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 fragments", parameters));

    // Repaint the window to reflect the change in the peak list
    MZmineCore.getDesktop().getMainFrame().repaint();
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      errorMessage = e.toString();
      return;
    }

    // Add task description to peakList
    peakList.addDescriptionOfAppliedTask(new SimplePeakListAppliedMethod(
        "Peak identification using database " + dataBaseFile,
        parameters));

    // Repaint the window to reflect the changes in the peak list
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    MZmineProject currentProject = MZmineCore.getCurrentProject();
    currentProject.addPeakList(processedPeakList);

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

    logger.log(Level.INFO, "Targeted peak detection on {0}", this.dataFile);
    setStatus(TaskStatus.FINISHED);
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          newPeakList.addDescriptionOfAppliedTask(method);
        }

        // Add task description to peak-list.
        newPeakList
            .addDescriptionOfAppliedTask(new SimplePeakListAppliedMethod(
                "Peaks smoothed by Savitzky-Golay filter",
                parameters));

        LOG.finest("Finished peak smoothing: " + progress
            + " rows processed");
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    }

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

    // Repaint the window to reflect the change in the peak list
    MZmineCore.getDesktop().getMainFrame().repaint();
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    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);
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    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);
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      newPeakList.addDescriptionOfAppliedTask(proc);
    }

    // Add task description to peakList
    newPeakList
        .addDescriptionOfAppliedTask(new SimplePeakListAppliedMethod(
            "Peaks shaped by " + shapeModelerType + " function",
            parameters));

    logger.finest("Finished peak shape modeler " + processedRows
        + " rows processed");
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      resolvedPeaks.addDescriptionOfAppliedTask(method);
    }

    // Add task description to peak list.
    resolvedPeaks
        .addDescriptionOfAppliedTask(new SimplePeakListAppliedMethod(
            "Peak deconvolution by " + resolver, resolver
                .getParameterSet()));

    // Initialise counters.
    processedRows = 0;
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      searchAdducts();

      if (!isCanceled()) {

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

        // Repaint the window to reflect the change in the peak list.
        MZmineCore.getDesktop().getMainFrame().repaint();
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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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