org.proteios.io.mzdata
Class MzDataImpCommonPeakList

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

Direct Known Subclasses:

MzDataImpAcqSpecificationBlock, MzDataImpAcquisitionBlock, MzDataImpActivationBlock, MzDataImpDataBlock, MzDataImpIntenArrayBinaryBlock, MzDataImpIonSelectionBlock, MzDataImpMzArrayBinaryBlock, MzDataImpPrecursorBlock, MzDataImpPrecursorListBlock, MzDataImpSpectrumBlock, MzDataImpSpectrumDescBlock, MzDataImpSpectrumInstrumentBlock, MzDataImpSpectrumListBlock, MzDataImpSpectrumSettingsBlock

public class MzDataImpCommonPeakList
extends MzDataImpCommonAnnotation

This class supports import of mzData files into Proteios. It contains common attributes and methods, and is intended to be the parent class for other classes that process an 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

MzDataImpCommonPeakList(SessionControl sc)
Default constructor.

Method Summary

PeakList	getPeakList() Get the PeakList.
PeakList	parse(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	setPeakList(PeakList peakList) Set the PeakList.

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, processInternalStartElement, setBlockTagName, setTempStrBuf

Methods inherited from class java.lang.Object

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

Constructor Detail

MzDataImpCommonPeakList

public MzDataImpCommonPeakList(SessionControl sc)

Default constructor.

Method Detail

getPeakList

public PeakList getPeakList()

Get the PeakList.

Returns:

peakList PeakList the current peakList

setPeakList

public void setPeakList(PeakList peakList)

Set the PeakList.

Parameters:

peakList - PeakList the peakList to set.

parse

public PeakList parse(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:

peakList PeakList the updated output peakList.

Throws:

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