Examples of Spectrum

ca.eandb.jmist.framework.color.Spectrum
Represents the "color" of something in an abstract sense. A Spectrum may be sampled given a WavelengthPacket from a compatible ColorModel. @author Brad Kimmel
com.compomics.util.experiment.massspectrometry.Spectrum
net.mindengine.rainbow4j.Spectrum
org.mcisb.massspectrometry.pride.model.ExperimentType.MzData.SpectrumList.Spectrum
uk.ac.ebi.jmzml.model.mzml.Spectrum
uk.ac.ebi.pride.jaxb.model.Spectrum

Examples of ca.eandb.jmist.framework.color.Spectrum


  /* (non-Javadoc)
   * @see ca.eandb.jmist.framework.DirectionalTexture3#evaluate(ca.eandb.jmist.math.Vector3)
   */
  public Spectrum evaluate(final Vector3 v) {
    return new Spectrum() {
      private static final long serialVersionUID = 7992544267450760499L;
      public Color sample(WavelengthPacket lambda) {
        return evaluate(v, lambda);
      }
    };

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Examples of ca.eandb.jmist.framework.color.Spectrum

      visitMaterial();
      currentMaterialName = name;
    }


    private Painter getPainter(String name) throws IOException {
      Spectrum color = getColor(name);
      if (maps.containsKey(name)) {
        File file = new File(directory, maps.get(name));
        return new ProductPainter(color, new Texture2Painter(new RasterTexture2(file)));
      }
      return new UniformPainter(color);

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Examples of ca.eandb.jmist.framework.color.Spectrum


  /* (non-Javadoc)
   * @see ca.eandb.jmist.framework.DirectionalTexture3#evaluate(ca.eandb.jmist.math.Vector3)
   */
  public Spectrum evaluate(final Vector3 v) {
    return new Spectrum() {
      private static final long serialVersionUID = -3558496271642281773L;
      public Color sample(WavelengthPacket lambda) {
        return evaluate(v, lambda);
      }
    };

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Examples of ca.eandb.jmist.framework.color.Spectrum

  /* (non-Javadoc)
   * @see ca.eandb.jmist.framework.color.ColorModel#getGray(double, ca.eandb.jmist.framework.color.WavelengthPacket)
   */
  @Override
  public Color getGray(double value, WavelengthPacket lambda) {
    Spectrum s = new XYZColor(value, value, value, this);
    return s.sample(lambda);
  }

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Examples of com.compomics.util.experiment.massspectrometry.Spectrum

                return peptideAssumption.getIsotopeNumber(precursor.getMz()) + "";
            case mz:
                precursor = SpectrumFactory.getInstance().getPrecursor(spectrumKey);
                return precursor.getMz() + "";
            case total_spectrum_intensity:
                Spectrum spectrum = SpectrumFactory.getInstance().getSpectrum(spectrumKey);
                return spectrum.getTotalIntensity() + "";
            case max_intensity:
                spectrum = SpectrumFactory.getInstance().getSpectrum(spectrumKey);
                return spectrum.getMaxIntensity() + "";
            case intensity_coverage:
                spectrum = SpectrumFactory.getInstance().getSpectrum(spectrumKey);
                double coveredIntensity = 0;
                Peptide peptide = peptideAssumption.getPeptide();
                ArrayList<IonMatch> matches = peptideSpectrumAnnotator.getSpectrumAnnotation(
                        annotationPreferences.getIonTypes(), annotationPreferences.getNeutralLosses(), annotationPreferences.getValidatedCharges(),
                        peptideAssumption.getIdentificationCharge().value,
                        (MSnSpectrum) spectrum, peptide, 0, searchParameters.getFragmentIonAccuracy(), false, true);
                for (IonMatch ionMatch : matches) {
                    coveredIntensity += ionMatch.peak.intensity;
                }
                double coverage = 100 * coveredIntensity / spectrum.getTotalIntensity();
                return coverage + "";
            case mz_error:
                precursor = SpectrumFactory.getInstance().getPrecursor(spectrumKey);
                return peptideAssumption.getDeltaMass(precursor.getMz(), true) + "";
            case rt:

