org.proteios.io.mzdata
Class MzDataExpSpectrumBlock

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.MzDataExpSpectrumBlock

public class MzDataExpSpectrumBlock
extends MzDataExpCommonPeakList

This class processes a "spectrum" 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: 2006-10-16 16:40:00 +0200 (Mon, 16 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

MzDataExpSpectrumBlock(SessionControl sc)
Default constructor.

Method Summary

void	fetchPeakListAnnotations(PeakList peakList, DbControl dc) Fetches variable values stored as annotations for peakList.
String	stringPrecision(boolean doublePrecision) Get the precision as a String.
void	write(XMLCrudeWriter xmlCrudeWriter, PeakList peakList) Creates a spectrum 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

MzDataExpSpectrumBlock

public MzDataExpSpectrumBlock(SessionControl sc)

Default constructor.

Parameters:

sc -

Method Detail

stringPrecision

public String stringPrecision(boolean doublePrecision)

Get the precision as a String.

Parameters:

doublePrecision - boolean doublePrecision

Returns:

precision String precision based on boolean doublePrecision

write

public void write(XMLCrudeWriter xmlCrudeWriter,
                  PeakList peakList)
           throws javax.xml.stream.XMLStreamException

Creates a spectrum block.

Parameters:

xmlCrudeWriter - the XMLCrudeWriter instance to use.

peakList - PeakList peakList (spectrum)

Throws:

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

fetchPeakListAnnotations

public void fetchPeakListAnnotations(PeakList peakList,
                                     DbControl dc)

Fetches variable values stored as annotations for peakList.

Parameters:

peakList - PeakList peakList (spectrum)

dc - DbControl used to retrieve data