org.expasy.mzjava.proteomics.io.ms.ident

Class MzIdentMlReader

java.lang.Object

org.expasy.mzjava.proteomics.io.ms.ident.MzIdentMlReader

All Implemented Interfaces:

PsmReader

public class MzIdentMlReader
extends Object
implements PsmReader

Version:

sqrt -1

Author:

Oliver Horlacher

Field Summary

Fields

Modifier and Type	Field and Description
static String	RETENTION_TIME_CV
static String	SCAN_NUMBER_CV
static String	TITLE_CV

Constructor Summary

Constructors

Constructor and Description
MzIdentMlReader()
MzIdentMlReader(ModificationResolver modResolver)

Method Summary

Methods

Modifier and Type	Method and Description
void	parse(File file, PSMReaderCallback callback) Parse file and call back PSMReaderCallback on each found PSM
void	parse(InputSource is, PSMReaderCallback callback)
void	parse(InputStream inputStream, PSMReaderCallback callback) Parse inputStream and call back PSMReaderCallback on each found PSM
void	parse(Reader reader, PSMReaderCallback callback) Parse reader and call back PSMReaderCallback on each found PSM
protected PeptideMatch	readPeptide(String peptideRef, SequenceCollectionType sequenceCollection)
protected void	readPeptideIDProteinMap(MzIdentMLType doc)
protected void	readPeptideIDProteinPositionMap(MzIdentMLType doc)

Methods inherited from class java.lang.Object

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

Field Detail

SCAN_NUMBER_CV

public static final String SCAN_NUMBER_CV

See Also:

Constant Field Values

RETENTION_TIME_CV

public static final String RETENTION_TIME_CV

See Also:

Constant Field Values

TITLE_CV

public static final String TITLE_CV

See Also:

Constant Field Values

Constructor Detail

MzIdentMlReader

public MzIdentMlReader()

MzIdentMlReader

public MzIdentMlReader(ModificationResolver modResolver)

Method Detail

parse

public void parse(File file,
         PSMReaderCallback callback)

Description copied from interface: PsmReader

Parse file and call back PSMReaderCallback on each found PSM

Specified by:

parse in interface PsmReader

Parameters:

file - input file

callback - a PSMReaderCallback implementation

parse

public void parse(Reader reader,
         PSMReaderCallback callback)

Description copied from interface: PsmReader

Parse reader and call back PSMReaderCallback on each found PSM

Specified by:

parse in interface PsmReader

Parameters:

reader - input stream

callback - a PSMReaderCallback implementation

parse

public void parse(InputStream inputStream,
         PSMReaderCallback callback)

Description copied from interface: PsmReader

Parse inputStream and call back PSMReaderCallback on each found PSM

Specified by:

parse in interface PsmReader

Parameters:

inputStream - input stream

callback - a PSMReaderCallback implementation

parse

public void parse(InputSource is,
         PSMReaderCallback callback)
           throws SAXException,
                  JAXBException

Throws:

SAXException

JAXBException

readPeptideIDProteinMap

protected void readPeptideIDProteinMap(MzIdentMLType doc)

readPeptideIDProteinPositionMap

protected void readPeptideIDProteinPositionMap(MzIdentMLType doc)

readPeptide

protected PeptideMatch readPeptide(String peptideRef,
                       SequenceCollectionType sequenceCollection)