org.proteios.io.mzdata
Class MzDataImpSpectrumInstrumentBlock

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.MzDataImpSpectrumInstrumentBlock

public class MzDataImpSpectrumInstrumentBlock
extends MzDataImpCommonPeakList

This class processes a "spectrumInstrument" 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

MzDataImpSpectrumInstrumentBlock(SessionControl sc)
Default constructor.

Method Summary

void	blockEnd(javax.xml.stream.XMLStreamReader parser) Processes end of XML block processed by this class.
void	blockStart(javax.xml.stream.XMLStreamReader parser) Processes start of XML block processed by this class.
void	cvParamElementStart(javax.xml.stream.XMLStreamReader parser) Processes start of cvParam XML element.
int	getMsLevel() Get the msLevel.
float	getMzRangeStart() Get the mzRangeStart.
float	getMzRangeStop() Get the mzRangeStop.
float	getTimeInMinutes() Get the timeInMinutes.
void	processInternalStartElement(javax.xml.stream.XMLStreamReader parser) Processes an internal StartElement event.
void	setMsLevel(int msLevel) Set the msLevel.
void	setMzRangeStart(float mzRangeStart) Set the mzRangeStart.
void	setMzRangeStop(float mzRangeStop) Set the mzRangeStop.
void	setTimeInMinutes(float timeInMinutes) Set the timeInMinutes.
HardwareConfiguration	spectrumInstrumentItem(PeakList peakList) Creates a spectrumInstrument item.
void	storeSpectrumInstrumentAnnotations(HardwareConfiguration spectrumInstrument) Stores variable values as annotations for spectrumInstrument.
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

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

MzDataImpSpectrumInstrumentBlock

public MzDataImpSpectrumInstrumentBlock(SessionControl sc)

Default constructor.

Parameters:

sc -

Method Detail

getMsLevel

public int getMsLevel()

Get the msLevel.

Returns:

msLevel int the msLevel

setMsLevel

public void setMsLevel(int msLevel)

Set the msLevel.

Parameters:

msLevel - int the msLevel to set.

getMzRangeStart

public float getMzRangeStart()

Get the mzRangeStart.

Returns:

mzRangeStart float the mzRangeStart

setMzRangeStart

public void setMzRangeStart(float mzRangeStart)

Set the mzRangeStart.

Parameters:

mzRangeStart - float the mzRangeStart to set.

getMzRangeStop

public float getMzRangeStop()

Get the mzRangeStop.

Returns:

mzRangeStop float the mzRangeStop

setMzRangeStop

public void setMzRangeStop(float mzRangeStop)

Set the mzRangeStop.

Parameters:

mzRangeStop - float the mzRangeStop to set.

getTimeInMinutes

public float getTimeInMinutes()

Get the timeInMinutes.

Returns:

timeInMinutes float the timeInMinutes

setTimeInMinutes

public void setTimeInMinutes(float timeInMinutes)

Set the timeInMinutes.

Parameters:

timeInMinutes - float the timeInMinutes to set.

blockStart

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

Processes start of XML block processed by this class. Extracts data from attributes.

Overrides:

blockStart 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. 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. A userParam tag has the format: where [userParamName} and {userParamValue} are the strings that are extracted.

Parameters:

parser - XMLStreamReader instance.

Throws:

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

spectrumInstrumentItem

public HardwareConfiguration spectrumInstrumentItem(PeakList peakList)

Creates a spectrumInstrument item.

Parameters:

peakList - PeakList peakList

Returns:

spectrumInstrument HardwareConfiguration spectrumInstrument

storeSpectrumInstrumentAnnotations

public void storeSpectrumInstrumentAnnotations(HardwareConfiguration spectrumInstrument)

Stores variable values as annotations for spectrumInstrument.

Parameters:

spectrumInstrument - HardwareConfiguration spectrumInstrument