/** {@inheritDoc} */ @Override public @Nonnull float[] getIntensityValues() { return getIntensityValues(null); }
/** {@inheritDoc} */ @Override public @Nonnull double[] getMzValues() { return getMzValues(null); }
/** {@inheritDoc} */ @Override public @Nonnull float[] getRetentionTimes() { return getRetentionTimes(null); }
buildingChromatogram = new SimpleChromatogram(); chromatogramMap.put(q1 + ";" + q3, buildingChromatogram); buildingChromatogram.addDataPoint(rt, null, intenstiy); double q1 = Double.parseDouble(strs[0]); double q3 = Double.parseDouble(strs[1]); List<IsolationInfo> isolations = chromatogram.getIsolations(); isolations.add(isolationInfo); if ((chromatogram.getMz() == null) && (chromatogram.getMzValues() != null)) { double mzValues[] = chromatogram.getMzValues(); Integer size = chromatogram.getNumberOfDataPoints(); Double newMz = ChromatogramUtil.getMedianMz(mzValues, size); chromatogram.setMz(newMz);
chromatogram = new SimpleChromatogram(); chromatogram.setChromatogramNumber(chromatogramNumber); float[] intensityValues = buildingChromatogram.getIntensityValues(); int size = buildingChromatogram.getSize(); chromatogram.setDataPoints(rtValues, mzValues, intensityValues, size); newMz = ChromatogramUtil.calculateMz(mzValues, intensityValues, size, CalculationMethod.allAverage); chromatogram.setMz(newMz); chromatogram.setIonAnnotation(ionAnnotation);
if (sx.getMaxDatumScans() >= tolScans && (sx.getContigousMaxDatumScans() >= tolScans || sx.getContigousToMaxDatumScansRatio() > 0.5)) { SimpleChromatogram peak = new SimpleChromatogram(); peak.setRawDataFile(rawDataFile); if (addMaxDatumFromScans(sx, peak) > 0) { float area = ChromatogramUtil.getArea(peak.getRetentionTimes(), peak.getIntensityValues(), peak.getNumberOfDataPoints()); if (area > 1e-6) { SimpleFeatureTableRow newRow = new SimpleFeatureTableRow(newPeakList); newFeature.setArea(area); newFeature.setChromatogram(peak); float height = ChromatogramUtil.getMaxHeight(peak.getIntensityValues(), peak.getNumberOfDataPoints()); newFeature.setHeight(height);
SimpleChromatogram newChromatogram = new SimpleChromatogram(); intensityBuffer = buildingChromatogram.getIntensityValues(intensityBuffer); int size = buildingChromatogram.size(); newChromatogram.setDataPoints(rtBuffer, mzBuffer, intensityBuffer, size); newChromatogram.setMz(mz);
SimpleChromatogram chromatogram = new SimpleChromatogram(); chromatogram.setDataPoints(rtArray, mzArray, intensityArray, upperScanBound - lowerScanBound + 1);
chr.addDataPoint(scans.get(i).getRetentionTime(), mzMax.mz, new Float(mzMax.intensity));
buildingChromatogram = new SimpleChromatogram(); chromatogramMap.put(q1 + ";" + q3, buildingChromatogram); buildingChromatogram.addDataPoint(rt, null, intenstiy); double q1 = Double.parseDouble(strs[0]); double q3 = Double.parseDouble(strs[1]); List<IsolationInfo> isolations = chromatogram.getIsolations(); isolations.add(isolationInfo); if ((chromatogram.getMz() == null) && (chromatogram.getMzValues() != null)) { double mzValues[] = chromatogram.getMzValues(); Integer size = chromatogram.getNumberOfDataPoints(); Double newMz = ChromatogramUtil.getMedianMz(mzValues, size); chromatogram.setMz(newMz);
