Examples of 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

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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Examples of net.sf.mzmine.project.MZmineProject

      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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Examples of net.sf.mzmine.project.MZmineProject

      }


    } // 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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