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Examples of com.compomics.util.experiment.massspectrometry.Spectrum

                return tagAssumption.getIsotopeNumber(precursor.getMz()) + "";
            case mz:
                precursor = SpectrumFactory.getInstance().getPrecursor(spectrumKey);
                return precursor.getMz() + "";
            case total_spectrum_intensity:
                Spectrum spectrum = SpectrumFactory.getInstance().getSpectrum(spectrumKey);
                return spectrum.getTotalIntensity() + "";
            case max_intensity:
                spectrum = SpectrumFactory.getInstance().getSpectrum(spectrumKey);
                return spectrum.getMaxIntensity() + "";
            case mz_error:
                precursor = SpectrumFactory.getInstance().getPrecursor(spectrumKey);
                return tagAssumption.getDeltaMass(precursor.getMz(), true) + "";
            case rt:
                precursor = SpectrumFactory.getInstance().getPrecursor(spectrumKey);

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Examples of net.mindengine.rainbow4j.Spectrum

        
        
        
        
        
        Spectrum spectrum;
        try {
            spectrum = Rainbow4J.readSpectrum(pageImage, new Rectangle(area.getLeft(), area.getTop(), area.getWidth(), area.getHeight()), PRECISION);
        } catch (Exception e) {
            throw new ValidationErrorException(String.format("Couldn't fetch spectrum for \"%s\"", objectName));
        }
        
        List<String> messages = new LinkedList<String>();
        
        for (ColorRange colorRange : spec.getColorRanges()) {
            Color color = colorRange.getColor();
            int percentage = (int)spectrum.getPercentage(color.getRed(), color.getGreen(), color.getBlue(), TEST_RANGE);
            
            if (!colorRange.getRange().holds(percentage)) {
                messages.add(String.format("color %s on \"%s\" is %d%% %s", toHexColor(color), objectName, (int)percentage, colorRange.getRange().getErrorMessageSuffix("%")));
            }
        }

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Examples of org.mcisb.massspectrometry.pride.model.ExperimentType.MzData.SpectrumList.Spectrum

      {
        final Peptide labelledPeptide = entry.getValue();
        final List<Object> cvParamOrUserParam = labelledPeptide.getAdditional().getCvParamOrUserParam();
        
        // Generate XIC:
        final Spectrum labelledXic = xicFactory.getSpectrum( labelledPeptide );
        final float labelledRt = Float.valueOf( PrideUtils.getCvParamValue( labelledPeptide.getAdditional(), PrideUtils.PARENT_ION_RETENTION_TIME_ACCESSION ) ).floatValue();
        
        if( xicFactory.addPeakStartAndEnd( labelledXic, labelledRt ) )
        {
          // Add precursor spectrum:
          double startRt = NumberUtils.UNDEFINED;
          double endRt = NumberUtils.UNDEFINED;
          
          for( final String comment : labelledXic.getSpectrumDesc().getComments() )
          {
            if( comment.startsWith( org.mcisb.massspectrometry.pride.converter.qconcat.PropertyNames.PEAK_START ) )
            {
              startRt = Double.parseDouble( comment.substring( org.mcisb.massspectrometry.pride.converter.qconcat.PropertyNames.PEAK_START.length() ) );
            }
            else if( comment.startsWith( org.mcisb.massspectrometry.pride.converter.qconcat.PropertyNames.PEAK_END ) )
            {
              endRt = Double.parseDouble( comment.substring( org.mcisb.massspectrometry.pride.converter.qconcat.PropertyNames.PEAK_END.length() ) );
            }
          }
          
          final Spectrum[] precursorSpectra = precursorSpectrumFactory.getSpectra( labelledPeptide, startRt, endRt );
          
          if( precursorSpectra.length > 0 )
          {
            quantified = true;
            
            for( Spectrum precursorSpectrum : precursorSpectra )
            {
              spectra.add( precursorSpectrum );
              matchedSpectrumReferences.add( Integer.valueOf( precursorSpectrum.getId() ) );
              cvParamOrUserParam.add( PrideParamFactory.getUserParam( PrecursorSpectrumFactory.PRECURSOR_SPECTRUM_ID, Integer.toString( precursorSpectrum.getId() ) ) );
            }
            
