Package net.sf.mzmine.data.impl

Examples of net.sf.mzmine.data.impl.SimplePeakListRow.addPeak()

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      PeakListRow row = new SimplePeakListRow(++id);
      row.setComment(name);

      for (FameAlignmentProcessingTask task : processingTasks) {
        if (task.getResults().containsKey(name))
          row.addPeak(task.getResults().get(name).getDataFile(), task
              .getResults().get(name));
      }

      peakList.addRow(row);
    }
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    for (Double averageRT : matchedCandidates.keySet()) {
      List<MassCandidate> masses = matchedCandidates.get(averageRT);
      PeakListRow row = new SimplePeakListRow(id++);

      for (MassCandidate m : masses)
        row.addPeak(m.getDataFile(), m);

      peakList.addRow(row);
    }

    MZmineCore.getCurrentProject().addPeakList(peakList);
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          double normalizedArea = originalPeak.getArea()
              / normalizationFactor;
          normalizedPeak.setHeight(normalizedHeight);
          normalizedPeak.setArea(normalizedArea);

          normalizedRow.addPeak(file, normalizedPeak);
        }

      }

      normalizedPeakList.addRow(normalizedRow);
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    for (final ChromatographicPeak peak : row.getPeaks()) {

      final ChromatographicPeak newPeak = new SimpleChromatographicPeak(
          peak);
      PeakUtils.copyPeakProperties(peak, newPeak);
      newRow.addPeak(peak.getDataFile(), newPeak);
    }

    return newRow;
  }
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        // keep old ID
        int oldID = oldRow.getID();
        SimplePeakListRow newRow = new SimplePeakListRow(oldID);
        PeakUtils.copyPeakListRowProperties(oldRow, newRow);
        newRow.addPeak(dataFile, newPeak);
        extendedPeakList.addRow(newRow);
      }

      // Update completion rate
      processedPeaks++;
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      if (originalPeak != null) {
        SimpleChromatographicPeak normalizedPeak = new SimpleChromatographicPeak(
            originalPeak);
        PeakUtils.copyPeakProperties(originalPeak, normalizedPeak);
        normalizedPeak.setRT(normalizedRT);
        normalizedRow.addPeak(file, normalizedPeak);
      }
    }

    return normalizedRow;
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                originalpeakListRow, normalizedRow);

            rowMap.put(originalpeakListRow, normalizedRow);
          }

          normalizedRow.addPeak(file, normalizedPeak);

        }

      }
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