org.proteios.io.mzdata
Class MzDataImpSpectrumDescBlock

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.MzDataImpSpectrumDescBlock

public class MzDataImpSpectrumDescBlock
extends MzDataImpCommonPeakList

This class processes a "spectrumDesc" 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.MzDataImpCommonDc

anna, dc, factory

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

log

Constructor Summary

MzDataImpSpectrumDescBlock(SessionControl sc)
Default constructor.

Method Summary

String	getSpectrumDescComment() Get the spectrumDescComment.
String	getSpectrumType() Get the spectrumType.
void	processInternalEndElement(javax.xml.stream.XMLStreamReader parser) Processes an internal EndElement event.
void	processInternalStartElement(javax.xml.stream.XMLStreamReader parser) Processes an Internal StartElement event.
void	setSpectrumDescComment(String spectrumDescComment) Set the spectrumDescComment.
void	setSpectrumType(String spectrumType) Set the spectrumType.

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

blockEnd, blockStart, getBlockTagName, getTempStrBuf, parse, processCData, processCharacters, setBlockTagName, setTempStrBuf

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

MzDataImpSpectrumDescBlock

public MzDataImpSpectrumDescBlock(SessionControl sc)

Default constructor.

Parameters:

sc -

Method Detail

getSpectrumType

public String getSpectrumType()

Get the spectrumType.

Returns:

spectrumType String the spectrumType

setSpectrumType

public void setSpectrumType(String spectrumType)

Set the spectrumType.

Parameters:

spectrumType - String the spectrumType to set.

getSpectrumDescComment

public String getSpectrumDescComment()

Get the spectrumDescComment.

Returns:

spectrumDescComment String the spectrumDescComment

setSpectrumDescComment

public void setSpectrumDescComment(String spectrumDescComment)

Set the spectrumDescComment.

Parameters:

spectrumDescComment - String the spectrumDescComment to set.

processInternalStartElement

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

Processes an Internal StartElement event. The blocks in the if-else section are placed in the order of appearance of the start elements in the mzData XML file. This not essential for the functionality, but makes it easier to see if a specific element is handled or not. Elements that may be daughter elements to different types of parent elements, e.g. and , are placed at a suitable location.

Overrides:

processInternalStartElement in class MzDataImpCommon

Parameters:

parser - XMLStreamReader instance.

Throws:

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

processInternalEndElement

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

Processes an internal EndElement event.

Overrides:

processInternalEndElement in class MzDataImpCommon

Parameters:

parser - XMLStreamReader instance.

Throws:

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