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

      numberOfGroups = selectedRawDataFiles.length;
    }


    if (coloringType.isByParameter()) {
      // Group files with same parameter value to same group
      MZmineProject project = MZmineCore.getCurrentProject();
      Vector<Object> availableParameterValues = new Vector<Object>();
      UserParameter selectedParameter = coloringType.getParameter();
      for (RawDataFile rawDataFile : selectedRawDataFiles) {
        Object paramValue = project.getParameterValue(
            selectedParameter, rawDataFile);
        if (!availableParameterValues.contains(paramValue))
          availableParameterValues.add(paramValue);
      }


      for (int ind = 0; ind < selectedRawDataFiles.length; ind++) {
        Object paramValue = project.getParameterValue(
            selectedParameter, selectedRawDataFiles[ind]);
        groupsForSelectedRawDataFiles[ind] = availableParameterValues
            .indexOf(paramValue);
      }
      parameterValuesForGroups = availableParameterValues.toArray();

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      numberOfGroups = selectedRawDataFiles.length;
    }


    if (coloringType.isByParameter()) {
      // Group files with same parameter value to same group
      MZmineProject project = MZmineCore.getCurrentProject();
      Vector<Object> availableParameterValues = new Vector<Object>();
      UserParameter selectedParameter = coloringType.getParameter();
      for (RawDataFile rawDataFile : selectedRawDataFiles) {
        Object paramValue = project.getParameterValue(
            selectedParameter, rawDataFile);
        if (!availableParameterValues.contains(paramValue))
          availableParameterValues.add(paramValue);
      }


      for (int ind = 0; ind < selectedRawDataFiles.length; ind++) {
        Object paramValue = project.getParameterValue(
            selectedParameter, selectedRawDataFiles[ind]);
        groupsForSelectedRawDataFiles[ind] = availableParameterValues
            .indexOf(paramValue);
      }
      parameterValuesForGroups = availableParameterValues.toArray();

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      }
    }


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


    // Add task description to peakList
    processedPeakList
        .addDescriptionOfAppliedTask(new SimplePeakListAppliedMethod(
            "Gap filling ", parameters));


    // Remove the original peaklist if requested
    if (removeOriginal)
      currentProject.removePeakList(peakList);


    logger.info("Finished gap-filling on " + peakList);
    setStatus(TaskStatus.FINISHED);


  }

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      processedRows++;


    }


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


    // Add task description to peakList
    processedPeakList
        .addDescriptionOfAppliedTask(new SimplePeakListAppliedMethod(
            "Gap filling using RT and m/z range", parameters));


    // Remove the original peaklist if requested
    if (removeOriginal)
      currentProject.removePeakList(peakList);


    setStatus(TaskStatus.FINISHED);


    logger.info("Finished gap-filling " + peakList);

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      newPeakID++;
      processedRows++;
    }


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


    // Remove the original peaklist if requested
    if (removeOriginal)
      currentProject.removePeakList(originalPeakList);


    // Load previous applied methods
    for (PeakListAppliedMethod proc : originalPeakList.getAppliedMethods()) {
      newPeakList.addDescriptionOfAppliedTask(proc);
    }

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          newPeakList = resolvePeaks(originalPeakList);


          if (!isCanceled()) {


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


            // Remove the original peaklist if requested.
            if (parameters.getParameter(AUTO_REMOVE).getValue()) {


              currentProject.removePeakList(originalPeakList);
            }


            setStatus(TaskStatus.FINISHED);
            LOG.info("Finished peak recognition on "
                + originalPeakList);

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          processEI();
          break;
      }


      // 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(dataFile);
    } catch (IOException e) {
      logger.log(Level.SEVERE,
          "Retention correction initialization error", e);
      setStatus(TaskStatus.ERROR);
      errorMessage = e.getMessage();

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                .getValue());


        if (!isCanceled()) {


          // Add new peakList to the project.
          final MZmineProject project = MZmineCore
              .getCurrentProject();
          project.addPeakList(filteredPeakList);


          // Remove the original peakList if requested.
          if (parameters.getParameter(
              DuplicateFilterParameters.autoRemove).getValue()) {


            project.removePeakList(peakList);
          }


          // Finished.
          LOG.info("Finished filtering duplicate peak list rows on "
              + peakList);

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      processedPeaks++;


    }


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


    // Load previous applied methods
    for (PeakListAppliedMethod proc : peakList.getAppliedMethods()) {
      deisotopedPeakList.addDescriptionOfAppliedTask(proc);
    }


    // Add task description to peakList
    deisotopedPeakList
        .addDescriptionOfAppliedTask(new SimplePeakListAppliedMethod(
            "Isotopic peaks grouper", parameters));


    // Remove the original peakList if requested
    if (removeOriginal)
      currentProject.removePeakList(peakList);


    logger.info("Finished isotopic peak grouper on " + peakList);
    setStatus(TaskStatus.FINISHED);


  }

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      // the TaskProgressWindow from disposing
      frame.doDefaultCloseAction();
    }


    // Create a new, empty project
    MZmineProject newProject = new MZmineProjectImpl();


    // Replace the current project with the new one
    ProjectManager projectManager = MZmineCore.getProjectManager();
    projectManager.setCurrentProject(newProject);

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Related Classes of net.sf.mzmine.project.MZmineProject

net.sf.mzmine.desktop.impl.projecttree.ProjectTreeDnDHandler

net.sf.mzmine.modules.deconvolutedanalysis.famealignment.FameAlignmentProcessingTask

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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