org.proteios.io.mzdata
Class MzDataImpIonSelectionBlock

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.MzDataImpIonSelectionBlock

public class MzDataImpIonSelectionBlock
extends MzDataImpCommonPeakList

This class processes an "ionSelection" 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

MzDataImpIonSelectionBlock(SessionControl sc)
Default constructor.

Method Summary

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.
int	getChargeState() Get the chargeState.
float	getMassToChargeRatio() Get the massToChargeRatio.
HardwareConfiguration	ionSelectionItem(PeakList peakList) Creates an ionSelection item.
HardwareConfiguration	parseIonSelection(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	setChargeState(int chargeState) Set the chargeState.
void	setMassToChargeRatio(float massToChargeRatio) Set the massToChargeRatio.
void	storeIonSelectionAnnotations(HardwareConfiguration ionSelection) Stores variable values as annotations for ionSelection.
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

MzDataImpIonSelectionBlock

public MzDataImpIonSelectionBlock(SessionControl sc)

Default constructor.

Parameters:

sc -

Method Detail

getMassToChargeRatio

public float getMassToChargeRatio()

Get the massToChargeRatio.

Returns:

massToChargeRatio float the massToChargeRatio

setMassToChargeRatio

public void setMassToChargeRatio(float massToChargeRatio)

Set the massToChargeRatio.

Parameters:

massToChargeRatio - float the massToChargeRatio to set.

getChargeState

public int getChargeState()

Get the chargeState.

Returns:

chargeState int the chargeState

setChargeState

public void setChargeState(int chargeState)

Set the chargeState.

Parameters:

chargeState - int the chargeState to set.

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

ionSelectionItem

public HardwareConfiguration ionSelectionItem(PeakList peakList)

Creates an ionSelection item.

Parameters:

peakList - PeakList peakList

Returns:

ionSelection HardwareConfiguration ionSelection

storeIonSelectionAnnotations

public void storeIonSelectionAnnotations(HardwareConfiguration ionSelection)

Stores variable values as annotations for ionSelection.

Parameters:

ionSelection - HardwareConfiguration ionSelection

parseIonSelection

public HardwareConfiguration parseIonSelection(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 ionSelection an ionSelection object with retrieved data.

Throws:

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