Examples of net.sf.mzmine.project.MZmineProject

net.sf.mzmine.project.MZmineProject
MZmineProject collects all items user has opened or created during an MZmine session. This includes
- Experimental parameters and their values for each RawDataFile. Experimental parameters are available for defining any properties of the sample, for instance concentration or a class label.
- Opened RawDataFiles
- PeakLists of each RawDataFile. A peak list represents results of peak detection on a single RawDataFile or a processed version of a preceding PeakList.
- PeakLists of multiple aligned PeakLists. An aligned peak list represent results of aligning multiple PeakLists of individual runs or a processed version of a preceding aligned PeakList.
@see UserParameter @see ParameterValue @see RawDataFile @see PeakList

      newRow.addPeak(dataFile, finishedPeak);
      newPeakList.addRow(newRow);
    }


    // Add new peaklist to the project
    MZmineProject currentProject = MZmineCore.getCurrentProject();
    currentProject.addPeakList(newPeakList);


    setStatus(TaskStatus.FINISHED);


    logger.info("Finished chromatogram builder on " + dataFile);

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  }


  private void copyParameterValuesToRawDataFiles() {


    MZmineProject currentProject = MZmineCore.getCurrentProject();


    // Remove all previous parameters from project
    UserParameter[] parameters = currentProject.getParameters();
    for (UserParameter parameter : parameters) {
      currentProject.removeParameter(parameter);
    }


    // Add new parameters
    parameters = parameterValues.keySet().toArray(new UserParameter[0]);
    for (UserParameter parameter : parameters) {
      currentProject.addParameter(parameter);
    }


    // Set values for new parameters
    for (int columnIndex = 0; columnIndex < parameterValues.keySet().size(); columnIndex++) {
      UserParameter parameter = tablemodelParameterValues
          .getParameter(columnIndex + 1);


      for (int dataFileIndex = 0; dataFileIndex < dataFiles.length; dataFileIndex++) {
        RawDataFile file = dataFiles[dataFileIndex];


        Object value = tablemodelParameterValues.getValueAt(
            dataFileIndex, columnIndex + 1);
        if (parameter instanceof DoubleParameter) {
          Double doubleValue = null;
          if (value instanceof Double)
            doubleValue = (Double) value;
          if (value instanceof String)
            doubleValue = Double.parseDouble((String) value);
          currentProject.setParameterValue(parameter, file,
              doubleValue);
        }
        if (parameter instanceof StringParameter) {
          if (value == null)
            value = "";
          currentProject.setParameterValue(parameter, file,
              (String) value);
        }
        if (parameter instanceof ComboParameter) {
          if (value == null)
            value = "";
          currentProject.setParameterValue(parameter, file,
              (String) value);
        }


      }

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  }


  private void copyParameterValuesFromRawDataFiles() {


    MZmineProject currentProject = MZmineCore.getCurrentProject();


    for (int dataFileIndex = 0; dataFileIndex < dataFiles.length; dataFileIndex++) {


      RawDataFile file = dataFiles[dataFileIndex];
      UserParameter[] parameters = currentProject.getParameters();


      // Loop through all parameters defined for this file
      for (UserParameter p : parameters) {


        // Check if this parameter has been seen before?
        Object[] values;
        if (!(parameterValues.containsKey(p))) {
          // No, initialize a new array of values for this parameter
          values = new Object[dataFiles.length];
          for (int i = 0; i < values.length; i++)
            values[i] = p.getValue();
          parameterValues.put(p, values);
        } else {
          values = parameterValues.get(p);
        }


        // Set value of this parameter for the current raw data file
        values[dataFileIndex] = currentProject.getParameterValue(p,
            file);


      }


    }

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      newPeakList.addRow(entry);
      processedScans++;
    }


    MZmineProject currentProject = MZmineCore.getCurrentProject();
    currentProject.addPeakList(newPeakList);
    logger.info("Finished MS/MS peak builder on " + dataFile + ", "
        + processedScans + " scans processed");


    setStatus(TaskStatus.FINISHED);
  }

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    for (Gap gap : gaps) {
      gap.noMoreOffers();
    }


    // Append processed peak list to the project
    MZmineProject currentProject = MZmineCore.getCurrentProject();
    currentProject.addPeakList(processedPeakList);


    // Add task description to peakList
    processedPeakList
        .addDescriptionOfAppliedTask(new SimplePeakListAppliedMethod(
            "Targeted peak detection ", parameters));

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    }


    ProjectTree projectTree = (ProjectTree) info.getComponent();
    ProjectTreeModel treeModel = (ProjectTreeModel) projectTree.getModel();


    MZmineProject project = MZmineCore.getCurrentProject();


    JTree.DropLocation dl = (JTree.DropLocation) info.getDropLocation();
    TreePath dropPath = dl.getPath();
    DefaultMutableTreeNode droppedLocationNode = (DefaultMutableTreeNode) dropPath
        .getLastPathComponent();


    Object droppedLocationObject = droppedLocationNode.getUserObject();
    int childIndex = dl.getChildIndex();


    TreePath transferedPaths[] = projectTree.getSelectionPaths();


