Examples of MassList

net.sf.mzmine.data.MassList
This class represent detected masses (ions) in one mass spectrum. Each ion is represented by MzPeak

Examples of net.sf.mzmine.data.MassList

      if (isCanceled())
        return;


      Scan scan = dataFile.getScan(scanNumbers[i]);


      MassList massList = scan.getMassList(massListName);
      if (massList == null) {
        setStatus(TaskStatus.ERROR);
        this.errorMessage = "Scan " + dataFile + " #" + scanNumbers[i]
            + " does not have a mass list " + massListName;
        return;
      }


      DataPoint mzValues[] = massList.getDataPoints();


      if (mzValues == null) {
        setStatus(TaskStatus.ERROR);
        this.errorMessage = "Mass list " + massListName
            + " does not contain m/z values for scan "

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Examples of net.sf.mzmine.data.MassList


  @Override
  public synchronized void addMassList(final @Nonnull MassList massList) {


    // Remove all mass lists with same name, if there are any
    MassList currentMassLists[] = massLists.toArray(new MassList[0]);
    for (MassList ml : currentMassLists) {
      if (ml.getName().equals(massList.getName()))
        removeMassList(ml);
    }


    StorableMassList storedMassList;
    if (massList instanceof StorableMassList) {
      storedMassList = (StorableMassList) massList;
    } else {
      DataPoint massListDataPoints[] = massList.getDataPoints();
      try {
        int mlStorageID = rawDataFile
            .storeDataPoints(massListDataPoints);
        storedMassList = new StorableMassList(rawDataFile, mlStorageID,
            massList.getName(), this);
      } catch (IOException e) {
        logger.severe("Could not write data to temporary file "
            + e.toString());
        return;
      }
    }


    // Add the new mass list
    massLists.add(storedMassList);


    // Add the mass list to the tree model
    MZmineProjectImpl project = (MZmineProjectImpl) MZmineCore
        .getCurrentProject();


    // Check if we are adding to the current project
    if (Arrays.asList(project.getDataFiles()).contains(rawDataFile)) {
      final ProjectTreeModel treeModel = project.getTreeModel();
      final MassList newMassList = storedMassList;
      Runnable swingCode = new Runnable() {
        @Override
        public void run() {
          treeModel.addObject(newMassList);
        }

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Examples of net.sf.mzmine.data.MassList

        DefaultMutableTreeNode scanNode = new DefaultMutableTreeNode(
            scan);
        treeObjects.put(scan, scanNode);
        insertNodeInto(scanNode, newNode, i);


        MassList massLists[] = scan.getMassLists();
        for (int j = 0; j < massLists.length; j++) {
          DefaultMutableTreeNode mlNode = new DefaultMutableTreeNode(
              massLists[j]);
          treeObjects.put(massLists[j], mlNode);
          insertNodeInto(mlNode, scanNode, j);

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Examples of net.sf.mzmine.data.MassList

            scan.getDataFile(), scan.getScanNumber());
      }
    }


    if (command.equals("SHOW_MASSLIST")) {
      MassList selectedMassLists[] = tree
          .getSelectedObjects(MassList.class);
      for (MassList massList : selectedMassLists) {
        Scan scan = massList.getScan();
        SpectraVisualizerWindow window = SpectraVisualizerModule
            .showNewSpectrumWindow(scan.getDataFile(),
                scan.getScanNumber());
        MassListDataSet dataset = new MassListDataSet(massList);
        window.addDataSet(dataset, Color.green);
      }
    }


    if (command.equals("REMOVE_MASSLIST")) {
      MassList selectedMassLists[] = tree
          .getSelectedObjects(MassList.class);
      for (MassList massList : selectedMassLists) {
        Scan scan = massList.getScan();
        scan.removeMassList(massList);
      }
    }


    if (command.equals("REMOVE_ALL_MASSLISTS")) {
      MassList selectedMassLists[] = tree
          .getSelectedObjects(MassList.class);
      for (MassList massList : selectedMassLists) {
        String massListName = massList.getName();
        RawDataFile dataFiles[] = MZmineCore.getCurrentProject()
            .getDataFiles();
        for (RawDataFile dataFile : dataFiles) {
          int scanNumbers[] = dataFile.getScanNumbers();
          for (int scanNum : scanNumbers) {
            Scan scan = dataFile.getScan(scanNum);
            MassList ml = scan.getMassList(massListName);
            if (ml != null)
              scan.removeMassList(ml);
          }
        }
      }

