org.proteios.io.mzdata
Class MzDataExpSpectrumInstrumentBlock

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.MzDataExpSpectrumInstrumentBlock

public class MzDataExpSpectrumInstrumentBlock
extends MzDataExpCommonPeakList

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: 2006-09-19 11:38:54 +0200 (Tue, 19 Sep 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

MzDataExpSpectrumInstrumentBlock(SessionControl sc)
Default constructor.

Method Summary

void	fetchPeakListAnnotations(PeakList peakList, DbControl dc) Fetches variable values stored as annotations for peakList.
float	getTimeInMinutes() Get the timeInMinutes.
void	setTimeInMinutes(float timeInMinutes) Set the timeInMinutes.
void	write(XMLCrudeWriter xmlCrudeWriter, PeakList peakList) Creates a spectrumInstrument 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

MzDataExpSpectrumInstrumentBlock

public MzDataExpSpectrumInstrumentBlock(SessionControl sc)

Default constructor.

Parameters:

sc -

Method Detail

getTimeInMinutes

public float getTimeInMinutes()

Get the timeInMinutes.

Returns:

timeInMinutes float the timeInMinutes

setTimeInMinutes

public void setTimeInMinutes(float timeInMinutes)

Set the timeInMinutes.

Parameters:

timeInMinutes - float the timeInMinutes to set.

write

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

Creates a spectrumInstrument 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) used to retrieve data