List of addPeak() Examples

Examples of addPeak()

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

        for (final ChromatographicPeak peak : row.getPeaks()) {


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


        newPeakList.addRow(newRow);
      }
    }

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


      // Keep old ID
      int oldID = oldRow.getID();
      SimplePeakListRow newRow = new SimplePeakListRow(oldID);
      PeakUtils.copyPeakListRowProperties(oldRow, newRow);
      newRow.addPeak(dataFile, newPeak);
      deisotopedPeakList.addRow(newRow);


      // Remove all peaks already assigned to isotope pattern
      for (int i = 0; i < sortedPeaks.length; i++) {
        if (bestFitPeaks.contains(sortedPeaks[i]))

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

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

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

          double normalizedArea = originalPeak.getArea()
              / normalizationFactor;
          normalizedPeak.setHeight(normalizedHeight);
          normalizedPeak.setArea(normalizedArea);


          normalizedRow.addPeak(file, normalizedPeak);
        }


      }


      normalizedPeakList.addRow(normalizedRow);

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

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


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

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

                originalpeakListRow, normalizedRow);


            rowMap.put(originalpeakListRow, normalizedRow);
          }


          normalizedRow.addPeak(file, normalizedPeak);


        }


      }

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Examples of org.bmdrc.mass.PeakList.addPeak()

        PeakList thePeakList = new PeakList();


        while ((theFileString = theFileReader.readLine()) != null) {
            String[] theSplitedString = theFileString.split(theColumnSeparator);


            thePeakList.addPeak(new PeakUnit(Double.parseDouble(theSplitedString[this.MW_INDEX]), Double.parseDouble(theSplitedString[this.INTENSITY_INDEX]), theInputFile.toString()));
        }


        return thePeakList;
    }

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