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Examples of net.sf.mzmine.data.MassList

      SpectraVisualizerModule.showNewSpectrumWindow(
          clickedScan.getDataFile(), clickedScan.getScanNumber());
    }


    if (clickedObject instanceof MassList) {
      MassList clickedMassList = (MassList) clickedObject;
      Scan clickedScan = clickedMassList.getScan();
      SpectraVisualizerWindow window = SpectraVisualizerModule
          .showNewSpectrumWindow(clickedScan.getDataFile(),
              clickedScan.getScanNumber());
      MassListDataSet dataset = new MassListDataSet(clickedMassList);
      window.addDataSet(dataset, Color.green);

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Examples of net.sf.mzmine.data.MassList

          .getDataFiles();
      for (RawDataFile dataFile : dataFiles) {
        int scanNums[] = dataFile.getScanNumbers();
        for (int scanNum : scanNums) {
          Scan scan = dataFile.getScan(scanNum);
          MassList massLists[] = scan.getMassLists();
          for (MassList massList : massLists) {
            String name = massList.getName();
            if (!currentNames.contains(name))
              currentNames.add(name);
          }

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Examples of net.sf.mzmine.data.MassList


    if ((checkMSMS) && (msmsScanNumber > 0)) {
      Scan msmsScan = dataFile.getScan(msmsScanNumber);
      String massListName = msmsParameters.getParameter(
          MSMSScoreParameters.massList).getValue();
      MassList ms2MassList = msmsScan.getMassList(massListName);
      if (ms2MassList == null) {
        setStatus(TaskStatus.ERROR);
        this.errorMessage = "The MS/MS scan #" + msmsScanNumber
            + " in file " + dataFile.getName()
            + " does not have a mass list called '" + massListName

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Examples of net.sf.mzmine.data.MassList

            statement.setNull(i + 1, Types.BLOB);
            break;
          }
          RawDataFile dataFile = row.getBestPeak().getDataFile();
          Scan msmsScan = dataFile.getScan(msmsScanNum);
          MassList msmsMassList = msmsScan.getMassList(dataValue);
          // Check if there is a masslist for the scan
          if (msmsMassList == null) {
            statement.setNull(i + 1, Types.BLOB);
            break;
          }
          dataPoints = msmsMassList.getDataPoints();
          bytes = ScanUtils.encodeDataPointsToBytes(dataPoints);
          is = new ByteArrayInputStream(bytes);
          statement.setBlob(i + 1, is);


          break;

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Examples of net.sf.mzmine.data.MassList

      hd.endElement("", "",
          RawDataElementName.QUANTITY_FRAGMENT_SCAN.getElementName());
    }


    // <MASS_LIST>
    MassList massLists[] = scan.getMassLists();
    for (MassList massList : massLists) {
      StorableMassList stMassList = (StorableMassList) massList;
      atts.addAttribute("", "", RawDataElementName.NAME.getElementName(),
          "CDATA", stMassList.getName());
      atts.addAttribute("", "",

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Examples of net.sf.mzmine.data.MassList

    MZTolerance msmsTolerance = parameters.getParameter(
        MSMSScoreParameters.msmsTolerance).getValue();
    String massListName = parameters.getParameter(
        MSMSScoreParameters.massList).getValue();


    MassList massList = msmsScan.getMassList(massListName);


    if (massList == null) {
      throw new IllegalArgumentException("Scan #"
          + msmsScan.getScanNumber()
          + " does not have a mass list called '" + massListName
          + "'");
    }


    DataPoint msmsIons[] = massList.getDataPoints();


    if (msmsIons == null) {
      throw new IllegalArgumentException("Mass list " + massList
          + " does not contain data for scan #"
          + msmsScan.getScanNumber());

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