org.proteios.io.mzdata
Class MzDataImpProcessingMethodBlock

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.MzDataImpProcessingMethodBlock

public class MzDataImpProcessingMethodBlock
extends MzDataImpCommonPeakListSet

This class processes a "processingMethod" 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.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

MzDataImpProcessingMethodBlock(SessionControl sc)
Default constructor.

Method Summary

void	cvParamElementStart(javax.xml.stream.XMLStreamReader parser) Processes start of cvParam XML element.
String	getChargeDeconvolution() Get the chargeDeconvolution.
List<CvParam>	getCvParamList() Get the cvParamList.
String	getDeisotoping() Get the deisotoping.
String	getPeakProcessing() Get the peakProcessing.
List<UserParam>	getUserParamList() Get the userParamList.
void	processInternalStartElement(javax.xml.stream.XMLStreamReader parser) Processes an internal StartElement event.
void	setChargeDeconvolution(String chargeDeconvolution) Set the chargeDeconvolution.
void	setCvParamList(List<CvParam> cvParamList) Set the cvParamList.
void	setDeisotoping(String deisotoping) Set the deisotoping.
void	setPeakProcessing(String peakProcessing) Set the peakProcessing.
void	setUserParamList(List<UserParam> userParamList) Set the userParamList.
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

blockEnd, 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

MzDataImpProcessingMethodBlock

public MzDataImpProcessingMethodBlock(SessionControl sc)

Default constructor.

Parameters:

sc -

Method Detail

getDeisotoping

public String getDeisotoping()

Get the deisotoping.

Returns:

deisotoping String the deisotoping

setDeisotoping

public void setDeisotoping(String deisotoping)

Set the deisotoping.

Parameters:

deisotoping - String the deisotoping to set.

getChargeDeconvolution

public String getChargeDeconvolution()

Get the chargeDeconvolution.

Returns:

chargeDeconvolution String the chargeDeconvolution

setChargeDeconvolution

public void setChargeDeconvolution(String chargeDeconvolution)

Set the chargeDeconvolution.

Parameters:

chargeDeconvolution - String the chargeDeconvolution to set.

getPeakProcessing

public String getPeakProcessing()

Get the peakProcessing.

Returns:

peakProcessing String the peakProcessing

setPeakProcessing

public void setPeakProcessing(String peakProcessing)

Set the peakProcessing.

Parameters:

peakProcessing - String the peakProcessing to set.

getCvParamList

public List<CvParam> getCvParamList()

Get the cvParamList.

Returns:

cvParamList List the cvParamList.

setCvParamList

public void setCvParamList(List<CvParam> cvParamList)

Set the cvParamList.

Parameters:

cvParamList - List the cvParamList to set.

getUserParamList

public List<UserParam> getUserParamList()

Get the userParamList.

Returns:

userParamList List the userParamList.

setUserParamList

public void setUserParamList(List<UserParam> userParamList)

Set the userParamList.

Parameters:

userParamList - List the userParamList to set.

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