org.proteios.io.mzdata
Class MzDataExpSourceFileBlock

java.lang.Object
  org.proteios.io.mzdata.MzDataExpCommon
      org.proteios.io.mzdata.MzDataExpCommonDc
          org.proteios.io.mzdata.MzDataExpCommonAnnotation
              org.proteios.io.mzdata.MzDataExpCommonPeakListSet
                  org.proteios.io.mzdata.MzDataExpSourceFileBlock

public class MzDataExpSourceFileBlock
extends MzDataExpCommonPeakListSet

This class processes a "sourceFile" XML block in an mzData file. This class supports export of mzData files from Proteios. An mzData file contains information on a mass spectrometry experiment. Given a Proteios peakListSet, MzDataExporter fetches stored data related to this peakListSet and stores it in an mzData file.

Version:

2.0

Author:

Olle

Last modified

$Date: 2006-10-25 14:40:28 +0200 (Wed, 25 Oct 2006) $

Field Summary

Fields inherited from class org.proteios.io.mzdata.MzDataExpCommonDc

anna, dc, factory

Fields inherited from class org.proteios.io.mzdata.MzDataExpCommon

log

Constructor Summary

MzDataExpSourceFileBlock(SessionControl sc)
Default constructor.

Method Summary

void	fetchPeakListSetAnnotations(PeakListSet peakListSet) Fetches variable values stored as annotations for peakListSet.
String	getFileType() Get the source file fileType.
String	getNameOfFile() Get the source file nameOfFile.
String	getPathToFile() Get the source file pathToFile.
void	setFileType(String fileType) Set the source file fileType.
void	setNameOfFile(String nameOfFile) Set the source file nameOfFile.
void	setPathToFile(String pathToFile) Set the source file pathToFile.
void	write(XMLCrudeWriter xmlCrudeWriter, PeakListSet peakListSet) Creates a sourceFile block.

Methods inherited from class org.proteios.io.mzdata.MzDataExpCommonPeakListSet

getPeakListSet, setPeakListSet

Methods inherited from class org.proteios.io.mzdata.MzDataExpCommonAnnotation

createAddedParamAnnotationType, createAnnotationType, createCvLookupAnnotationType, createCvParamAnnotationType, createUserParamAnnotationType, fetchAddedParamAnnotationType, fetchAnnotation, fetchCvLookupAnnotation, fetchCvLookupAnnotationList, fetchCvLookupAnnotationType, fetchCvParamAnnotation, fetchCvParamAnnotationList, fetchUserParamAnnotation, fetchUserParamAnnotationList, obtainAddedParamAnnotationType, obtainCvLookupAnnotationType, storeAnnotation, storeCvLookupAnnotation, storeCvParamAnnotation, storeUserParamAnnotation

Methods inherited from class org.proteios.io.mzdata.MzDataExpCommonDc

enableAnnotator, enableDbControl, enableDbControl, getDbControl, getSessionControl, setDbControl

Methods inherited from class org.proteios.io.mzdata.MzDataExpCommon

getBlockTagName, setBlockTagName, write, writeAttribute, writeEndTag, writeNamespace, writeSimpleElementPair, writeSimpleElementPair, writeSingleElementEnd, writeStartElement, writeStartElementEnd, writeStartListTag, writeStartTag, zeroPad, zeroPad, zeroPad

Methods inherited from class java.lang.Object

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

Constructor Detail

MzDataExpSourceFileBlock

public MzDataExpSourceFileBlock(SessionControl sc)

Default constructor.

Parameters:

sc -

Method Detail

getNameOfFile

public String getNameOfFile()

Get the source file nameOfFile.

Returns:

nameOfFile String the nameOfFile

setNameOfFile

public void setNameOfFile(String nameOfFile)

Set the source file nameOfFile.

Parameters:

nameOfFile - String the nameOfFile to set.

getPathToFile

public String getPathToFile()

Get the source file pathToFile.

Returns:

pathToFile String the pathToFile

setPathToFile

public void setPathToFile(String pathToFile)

Set the source file pathToFile.

Parameters:

pathToFile - String the pathToFile to set.

getFileType

public String getFileType()

Get the source file fileType.

Returns:

fileType String the fileType

setFileType

public void setFileType(String fileType)

Set the source file fileType.

Parameters:

fileType - String the fileType to set.

write

public void write(XMLCrudeWriter xmlCrudeWriter,
                  PeakListSet peakListSet)
           throws javax.xml.stream.XMLStreamException

Creates a sourceFile block.

Parameters:

xmlCrudeWriter - the XMLCrudeWriter instance to use.

peakListSet - PeakListSet peakListSet used

Throws:

javax.xml.stream.XMLStreamException - If there is an XML Stream related error

fetchPeakListSetAnnotations

public void fetchPeakListSetAnnotations(PeakListSet peakListSet)

Fetches variable values stored as annotations for peakListSet.

Parameters:

peakListSet - PeakListSet peakListSet used