrorList return by getErrorList()

Returns:

the error list

Throws:

IOException - if any io related errors occur.

parse

public uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorList parse(OutputStream out,
                                                                 uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorType.Level level)
                                                          throws IOException

Create a new MZTabParserContext and MZTabErrorList for the given file URI. Parsing output and errors are written to the provided OutputStream. Reports up to MZTabProperties.MAX_ERROR_COUNT errors.

Parameters:

out - the output stream for parsing messages

level - the minimum error level to report errors for

Returns:

the error list

Throws:

IOException - if any io related errors occur.

parse

public uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorList parse(OutputStream out)
                                                          throws IOException

Create a new MZTabParserContext and MZTabErrorList for the given file URI. Parsing output and errors are written to the provided OutputStream. Reports up to MZTabProperties.MAX_ERROR_COUNT errors on level MZTabProperties.LEVEL.

Parameters:

out - the output stream for parsing messages

Returns:

the error list

Throws:

IOException - if any io related errors occur.

getErrorList

public uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorList getErrorList()

Getter for the field errorList.

Returns:

a MZTabErrorList object.

checkColunitMapping

protected void checkColunitMapping(MZTabColumnFactory columnFactory,
                                   Optional<Collection<de.isas.mztab2.model.ColumnParameterMapping>> columnParameterMapping,
                                   de.isas.mztab2.model.Metadata.Properties colUnitProperty,
                                   de.isas.mztab2.model.MzTab.Properties mzTabSection)

getMZTabFile

public de.isas.mztab2.model.MzTab getMZTabFile()

getMZTabFile.

Returns:

a MzTab object.