org.proteios.io.mzdata
Class MzDataImpContactBlock

java.lang.Object
  org.proteios.io.mzdata.MzDataImpCommon
      org.proteios.io.mzdata.MzDataImpCommonDc
          org.proteios.io.mzdata.MzDataImpCommonAnnotation
              org.proteios.io.mzdata.MzDataImpCommonPeakListSet
                  org.proteios.io.mzdata.MzDataImpContactBlock

public class MzDataImpContactBlock
extends MzDataImpCommonPeakListSet

This class processes a "contact" 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.MzDataImpCommonPeakListSet

aPeakListSet

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

anna, dc, factory

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

log

Constructor Summary

MzDataImpContactBlock(SessionControl sc)
Default constructor.

Method Summary

String	getContactInfo() Get the contactInfo.
String	getContactInstitution() Get the contactInstitution.
String	getContactName() Get the contactName.
void	processInternalEndElement(javax.xml.stream.XMLStreamReader parser) Processes an internal EndElement event.
void	setContactInfo(String contactInfo) Set the contactInfo.
void	setContactInstitution(String contactInstitution) Set the contactInstitution.
void	setContactName(String contactName) Set the contactName.

Methods inherited from class org.proteios.io.mzdata.MzDataImpCommonPeakListSet

getPeakListSet, getXMLFilePath, parse, setPeakListSet, setXMLFilePath

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, processInternalStartElement, setBlockTagName, setTempStrBuf

Methods inherited from class java.lang.Object

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

Constructor Detail

MzDataImpContactBlock

public MzDataImpContactBlock(SessionControl sc)

Default constructor.

Method Detail

getContactName

public String getContactName()

Get the contactName.

Returns:

contactName String the contactName

setContactName

public void setContactName(String contactName)

Set the contactName.

Parameters:

contactName - String the contactName to set.

getContactInstitution

public String getContactInstitution()

Get the contactInstitution.

Returns:

contactInstitution String the contactInstitution

setContactInstitution

public void setContactInstitution(String contactInstitution)

Set the contactInstitution.

Parameters:

contactInstitution - String the contactInstitution to set.

getContactInfo

public String getContactInfo()

Get the contactInfo.

Returns:

contactInfo String the contactInfo

setContactInfo

public void setContactInfo(String contactInfo)

Set the contactInfo.

Parameters:

contactInfo - String the contactInfo to set.

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