Package net.sf.mzmine.data.impl

Examples of net.sf.mzmine.data.impl.SimplePeakListAppliedMethod

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      }
    }

    // Add task description to peakList
    ((SimplePeakList) peakList)
        .addDescriptionOfAppliedTask(new SimplePeakListAppliedMethod(
            "Identification of glycerophospholipids", parameters));

    // Repaint the window to reflect the change in the peak list
    MZmineCore.getDesktop().getMainFrame().repaint();
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    buildingPeakList = new SimplePeakList(peakListName, dataFiles);

    for (int i = 0; i < appliedMethods.size(); i++) {
      String methodName = appliedMethods.elementAt(i);
      String methodParams = appliedMethodParameters.elementAt(i);
      PeakListAppliedMethod pam = new SimplePeakListAppliedMethod(
          methodName, methodParams);
      buildingPeakList.addDescriptionOfAppliedTask(pam);
    }
    buildingPeakList.setDateCreated(dateCreated);
  }
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    buildingPeakList = new SimplePeakList(peakListName, dataFiles);

    for (int i = 0; i < appliedMethods.size(); i++) {
      String methodName = appliedMethods.elementAt(i);
      String methodParams = appliedMethodParameters.elementAt(i);
      PeakListAppliedMethod pam = new SimplePeakListAppliedMethod(
          methodName, methodParams);
      buildingPeakList.addDescriptionOfAppliedTask(pam);
    }
    buildingPeakList.setDateCreated(dateCreated);
  }
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        newPeakList.addDescriptionOfAppliedTask(method);
      }

      // Add task description to peakList
      newPeakList
          .addDescriptionOfAppliedTask(new SimplePeakListAppliedMethod(
              "Duplicate peak list rows filter", parameters));
    }

    return newPeakList;
  }
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      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);
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    buildingPeakList = new SimplePeakList(peakListName, dataFiles);

    for (int i = 0; i < appliedMethods.size(); i++) {
      String methodName = appliedMethods.elementAt(i);
      String methodParams = appliedMethodParameters.elementAt(i);
      PeakListAppliedMethod pam = new SimplePeakListAppliedMethod(
          methodName, methodParams);
      buildingPeakList.addDescriptionOfAppliedTask(pam);
    }
    buildingPeakList.setDateCreated(dateCreated);
  }
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      normalizedPeakList.addDescriptionOfAppliedTask(proc);
    }

    // Add task description to peakList
    normalizedPeakList
        .addDescriptionOfAppliedTask(new SimplePeakListAppliedMethod(
            "Standard compound normalization", parameters));

    // Remove the original peaklist if requested
    if (removeOriginal)
      currentProject.removePeakList(originalPeakList);
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    MZmineProject currentProject = MZmineCore.getCurrentProject();
    currentProject.addPeakList(alignedPeakList);

    // Add task description to peakList
    alignedPeakList
        .addDescriptionOfAppliedTask(new SimplePeakListAppliedMethod(
            "Path aligner", parameters));

    logger.info("Finished Path aligner");
    setStatus(TaskStatus.FINISHED);
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      newPeakList.addDescriptionOfAppliedTask(method);
    }

    // Add task description to peakList.
    newPeakList
        .addDescriptionOfAppliedTask(new SimplePeakListAppliedMethod(
            getTaskDescription(), parameters));

    // Get parameters.
    final boolean identified = parameters.getParameter(HAS_IDENTITIES)
        .getValue();
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    MZmineProject currentProject = MZmineCore.getCurrentProject();
    currentProject.addPeakList(alignedPeakList);

    // Add task description to peakList
    alignedPeakList
        .addDescriptionOfAppliedTask(new SimplePeakListAppliedMethod(
            "Ransac aligner", parameters));

    logger.info("Finished RANSAC aligner");
    setStatus(TaskStatus.FINISHED);
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Related Classes of net.sf.mzmine.data.impl.SimplePeakListAppliedMethod

  • 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.filtering.duplicatefilter.DuplicateFilterTask
  • net.sf.mzmine.modules.peaklistmethods.filtering.rowsfilter.RowsFilterTask
  • net.sf.mzmine.modules.peaklistmethods.gapfilling.peakfinder.PeakFinderTask
  • net.sf.mzmine.modules.peaklistmethods.gapfilling.samerange.SameRangeTask
  • net.sf.mzmine.modules.peaklistmethods.identification.adductsearch.AdductSearchTask
  • net.sf.mzmine.modules.peaklistmethods.identification.complexsearch.ComplexSearchTask
  • net.sf.mzmine.modules.peaklistmethods.identification.custom.CustomDBSearchTask
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