org.proteios.io.mzdata
Class MzDataExpSoftwareBlock

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.MzDataExpSoftwareBlock

public class MzDataExpSoftwareBlock
extends MzDataExpCommonPeakListSet

This class processes a "software" 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

MzDataExpSoftwareBlock(SessionControl sc)
Default constructor.

Method Summary

void	fetchDataProcessingStepAnnotations(DataProcessingStep dataProcessingStep) Fetches variable values stored as annotations for dataProcessingStep.
String	getSoftwareComment() Get the softwareComment.
String	getSoftwareCompletionTime() Get the softwareCompletionTime.
String	getSoftwareVersion() Get the softwareVersion.
void	setSoftwareComment(String softwareComment) Set the softwareComment.
void	setSoftwareCompletionTime(String softwareCompletionTime) Set the softwareCompletionTime.
void	setSoftwareVersion(String softwareVersion) Set the softwareVersion.
void	write(XMLCrudeWriter xmlCrudeWriter, DataProcessingStep dataProcessingStep) Creates a software 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

MzDataExpSoftwareBlock

public MzDataExpSoftwareBlock(SessionControl sc)

Default constructor.

Parameters:

sc -

Method Detail

getSoftwareCompletionTime

public String getSoftwareCompletionTime()

Get the softwareCompletionTime.

Returns:

softwareCompletionTime String the softwareCompletionTime

setSoftwareCompletionTime

public void setSoftwareCompletionTime(String softwareCompletionTime)

Set the softwareCompletionTime.

Parameters:

softwareCompletionTime - String the softwareCompletionTime to set.

getSoftwareVersion

public String getSoftwareVersion()

Get the softwareVersion.

Returns:

softwareVersion String the softwareVersion

setSoftwareVersion

public void setSoftwareVersion(String softwareVersion)

Set the softwareVersion.

Parameters:

softwareVersion - String the softwareVersion to set.

getSoftwareComment

public String getSoftwareComment()

Get the softwareComment.

Returns:

softwareComment String the softwareComment

setSoftwareComment

public void setSoftwareComment(String softwareComment)

Set the softwareComment.

Parameters:

softwareComment - String the softwareComment to set.

write

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

Creates a software 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

fetchDataProcessingStepAnnotations

public void fetchDataProcessingStepAnnotations(DataProcessingStep dataProcessingStep)

Fetches variable values stored as annotations for dataProcessingStep.

Parameters:

dataProcessingStep - DataProcessingStep dataProcessingStep used