    // Check if the drop target is among the project data files
    if (droppedLocationObject == ProjectTreeModel.dataFilesNodeName) {


      for (TreePath path : transferedPaths) {
        DefaultMutableTreeNode node = (DefaultMutableTreeNode) path
            .getLastPathComponent();
        int currentIndex = node.getParent().getIndex(node);
        Object transferObject = node.getUserObject();
        if (transferObject instanceof RawDataFile) {
          treeModel.removeNodeFromParent(node);


          if (childIndex > currentIndex)
            childIndex--;
          treeModel.insertNodeInto(node, droppedLocationNode,
              childIndex);


          childIndex++;


        }
      }


    }


    // Check if the drop target is AFTER the data files (last position)
    if ((droppedLocationObject == project) && (childIndex == 1)) {
      int numOfFiles = project.getDataFiles().length;
      DefaultMutableTreeNode filesNode = (DefaultMutableTreeNode) droppedLocationNode
          .getChildAt(0);


      for (TreePath path : transferedPaths) {
        DefaultMutableTreeNode node = (DefaultMutableTreeNode) path
            .getLastPathComponent();
        Object transferObject = node.getUserObject();
        if (transferObject instanceof RawDataFile) {
          treeModel.removeNodeFromParent(node);
          treeModel.insertNodeInto(node, filesNode, numOfFiles - 1);
        }
      }


    }


    // Check if the drop target is among the project peak lists
    if (droppedLocationObject == ProjectTreeModel.peakListsNodeName) {
      for (TreePath path : transferedPaths) {
        DefaultMutableTreeNode node = (DefaultMutableTreeNode) path
            .getLastPathComponent();
        int currentIndex = node.getParent().getIndex(node);
        Object transferObject = node.getUserObject();
        if (childIndex > currentIndex)
          childIndex--;
        if (transferObject instanceof PeakList) {
          treeModel.removeNodeFromParent(node);
          treeModel.insertNodeInto(node, droppedLocationNode,
              childIndex);
          childIndex++;
        }
      }
    }


    // Check if the drop target is AFTER the peak lists (last position)
    if ((droppedLocationObject == project) && (childIndex == 2)) {
      DefaultMutableTreeNode peakListsNode = (DefaultMutableTreeNode) droppedLocationNode
          .getChildAt(1);


      int numOfPeakLists = project.getPeakLists().length;
      for (TreePath path : transferedPaths) {
        DefaultMutableTreeNode node = (DefaultMutableTreeNode) path
            .getLastPathComponent();
        Object transferObject = node.getUserObject();
        if (transferObject instanceof PeakList) {

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        // Finalize writing
        correctedDataFile = rawDataFileWriter.finishWriting();


        // Add the newly created file to the project
        final MZmineProject project = MZmineCore.getCurrentProject();
        project.addFile(correctedDataFile);


        // Remove the original data file if requested
        if (removeOriginal) {
          project.removeFile(origDataFile);
        }


        // Set task status to FINISHED
        setStatus(TaskStatus.FINISHED);

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    this.selectedRows = parameters.getParameter(
        IntensityPlotParameters.selectedRows).getValue();


    if (xAxisValueSource instanceof ParameterWrapper) {
      MZmineProject project = MZmineCore.getCurrentProject();
      UserParameter xAxisParameter = ((ParameterWrapper) xAxisValueSource)
          .getParameter();
      LinkedHashSet<Comparable> parameterValues = new LinkedHashSet<Comparable>();
      for (RawDataFile file : selectedFiles) {
        Object value = project.getParameterValue(xAxisParameter, file);
        parameterValues.add((Comparable<?>) value);
      }
      xValues = parameterValues.toArray(new Comparable[0]);


      // if we have a numerical axis, we don't want the values to be

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    }
    if (xAxisValueSource instanceof ParameterWrapper) {
      HashSet<RawDataFile> files = new HashSet<RawDataFile>();
      UserParameter xAxisParameter = ((ParameterWrapper) xAxisValueSource)
          .getParameter();
      MZmineProject project = MZmineCore.getCurrentProject();
      for (RawDataFile file : selectedFiles) {
        Object fileValue = project.getParameterValue(xAxisParameter,
            file);
        if (fileValue == null)
          continue;
        if (fileValue.equals(xValue))
          files.add(file);

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      // Finish up.
      if (!isCanceled()) {


        // Add new peak-list to the project.
        final MZmineProject currentProject = MZmineCore
            .getCurrentProject();
        currentProject.addPeakList(newPeakList);


        // Remove the original peak-list if requested.
        if (removeOriginal) {


          currentProject.removePeakList(origPeakList);
        }


        // Copy previously applied methods
        for (final PeakListAppliedMethod method : origPeakList
            .getAppliedMethods()) {

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net.sf.mzmine.modules.deconvolutedanalysis.spectrafilter.SpectraFilterTask

net.sf.mzmine.modules.masslistmethods.chromatogrambuilder.ChromatogramBuilderTask

net.sf.mzmine.modules.peaklistmethods.alignment.join.JoinAlignerTask

net.sf.mzmine.modules.peaklistmethods.alignment.path.PathAlignerTask

net.sf.mzmine.modules.peaklistmethods.alignment.ransac.RansacAlignerTask

net.sf.mzmine.modules.peaklistmethods.dataanalysis.heatmaps.HeatMapTask

net.sf.mzmine.modules.peaklistmethods.dataanalysis.projectionplots.CDADataset

net.sf.mzmine.modules.peaklistmethods.dataanalysis.projectionplots.PCADataset

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