org.proteios.io.mzdata
Class MzDataExpIonSelectionBlock

java.lang.Object
  org.proteios.io.mzdata.MzDataExpCommon
      org.proteios.io.mzdata.MzDataExpCommonDc
          org.proteios.io.mzdata.MzDataExpCommonAnnotation
              org.proteios.io.mzdata.MzDataExpCommonPeakList
                  org.proteios.io.mzdata.MzDataExpIonSelectionBlock

public class MzDataExpIonSelectionBlock
extends MzDataExpCommonPeakList

This class processes an "ionSelection" 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: 2006-10-31 11:05:43 +0100 (Tue, 31 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

MzDataExpIonSelectionBlock(SessionControl sc)
Default constructor.

Method Summary

void	fetchPrecursorAnnotations(Precursor precursor, DbControl dc) Fetches variable values stored as annotations for precursor.
void	write(XMLCrudeWriter xmlCrudeWriter, Precursor precursor) Creates an ionSelection block.

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

getPeakList, setPeakList

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

MzDataExpIonSelectionBlock

public MzDataExpIonSelectionBlock(SessionControl sc)

Default constructor.

Parameters:

sc -

Method Detail

write

public void write(XMLCrudeWriter xmlCrudeWriter,
                  Precursor precursor)
           throws javax.xml.stream.XMLStreamException

Creates an ionSelection block.

Parameters:

xmlCrudeWriter - the XMLCrudeWriter instance to use.

precursor - Precursor precursor

Throws:

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

fetchPrecursorAnnotations

public void fetchPrecursorAnnotations(Precursor precursor,
                                      DbControl dc)

Fetches variable values stored as annotations for precursor.

Parameters:

precursor - Precursor precursor used to retrieve data