org.proteios.io.mzdata
Class MzDataImpPrecursorBlock

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.MzDataImpPrecursorBlock

public class MzDataImpPrecursorBlock
extends MzDataImpCommonPeakList

This class processes a "precursor" 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

MzDataImpPrecursorBlock(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.
Precursor	parsePrecursor(javax.xml.stream.XMLStreamReader parser, PeakList peakList) Parse the current XML block, and return the created Precursor object after updating it with data from the current block.
Precursor	precursorItem(HardwareConfiguration ionSelection, HardwareConfiguration activation) Creates a precursor item.
void	processInternalStartElement(javax.xml.stream.XMLStreamReader parser) Processes an internal StartElement event.

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

MzDataImpPrecursorBlock

public MzDataImpPrecursorBlock(SessionControl sc)

Default constructor.

Parameters:

sc -

Method Detail

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

precursorItem

public Precursor precursorItem(HardwareConfiguration ionSelection,
                               HardwareConfiguration activation)

Creates a precursor item.

Parameters:

ionSelection - HardwareConfiguration ionSelection

activation - HardwareConfiguration activation

Returns:

precursor Precursor precursor

parsePrecursor

public Precursor parsePrecursor(javax.xml.stream.XMLStreamReader parser,
                                PeakList peakList)
                         throws javax.xml.stream.XMLStreamException

Parse the current XML block, and return the created Precursor object after updating 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:

Acquisition acquisition an acquisition object with retrieved data.

Throws:

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