org.proteios.io.mzdata
Class MzDataImpDescriptionBlock

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.MzDataImpDescriptionBlock

public class MzDataImpDescriptionBlock
extends MzDataImpCommonPeakListSet

This class processes a "description" 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

MzDataImpDescriptionBlock(SessionControl sc)
Default constructor.

Method Summary

void	blockEnd(javax.xml.stream.XMLStreamReader parser) Processes end of XML block processed by this class.
String	getMzDataAccessionNumber() Get the mzData accessionNumber.
List<CvLookup>	getMzDataCvLookupList() Get the mzData cvLookup list.
String	getMzDataNamespacePrefix() Get the mzData namespace prefix.
String	getMzDataNamespaceURI() Get the mzData namespace uri.
String	getMzDataVersion() Get the mzData version.
void	processInternalStartElement(javax.xml.stream.XMLStreamReader parser) Processes an Internal StartElement event.
void	setMzDataAccessionNumber(String mzDataAccessionNumber) Set the mzData accessionNumber.
void	setMzDataCvLookupList(List<CvLookup> mzDataCvLookupList) Set the mzData cvLookup list.
void	setMzDataNamespacePrefix(String mzDataNamespacePrefix) Set the mzData namespace prefix.
void	setMzDataNamespaceURI(String mzDataNamespaceURI) Set the mzData namespace uri.
void	setMzDataVersion(String mzDataVersion) Set the mzData version.
void	storePeakListSetAnnotations(PeakListSet peakListSet) Stores variable values as annotations for peakListSet.

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

blockStart, getBlockTagName, getTempStrBuf, parse, processCData, processCharacters, processInternalEndElement, setBlockTagName, setTempStrBuf

Methods inherited from class java.lang.Object

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

Constructor Detail

MzDataImpDescriptionBlock

public MzDataImpDescriptionBlock(SessionControl sc)

Default constructor.

Method Detail

getMzDataVersion

public String getMzDataVersion()

Get the mzData version.

Returns:

mzDataVersion String the mzDataVersion

setMzDataVersion

public void setMzDataVersion(String mzDataVersion)

Set the mzData version.

Parameters:

mzDataVersion - String the mzDataVersion to set.

getMzDataAccessionNumber

public String getMzDataAccessionNumber()

Get the mzData accessionNumber.

Returns:

mzDataAccessionNumber String the mzDataAccessionNumber

setMzDataAccessionNumber

public void setMzDataAccessionNumber(String mzDataAccessionNumber)

Set the mzData accessionNumber.

Parameters:

mzDataAccessionNumber - String the mzDataZccessionNumber to set.

getMzDataNamespacePrefix

public String getMzDataNamespacePrefix()

Get the mzData namespace prefix.

Returns:

mzDataNamespacePrefix String the mzDataNamespacePrefix

setMzDataNamespacePrefix

public void setMzDataNamespacePrefix(String mzDataNamespacePrefix)

Set the mzData namespace prefix.

Parameters:

mzDataNamespacePrefix - String the mzDataNamespacePrefix to set.

getMzDataNamespaceURI

public String getMzDataNamespaceURI()

Get the mzData namespace uri.

Returns:

mzDataNamespaceURI String the mzDataNamespaceURI

setMzDataNamespaceURI

public void setMzDataNamespaceURI(String mzDataNamespaceURI)

Set the mzData namespace uri.

Parameters:

mzDataNamespaceURI - String the mzDataNamespaceURI to set.

getMzDataCvLookupList

public List<CvLookup> getMzDataCvLookupList()

Get the mzData cvLookup list.

Returns:

mzDataCvLookupList List the mzDataCvLookupList

setMzDataCvLookupList

public void setMzDataCvLookupList(List<CvLookup> mzDataCvLookupList)

Set the mzData cvLookup list.

Parameters:

mzDataCvLookupList - List the mzDataCvLookupList to set.

processInternalStartElement

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

Processes an Internal StartElement event. The blocks in the if-else section are placed in the order of appearance of the start elements in the mzData XML file. This not essential for the functionality, but makes it easier to see if a specific element is handled or not. Elements that may be daughter elements to different types of parent elements, e.g. and , are placed at a suitable location.

Overrides:

processInternalStartElement in class MzDataImpCommon

Parameters:

parser - XMLStreamReader instance.

Throws:

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

blockEnd

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

Processes end of XML block processed by this class.

Overrides:

blockEnd in class MzDataImpCommon

Parameters:

parser - XMLStreamReader instance.

Throws:

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

storePeakListSetAnnotations

public void storePeakListSetAnnotations(PeakListSet peakListSet)

Stores variable values as annotations for peakListSet.

Parameters:

peakListSet - PeakListSet peakListSet