org.proteios.io.mzdata
Class MzDataImpAnalyzerBlock

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.MzDataImpAnalyzerBlock

public class MzDataImpAnalyzerBlock
extends MzDataImpCommonPeakListSet

This class processes an "analyzer" 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

MzDataImpAnalyzerBlock(SessionControl sc)
Default constructor.

Method Summary

HardwareConfiguration	analyzerItem(PeakListSet peakListSet, Hardware instrument) Creates an analyzer item.
void	blockEnd(javax.xml.stream.XMLStreamReader parser) Processes end of XML block processed by this class.
void	cvParamElementStart(javax.xml.stream.XMLStreamReader parser) Processes start of cvParam XML element.
HardwareConfiguration	parseAnalyzer(javax.xml.stream.XMLStreamReader parser, PeakListSet peakListSet) Parse the current XML block, and return the updated PeakListSet object after extending it with data from the current block.
void	processInternalStartElement(javax.xml.stream.XMLStreamReader parser) Processes an internal StartElement event.
void	storeAnalyzerAnnotations(HardwareConfiguration analyzer) Stores variable values as annotations for analyzer.
void	userParamElementStart(javax.xml.stream.XMLStreamReader parser) Processes start of userParam XML element.

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

MzDataImpAnalyzerBlock

public MzDataImpAnalyzerBlock(SessionControl sc)

Default constructor.

Method Detail

blockEnd

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

Processes end of XML block processed by this class. Extracts data in block.

Overrides:

blockEnd in class MzDataImpCommon

Parameters:

parser - XMLStreamReader instance.

Throws:

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

processInternalStartElement

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

Processes an internal StartElement event.

Overrides:

processInternalStartElement in class MzDataImpCommon

Parameters:

parser - XMLStreamReader instance.

Throws:

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

parseAnalyzer

public HardwareConfiguration parseAnalyzer(javax.xml.stream.XMLStreamReader parser,
                                           PeakListSet peakListSet)
                                    throws javax.xml.stream.XMLStreamException

Parse the current XML block, and return the updated PeakListSet object after extending it with data from the current block. The XMLStreamReader parser is updated to refer to the current position in the XML data.

Parameters:

parser - XMLStreamReader instance.

peakListSet - PeakListSet the input peakListSet.

Returns:

HardwareConfiguration analyzer an analyzer object with retrieved data.

Throws:

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

cvParamElementStart

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

Processes start of cvParam XML element. Extracts data from attributes.

Parameters:

parser - XMLStreamReader instance.

Throws:

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

userParamElementStart

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

Processes start of userParam XML element. Extracts data from attributes.

Parameters:

parser - XMLStreamReader instance.

Throws:

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

analyzerItem

public HardwareConfiguration analyzerItem(PeakListSet peakListSet,
                                          Hardware instrument)

Creates an analyzer item.

Parameters:

peakListSet - PeakListSet peakListSet

instrument - Hardware instrument

Returns:

analyzer HardwareConfiguration analyzer

storeAnalyzerAnnotations

public void storeAnalyzerAnnotations(HardwareConfiguration analyzer)

Stores variable values as annotations for analyzer.

Parameters:

analyzer - HardwareConfiguration analyzer