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

Class net.sf.mzmine.data.impl.SimplePeakListRow

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

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


    // Add the chromatograms to the new peak list
    for (ChromatographicPeak finishedPeak : chromatograms) {
      SimplePeakListRow newRow = new SimplePeakListRow(newPeakID);
      newPeakID++;
      newRow.addPeak(dataFile, finishedPeak);
      newPeakList.addRow(newRow);
    }


    // Add new peaklist to the project
    MZmineProject currentProject = MZmineCore.getCurrentProject();

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              bestScan.getRetentionTime()), new Range(
              scan.getPrecursorMZ()), new Range(
              maxPoint.getIntensity()));


      PeakListRow entry = new SimplePeakListRow(scan.getScanNumber());
      entry.addPeak(dataFile, c);


      newPeakList.addRow(entry);
      processedScans++;
    }

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              assert maxDataPoint != null;


              if (!isCanceled() && maxScanNumber >= 0) {


                // Create a new peak.
                newRow.addPeak(
                    dataFile,
                    new SimpleChromatographicPeak(
                        dataFile,
                        maxDataPoint.getMZ(),
                        peak.getRT(),

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                rtRange, intTolerance);


            gaps.add(newGap);


          } else {
            newRow.addPeak(dataFile, sourcePeak);
          }


        }


        // Stop processing this file if there are no gaps

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        if (currentPeak == null)
          currentPeak = fillGap(sourceRow, column);


        // If a peak was found or created, add it
        if (currentPeak != null)
          newRow.addPeak(column, currentPeak);


      }


      processedPeakList.addRow(newRow);

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          ChromatographicPeak shapePeak = (ChromatographicPeak) shapeModelConstruct
              .newInstance(peak, scanNumbers, intensities,
                  retentionTimes, resolution);


          newRow.addPeak(shapePeak.getDataFile(), shapePeak);
        }


      } catch (Exception e) {
        String message = "Error trying to make an instance of shape model class "
            + shapeModelClass;

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      // Add peaks to the new peak list.
      for (final ChromatographicPeak peak : peaks) {


        final PeakListRow newRow = new SimplePeakListRow(peakId++);
        newRow.addPeak(dataFile, peak);
        resolvedPeaks.addRow(newRow);
      }


      processedRows++;
    }

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    PeakListRow newRow = new SimplePeakListRow(ID);
    try {
      for (PeakListRow row : this.peaks) {
        if (row != null) {
          for (ChromatographicPeak peak : row.getPeaks()) {
            newRow.addPeak(peak.getDataFile(), peak);
          }
        }
      }
    } catch (NullPointerException e) {
      e.printStackTrace();

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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);
        }


        newPeakList.addRow(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);
      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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