org.proteios.io.mzdata
Class MzDataImpAdminBlock

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.MzDataImpAdminBlock

public class MzDataImpAdminBlock
extends MzDataImpCommonPeakListSet

This class processes a "admin" 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

MzDataImpAdminBlock(SessionControl sc)
Default constructor.

Method Summary

String	getAccessionNumber() Get the source file accessionNumber.
String	getContactInfo() Get the contactInfo.
String	getContactInstitution() Get the contactInstitution.
String	getContactName() Get the contactName.
String	getFileType() Get the source file fileType.
String	getNameOfFile() Get the source file nameOfFile.
String	getPathToFile() Get the source file pathToFile.
String	getSampleName() Get the sample name.
void	processInternalStartElement(javax.xml.stream.XMLStreamReader parser) Processes an internal StartElement event.
void	setAccessionNumber(String accessionNumber) Set the source file accessionNumber.
void	setContactInfo(String contactInfo) Set the contactInfo.
void	setContactInstitution(String contactInstitution) Set the contactInstitution.
void	setContactName(String contactName) Set the contactName.
void	setFileType(String fileType) Set the source file fileType.
void	setNameOfFile(String nameOfFile) Set the source file nameOfFile.
void	setPathToFile(String pathToFile) Set the source file pathToFile.
void	setSampleName(String sampleName) Set the sample name.

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, processInternalEndElement, setBlockTagName, setTempStrBuf

Methods inherited from class java.lang.Object

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

Constructor Detail

MzDataImpAdminBlock

public MzDataImpAdminBlock(SessionControl sc)

Default constructor.

Method Detail

getSampleName

public String getSampleName()

Get the sample name.

Returns:

sampleName String the sampleName

setSampleName

public void setSampleName(String sampleName)

Set the sample name.

Parameters:

sampleName - String the sampleName to set.

getAccessionNumber

public String getAccessionNumber()

Get the source file accessionNumber.

Returns:

accessionNumber String the accessionNumber

setAccessionNumber

public void setAccessionNumber(String accessionNumber)

Set the source file accessionNumber.

Parameters:

accessionNumber - String the accessionNumber to set.

getNameOfFile

public String getNameOfFile()

Get the source file nameOfFile.

Returns:

nameOfFile String the nameOfFile

setNameOfFile

public void setNameOfFile(String nameOfFile)

Set the source file nameOfFile.

Parameters:

nameOfFile - String the nameOfFile to set.

getPathToFile

public String getPathToFile()

Get the source file pathToFile.

Returns:

pathToFile String the pathToFile

setPathToFile

public void setPathToFile(String pathToFile)

Set the source file pathToFile.

Parameters:

pathToFile - String the pathToFile to set.

getFileType

public String getFileType()

Get the source file fileType.

Returns:

fileType String the fileType

setFileType

public void setFileType(String fileType)

Set the source file fileType.

Parameters:

fileType - String the fileType to set.

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.

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