            // Add XIC:
            spectra.add( labelledXic );
            matchedSpectrumReferences.add( Integer.valueOf( labelledXic.getId() ) );
            cvParamOrUserParam.add( PrideParamFactory.getUserParam( XicFactory.XIC_ID, Integer.toString( labelledXic.getId() ) ) );
            
            // Add quantitation:
            cvParamOrUserParam.add( PrideParamFactory.getCvParam( PrideUtils.PRIDE_LABEL, PrideUtils.STABLE_ISOTOPE_RATIO_ACCESSION, "Stable isotope ratio", Double.toString( precursorSpectrumFactory.getRatio( labelledPeptide ) ) ) ); //$NON-NLS-1$
            cvParamOrUserParam.add( PrideParamFactory.getUserParam( STABLE_ISOTOPE_RATIO_ACCESSION_ERROR_ID, Double.toString( precursorSpectrumFactory.getRatioStandardError( labelledPeptide ) ) ) );
            cvParamOrUserParam.add( PrideParamFactory.getUserParam( NUM_OBSERVATIONS_ID, Long.toString( precursorSpectrumFactory.getNumberOfObservations( labelledPeptide ) ) ) );
            
            // Add / find unlabelled peptide:
            Peptide unlabelledPeptide = peptidePairIdToPartnerPeptide.get( entry.getKey() );
            
            if( unlabelledPeptide != null )
            {
              for( Spectrum precursorSpectrum : precursorSpectra )
              {
                unlabelledPeptide.getAdditional().getCvParamOrUserParam().add( PrideParamFactory.getUserParam( PrecursorSpectrumFactory.PRECURSOR_SPECTRUM_ID, Integer.toString( precursorSpectrum.getId() ) ) );
              }
            }
            else
            {
              unlabelledPeptide = PrideUtils.clone( labelledPeptide, labelAccessions );
              unlabelledPeptide.setAdditional( new ParamType() );
              unlabelledPeptide.getAdditional().getCvParamOrUserParam().add( PrideParamFactory.getCvParam( PrideUtils.PSI_LABEL, PrideUtils.PARENT_ION_CHARGE_STATE_ACCESSION, "Charge state", Long.toString( PrideUtils.getZ( labelledPeptide, mzData ) ) ) ); //$NON-NLS-1$
              unlabelledPeptide.getAdditional().getCvParamOrUserParam().add( PrideParamFactory.getCvParam( PrideUtils.PRIDE_LABEL, PrideUtils.PARENT_ION_RETENTION_TIME_ACCESSION, "parent ion retention time", Float.toString( labelledRt ) ) ); //$NON-NLS-1$
              gelFreeIdentification.getPeptideItem().add( unlabelledPeptide );
            }
            
            final Spectrum unlabelledXic = xicFactory.getSpectrum( unlabelledPeptide );
            spectra.add( unlabelledXic );
            matchedSpectrumReferences.add( Integer.valueOf( unlabelledXic.getId() ) );
            unlabelledPeptide.getAdditional().getCvParamOrUserParam().add( PrideParamFactory.getUserParam( XicFactory.XIC_ID, Integer.toString( unlabelledXic.getId() ) ) );
            unlabelledPeptide.getAdditional().getCvParamOrUserParam().add( PrideParamFactory.getCvParam( PrideUtils.PRIDE_LABEL, PrideUtils.PEPTIDE_PAIR_ID_ACCESSION, PEPTIDE_PAIR_ID_NAME, entry.getKey() ) );
          }
        }
      }

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Examples of uk.ac.ebi.jmzml.model.mzml.Spectrum

            Spectrum.class);
    try {


      while (spectrumIterator.hasNext()) {


        Spectrum spectrum = spectrumIterator.next();


        String scanId = spectrum.getId();
        int scanNumber = convertScanIdToScanNumber(scanId);


        int msLevel = extractMSLevel(spectrum);
        double retentionTime = extractRetentionTime(spectrum);

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Examples of uk.ac.ebi.pride.jaxb.model.Spectrum

                    w.close();
                    progressDialog.setRunFinished();
                    return false;
                }


                Spectrum spectrum = prideXmlReader.getSpectrumById(spectrumId);
                boolean valid = asMgf(spectrum, bw);


                if (valid) {
                    validSpectrumCount++;
                }

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