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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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gaps.add(newGap); } } } else { newRow.addPeak(datafile1, 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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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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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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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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alignedPeakList.addRow(targetRow); } // Add all peaks from the original row to the aligned row for (RawDataFile file : row.getRawDataFiles()) { targetRow.addPeak(file, row.getPeak(file)); } // Add all non-existing identities from the original row to the // aligned row PeakUtils.copyPeakListRowProperties(row, targetRow);