chromatogram = new SimpleChromatogram(); chromatogram.setChromatogramNumber(chromatogramNumber); float[] intensityValues = buildingChromatogram.getIntensityValues(); int size = buildingChromatogram.getSize(); chromatogram.setDataPoints(rtValues, mzValues, intensityValues, size); newMz = ChromatogramUtil.calculateMz(mzValues, intensityValues, size, CalculationMethod.allAverage); chromatogram.setMz(newMz); chromatogram.setIonAnnotation(ionAnnotation);
if (sx.getMaxDatumScans() >= tolScans && (sx.getContigousMaxDatumScans() >= tolScans || sx.getContigousToMaxDatumScansRatio() > 0.5)) { SimpleChromatogram peak = new SimpleChromatogram(); peak.setRawDataFile(rawDataFile); if (addMaxDatumFromScans(sx, peak) > 0) { float area = ChromatogramUtil.getArea(peak.getRetentionTimes(), peak.getIntensityValues(), peak.getNumberOfDataPoints()); if (area > 1e-6) { SimpleFeatureTableRow newRow = new SimpleFeatureTableRow(newPeakList); newFeature.setArea(area); newFeature.setChromatogram(peak); float height = ChromatogramUtil.getMaxHeight(peak.getIntensityValues(), peak.getNumberOfDataPoints()); newFeature.setHeight(height);
SimpleChromatogram newChromatogram = new SimpleChromatogram(); intensityBuffer = buildingChromatogram.getIntensityValues(intensityBuffer); int size = buildingChromatogram.size(); newChromatogram.setDataPoints(rtBuffer, mzBuffer, intensityBuffer, size); newChromatogram.setMz(mz);
SimpleChromatogram chromatogram = new SimpleChromatogram(); chromatogram.setDataPoints(rtArray, mzArray, intensityArray, upperScanBound - lowerScanBound + 1);
chr.addDataPoint(scans.get(i).getRetentionTime(), mzMax.mz, new Float(mzMax.intensity));
int addMaxDatumFromScans(SpotByProbes s, SimpleChromatogram peak) { int i, j; int adds = 0; for (i = s.minScan; i <= s.maxScan; i++) { Datum[] di = roi[i]; if (di != null && di.length > 0) { Datum max = new Datum(new DataPoint(0, -1), 0, new DataPoint(0, -1)); int idx = findFirstMass(s.minMZ, di); for (j = idx; j < di.length && di[j].mz <= s.maxMZ; j++) { Datum d = di[j]; if (d.spotId == s.spotId) { if (d.intensity > max.intensity && d.mz >= s.minMZ && d.intensity > minimumHeight) { max = d; } } } if (max.intensity > 0) { adds++; peak.addDataPoint(scans.get(i).getRetentionTime(), max.mzOriginal, new Float(max.intensityOriginal)); } } } return adds; }
/** {@inheritDoc} */ @Override public @Nonnull float[] getRetentionTimes() { return getRetentionTimes(null); }
/** {@inheritDoc} */ @Override public @Nonnull float[] getIntensityValues() { return getIntensityValues(null); }
/** {@inheritDoc} */ @Override public @Nonnull double[] getMzValues() { return getMzValues(null); }
int addMaxDatumFromScans(SpotByProbes s, SimpleChromatogram peak) { int i, j; int adds = 0; for (i = s.minScan; i <= s.maxScan; i++) { Datum[] di = roi[i]; if (di != null && di.length > 0) { Datum max = new Datum(new DataPoint(0, -1), 0, new DataPoint(0, -1)); int idx = findFirstMass(s.minMZ, di); for (j = idx; j < di.length && di[j].mz <= s.maxMZ; j++) { Datum d = di[j]; if (d.spotId == s.spotId) { if (d.intensity > max.intensity && d.mz >= s.minMZ && d.intensity > minimumHeight) { max = d; } } } if (max.intensity > 0) { adds++; peak.addDataPoint(scans.get(i).getRetentionTime(), max.mzOriginal, new Float(max.intensityOriginal)); } } } return adds; }