Package org.mcisb.massspectrometry.pride.model.ExperimentType

Examples of org.mcisb.massspectrometry.pride.model.ExperimentType.Protocol

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  public static ExperimentCollection getExperimentCollection( final File mzDataFile ) throws JAXBException
  {
    final String mzDataFilename = mzDataFile.getName();
    final MzData mzData = JAXBContext.newInstance( "org.mcisb.massspectrometry.pride.model" ).createUnmarshaller().unmarshal( new StreamSource( mzDataFile ), MzData.class ).getValue(); //$NON-NLS-1$
   
    final Protocol protocol = new Protocol();
    protocol.setProtocolName( "undefined" ); //$NON-NLS-1$
   
    final ExperimentType experimentType = new ExperimentType();
    experimentType.setTitle( mzDataFilename );
    experimentType.setShortLabel( mzDataFilename );
    experimentType.setProtocol( protocol );
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   * @return ExperimentCollection
   */
  public static ExperimentCollection getExperimentCollection( final String version, final String title, final String experimentAccession, final String shortLabel, final String protocolName, final MzData mzData, final List<GelFreeIdentificationType> gelFreeIdentificationTypes )
  {
    // Create Protocol:
    final Protocol protocol = new Protocol();
    protocol.setProtocolName( protocolName );
   
    // Create ParamType:
    final ParamType paramType = new ParamType();
    paramType.getCvParamOrUserParam().add( PrideParamFactory.getCvParam( PrideUtils.PRIDE_LABEL, "PRIDE:0000175", "XML generation software", "PrideWizard" ) ); //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$
   
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    final CvParamType protocolDescription = PrideParamFactory.getCvParam( "PSI", "PSI:1000287", "Time-Of-Flight Mass Spectrometer", null ); //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$
    final ParamType stepDescription = new ParamType();
    stepDescription.getCvParamOrUserParam().add( protocolDescription );
    final ProtocolSteps steps = new ProtocolSteps();
    steps.getStepDescription().add( stepDescription );
    final Protocol protocol = new Protocol();
    protocol.setProtocolName( "Protocol" ); //$NON-NLS-1$
    protocol.setProtocolSteps( steps );
   
    final ParamType additional = new ParamType();
    additional.getCvParamOrUserParam().add( PrideParamFactory.getCvParam( "PRIDE", "PRIDE:0000175", "XML generation software", "QconCAT PrideWizard" ) ); //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$ //$NON-NLS-4$
    additional.getCvParamOrUserParam().add( PrideParamFactory.getCvParam( "PRIDE", "PRIDE:0000218", "Original MS data file format", "mzData" ) ); //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$ //$NON-NLS-4$
    additional.getCvParamOrUserParam().add( PrideParamFactory.getCvParam( "PRIDE", "PRIDE:0000097", "Project", "95% flux" ) ); //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$ //$NON-NLS-4$
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Related Classes of org.mcisb.massspectrometry.pride.model.ExperimentType.Protocol

  • org.mcisb.massspectrometry.pride.converter.PrideConverter
  • org.mcisb.massspectrometry.pride.converter.PrideUtils
  • org.mcisb.massspectrometry.pride.converter.QuickPrideWriter
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