org.proteios.io.mzdata
Class MzDataImpActivationBlock

java.lang.Object
  org.proteios.io.mzdata.MzDataImpCommon
      org.proteios.io.mzdata.MzDataImpCommonDc
          org.proteios.io.mzdata.MzDataImpCommonAnnotation
              org.proteios.io.mzdata.MzDataImpCommonPeakList
                  org.proteios.io.mzdata.MzDataImpActivationBlock

public class MzDataImpActivationBlock
extends MzDataImpCommonPeakList

This class processes an "activation" XML block in an mzData file. It collects data from name-value pairs in cvParam tags and makes it available through accessor methods to its instance variables.

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.MzDataImpCommonDc

anna, dc, factory

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

log

Constructor Summary

MzDataImpActivationBlock(SessionControl sc)
Default constructor.

Method Summary

HardwareConfiguration	activationItem(PeakList peakList) Creates an activation 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	parseActivation(javax.xml.stream.XMLStreamReader parser, PeakList peakList) Parse the current XML block, and return the updated PeakList object after extending it with data from the current block.
void	processInternalStartElement(javax.xml.stream.XMLStreamReader parser) Processes an internal StartElement event.
void	storeActivationAnnotations(HardwareConfiguration activation) Stores variable values as annotations for activation.
void	userParamElementStart(javax.xml.stream.XMLStreamReader parser) Processes start of userParam XML element.

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

getPeakList, parse, setPeakList

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

MzDataImpActivationBlock

public MzDataImpActivationBlock(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

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

activationItem

public HardwareConfiguration activationItem(PeakList peakList)

Creates an activation item.

Parameters:

peakList - PeakList peakList

Returns:

activation HardwareConfiguration activation

storeActivationAnnotations

public void storeActivationAnnotations(HardwareConfiguration activation)

Stores variable values as annotations for activation.

Parameters:

activation - HardwareConfiguration activation

parseActivation

public HardwareConfiguration parseActivation(javax.xml.stream.XMLStreamReader parser,
                                             PeakList peakList)
                                      throws javax.xml.stream.XMLStreamException

Parse the current XML block, and return the updated PeakList 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.

peakList - PeakList the input peakList.

Returns:

HardwareConfiguration activation an activation object with retrieved data.

Throws:

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