org.proteios.io.mzdata
Class MzDataExpDataProcessingBlock

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.MzDataExpDataProcessingBlock

public class MzDataExpDataProcessingBlock
extends MzDataExpCommonPeakListSet

This class processes a "dataProcessing" 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: 2006-10-16 16:40:00 +0200 (Mon, 16 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

MzDataExpDataProcessingBlock(SessionControl sc)
Default constructor.

Method Summary

void	dataProcessingBlock(XMLCrudeWriter xmlCrudeWriter, DataProcessingStep dataProcessingStep) Creates a dataProcessing block.
void	write(XMLCrudeWriter xmlCrudeWriter, PeakListSet peakListSet) Creates a number of dataProcessing blocks.

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

MzDataExpDataProcessingBlock

public MzDataExpDataProcessingBlock(SessionControl sc)

Default constructor.

Method Detail

write

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

Creates a number of dataProcessing blocks.

Parameters:

xmlCrudeWriter - the XMLCrudeWriter instance to use.

peakListSet - PeakListSet peakListSet used

Throws:

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

dataProcessingBlock

public void dataProcessingBlock(XMLCrudeWriter xmlCrudeWriter,
                                DataProcessingStep dataProcessingStep)
                         throws javax.xml.stream.XMLStreamException

Creates a dataProcessing block.

Parameters:

xmlCrudeWriter - the XMLCrudeWriter instance to use.

dataProcessingStep - DataProcessingStep dataProcessingStep used

Throws:

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