Package net.sf.mzmine.project

Examples of net.sf.mzmine.project.MZmineProject


    if (isCanceled()) {
      return;
    }

    // Add new peaklists to the project
    MZmineProject currentProject = MZmineCore.getCurrentProject();

    for (int i = 0; i < originalPeakLists.length; i++) {

      currentProject.addPeakList(normalizedPeakLists[i]);

      // Load previous applied methods
      for (PeakListAppliedMethod proc : originalPeakLists[i]
          .getAppliedMethods()) {
        normalizedPeakLists[i].addDescriptionOfAppliedTask(proc);
      }

      // Add task description to peakList
      normalizedPeakLists[i]
          .addDescriptionOfAppliedTask(new SimplePeakListAppliedMethod(
              "Retention time normalization", parameters));

      // Remove the original peaklists if requested
      if (removeOriginal)
        currentProject.removePeakList(originalPeakLists[i]);

    }

    logger.info("Finished retention time normalizer");
    setStatus(TaskStatus.FINISHED);
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      SimplePeakListRow normalizedRow = rowMap.get(originalpeakListRow);
      normalizedPeakList.addRow(normalizedRow);
    }

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

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

    // Add task description to peakList
    normalizedPeakList
        .addDescriptionOfAppliedTask(new SimplePeakListAppliedMethod(
            "Linear normalization of by " + normalizationType,
            parameters));

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

    logger.info("Finished linear normalizer");
    setStatus(TaskStatus.FINISHED);

  }
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      }

    } // Next peak list

    // Add new aligned peak list to the project
    MZmineProject currentProject = MZmineCore.getCurrentProject();
    currentProject.addPeakList(alignedPeakList);

    // Add task description to peakList
    alignedPeakList
        .addDescriptionOfAppliedTask(new SimplePeakListAppliedMethod(
            "Join aligner", parameters));
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Related Classes of net.sf.mzmine.project.MZmineProject

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