org.proteios.io.mzdata
Class MzDataImpSoftwareBlock

java.lang.Object
  org.proteios.io.mzdata.MzDataImpCommon
      org.proteios.io.mzdata.MzDataImpCommonDc
          org.proteios.io.mzdata.MzDataImpCommonAnnotation
              org.proteios.io.mzdata.MzDataImpCommonPeakListSet
                  org.proteios.io.mzdata.MzDataImpSoftwareBlock

public class MzDataImpSoftwareBlock
extends MzDataImpCommonPeakListSet

This class processes a "software" XML block in an mzData file. An mzData file contains information on a mass spectrometry experiment. The mzData file is first vaildated against the XML Schema Definition file mzdata.xsd. If the file is valid, its content is parsed and selected information stored in Proteios. The mzData file is parsed using cursor-based XML stream parsing. The StAX (Stream API for XML) parser finds start and stop (end) tags, which are then processed. Element attributes are located in the start tag, and elements of simple types are stored directly after the start tag is read. For more complex elements, values of attributes and sub-elements are collected in temporary variables, until the end tag is reached, and the colelcted contents are stored. Example: XML tag tagData At start tag: Method thisTagElementStart() stores attribute values. Between tags: tagData is stored in temporary StringBuffer. At end tag: Method thisTagItem() processes collected data. Tag data may be exchanged for a start/end tag pair, etc.

Version:

2.0

Author:

Olle

Last modified

$Date: 2009-04-09 08:48:11 +0200 (Thu, 09 Apr 2009) $

Field Summary

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

aPeakListSet

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

anna, dc, factory

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

log

Constructor Summary

MzDataImpSoftwareBlock(SessionControl sc)
Default constructor.

Method Summary

void	blockStart(javax.xml.stream.XMLStreamReader parser) Processes start of XML block processed by this class.
String	getSoftwareComment() Get the softwareComment.
String	getSoftwareCompletionTime() Get the softwareCompletionTime.
String	getSoftwareName() Get the softwareName.
String	getSoftwareVersion() Get the softwareVersion.
void	processInternalEndElement(javax.xml.stream.XMLStreamReader parser) Processes an internal EndElement event.
void	setSoftwareComment(String softwareComment) Set the softwareComment.
void	setSoftwareCompletionTime(String softwareCompletionTime) Set the softwareCompletionTime.
void	setSoftwareName(String softwareName) Set the softwareName.
void	setSoftwareVersion(String softwareVersion) Set the softwareVersion.

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

getPeakListSet, getXMLFilePath, parse, setPeakListSet, setXMLFilePath

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

fetchCvLookupAnnotation, fetchCvLookupAnnotationList, fetchCvParamAnnotation, fetchCvParamAnnotationList, fetchUserParamAnnotation, fetchUserParamAnnotationList, storeAnnotation, storeCvLookupAnnotation, storeCvParamAnnotation, storeUserParamAnnotation

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

enableDbControl, enableDbControl, getDbControl, getSessionControl, setDbControl

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

blockEnd, getBlockTagName, getTempStrBuf, parse, processCData, processCharacters, processInternalStartElement, setBlockTagName, setTempStrBuf

Methods inherited from class java.lang.Object

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

Constructor Detail

MzDataImpSoftwareBlock

public MzDataImpSoftwareBlock(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.

getSoftwareName

public String getSoftwareName()

Get the softwareName.

Returns:

softwareName String the softwareName

setSoftwareName

public void setSoftwareName(String softwareName)

Set the softwareName.

Parameters:

softwareName - String the softwareName 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.

blockStart

public void blockStart(javax.xml.stream.XMLStreamReader parser)
                throws javax.xml.stream.XMLStreamException

Processes start of XML block processed by this class. Extracts data from attributes.

Overrides:

blockStart in class MzDataImpCommon

Parameters:

parser - XMLStreamReader instance.

Throws:

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

processInternalEndElement

public void processInternalEndElement(javax.xml.stream.XMLStreamReader parser)
                               throws javax.xml.stream.XMLStreamException

Processes an internal EndElement event.

Overrides:

processInternalEndElement in class MzDataImpCommon

Parameters:

parser - XMLStreamReader instance.

Throws:

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