org.proteios.io.mzdata
Class MzDataExpSampleNameBlock

java.lang.Object
  org.proteios.io.mzdata.MzDataExpCommon
      org.proteios.io.mzdata.MzDataExpCommonDc
          org.proteios.io.mzdata.MzDataExpCommonAnnotation
              org.proteios.io.mzdata.MzDataExpCommonPeakListSet
                  org.proteios.io.mzdata.MzDataExpSampleNameBlock

public class MzDataExpSampleNameBlock
extends MzDataExpCommonPeakListSet

This class processes a "sampleName" XML block in an mzData file. This class supports export of mzData files from Proteios. An mzData file contains information on a mass spectrometry experiment. Given a Proteios peakListSet, MzDataExporter fetches stored data related to this peakListSet and stores it in an mzData file.

Version:

2.0

Author:

Olle

Last modified

$Date: 2006-10-25 14:40:28 +0200 (Wed, 25 Oct 2006) $

Field Summary

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

anna, dc, factory

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

log

Constructor Summary

MzDataExpSampleNameBlock(SessionControl sc)
Default constructor.

Method Summary

String	fetchSampleNameFromPeakListSetAnnotations(PeakListSet peakListSet) Fetches variable values stored as annotations for peakListSet.
String	fetchSampleNameFromSampleItem(PeakListSet peakListSet) Fetches sample name from Sample item.
String	getSampleName() Get the sample name.
void	setSampleName(String sampleName) Set the sample name.
void	write(XMLCrudeWriter xmlCrudeWriter, PeakListSet peakListSet) Creates a sampleName block.

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

getPeakListSet, setPeakListSet

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

createAddedParamAnnotationType, createAnnotationType, createCvLookupAnnotationType, createCvParamAnnotationType, createUserParamAnnotationType, fetchAddedParamAnnotationType, fetchAnnotation, fetchCvLookupAnnotation, fetchCvLookupAnnotationList, fetchCvLookupAnnotationType, fetchCvParamAnnotation, fetchCvParamAnnotationList, fetchUserParamAnnotation, fetchUserParamAnnotationList, obtainAddedParamAnnotationType, obtainCvLookupAnnotationType, storeAnnotation, storeCvLookupAnnotation, storeCvParamAnnotation, storeUserParamAnnotation

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

enableAnnotator, enableDbControl, enableDbControl, getDbControl, getSessionControl, setDbControl

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

getBlockTagName, setBlockTagName, write, writeAttribute, writeEndTag, writeNamespace, writeSimpleElementPair, writeSimpleElementPair, writeSingleElementEnd, writeStartElement, writeStartElementEnd, writeStartListTag, writeStartTag, zeroPad, zeroPad, zeroPad

Methods inherited from class java.lang.Object

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

Constructor Detail

MzDataExpSampleNameBlock

public MzDataExpSampleNameBlock(SessionControl sc)

Default constructor.

Parameters:

sc - SessionControl sc

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.

write

public void write(XMLCrudeWriter xmlCrudeWriter,
                  PeakListSet peakListSet)
           throws javax.xml.stream.XMLStreamException

Creates a sampleName block.

Parameters:

xmlCrudeWriter - the XMLCrudeWriter instance to use.

peakListSet - PeakListSet peakListSet used

Throws:

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

fetchSampleNameFromPeakListSetAnnotations

public String fetchSampleNameFromPeakListSetAnnotations(PeakListSet peakListSet)

Fetches variable values stored as annotations for peakListSet.

Parameters:

peakListSet - PeakListSet peakListSet used

fetchSampleNameFromSampleItem

public String fetchSampleNameFromSampleItem(PeakListSet peakListSet)

Fetches sample name from Sample item.

Parameters:

peakListSet - PeakListSet peakListSet used

Returns:

String name of sample item.