DataPoint[] getCachedDataPoints(MsScan scan) { if (dpCache == null) dpCache = new HashMap<>(); DataPoint[] dp = dpCache.get(scan); if (dp != null) { return dp; } dp = new DataPoint[scan.getNumberOfDataPoints()]; double mzValues[] = scan.getMzValues(); float intensityValues[] = scan.getIntensityValues(); for (int i = 0; i < scan.getNumberOfDataPoints(); i++) { dp[i] = new DataPoint(mzValues[i], intensityValues[i]); } dpCache.put(scan, dp); return dp; }
DataPoint[] getCachedDataPoints(MsScan scan) { if (dpCache == null) dpCache = new HashMap<>(); DataPoint[] dp = dpCache.get(scan); if (dp != null) { return dp; } dp = new DataPoint[scan.getNumberOfDataPoints()]; double mzValues[] = scan.getMzValues(); float intensityValues[] = scan.getIntensityValues(); for (int i = 0; i < scan.getNumberOfDataPoints(); i++) { dp[i] = new DataPoint(mzValues[i], intensityValues[i]); } dpCache.put(scan, dp); return dp; }
mzBuffer = scan.getMzValues(); intensityBuffer = scan.getIntensityValues(); numOfDataPoints = scan.getNumberOfDataPoints();
mzBuffer = scan.getMzValues(); intensityBuffer = scan.getIntensityValues(); numOfDataPoints = scan.getNumberOfDataPoints();
mzBuffer = scan.getMzValues(); intensityBuffer = scan.getIntensityValues(); numOfDataPoints = scan.getNumberOfDataPoints();
/** {@inheritDoc} */ @Override public @Nonnull MsScan centroidScan(@Nonnull MsScan inputScan) { // Copy all scan properties this.newScan = MsScanUtil.clone(inputScan, false); // Load data points mzBuffer = inputScan.getMzValues(); intensityBuffer = inputScan.getIntensityValues(); numOfDataPoints = inputScan.getNumberOfDataPoints(); newNumOfDataPoints = 0; // If there are no data points, just return the scan if (numOfDataPoints == 0) { newScan.setDataPoints(mzBuffer, intensityBuffer, 0); return newScan; } // Run the recursive search algorithm recursiveThreshold(0, numOfDataPoints - 1, 0); // Store the new data points newScan.setDataPoints(newMzBuffer, newIntensityBuffer, newNumOfDataPoints); return newScan; }
/** {@inheritDoc} */ @Override public @Nonnull MsScan centroidScan(@Nonnull MsScan inputScan) { // Copy all scan properties this.newScan = MsScanUtil.clone(inputScan, false); // Load data points mzBuffer = inputScan.getMzValues(); intensityBuffer = inputScan.getIntensityValues(); numOfDataPoints = inputScan.getNumberOfDataPoints(); newNumOfDataPoints = 0; // If there are no data points, just return the scan if (numOfDataPoints == 0) { newScan.setDataPoints(mzBuffer, intensityBuffer, 0); return newScan; } // Run the recursive search algorithm recursiveThreshold(0, numOfDataPoints - 1, 0); // Store the new data points newScan.setDataPoints(newMzBuffer, newIntensityBuffer, newNumOfDataPoints); return newScan; }
mzBuffer = inputScan.getMzValues(); intensityBuffer = inputScan.getIntensityValues(); numOfDataPoints = inputScan.getNumberOfDataPoints();
mzBuffer = inputScan.getMzValues(); intensityBuffer = inputScan.getIntensityValues(); numOfDataPoints = inputScan.getNumberOfDataPoints();
/** {@inheritDoc} */ @Override public @Nonnull MsScan centroidScan(@Nonnull MsScan inputScan) { // Copy all scan properties SimpleMsScan newScan = MsScanUtil.clone(inputScan, false); // Load data points double[] mzBuffer = inputScan.getMzValues(); float[] intensityBuffer = inputScan.getIntensityValues(); int numOfDataPoints = inputScan.getNumberOfDataPoints(); // If there are no data points, just return the scan if (numOfDataPoints == 0) { newScan.setDataPoints(mzBuffer, intensityBuffer, 0); return newScan; } float[] cwtDataPoints = performCWT(intensityBuffer, numOfDataPoints, scaleLevel, waveletWindow); int newNumOfDataPoints = extractMzPeaks(cwtDataPoints, mzBuffer, intensityBuffer); // Store the new data points newScan.setDataPoints(mzBuffer, intensityBuffer, newNumOfDataPoints); return newScan; }
/** {@inheritDoc} */ @Override public @Nonnull MsScan centroidScan(@Nonnull MsScan inputScan) { // Copy all scan properties SimpleMsScan newScan = MsScanUtil.clone(inputScan, false); // Load data points double[] mzBuffer = inputScan.getMzValues(); float[] intensityBuffer = inputScan.getIntensityValues(); int numOfDataPoints = inputScan.getNumberOfDataPoints(); // If there are no data points, just return the scan if (numOfDataPoints == 0) { newScan.setDataPoints(mzBuffer, intensityBuffer, 0); return newScan; } float[] cwtDataPoints = performCWT(intensityBuffer, numOfDataPoints, scaleLevel, waveletWindow); int newNumOfDataPoints = extractMzPeaks(cwtDataPoints, mzBuffer, intensityBuffer); // Store the new data points newScan.setDataPoints(mzBuffer, intensityBuffer, newNumOfDataPoints); return newScan; }
mzBuffer = inputScan.getMzValues(); intensityBuffer = inputScan.getIntensityValues(); final int numOfDataPoints = inputScan.getNumberOfDataPoints();
mzBuffer = inputScan.getMzValues(); intensityBuffer = inputScan.getIntensityValues(); final int numOfDataPoints = inputScan.getNumberOfDataPoints();
void addScan(RawDataFile dataFile, MsScan scan, MzTolerance mzTolerance) { mzBuffer = scan.getMzValues(); intensityBuffer = scan.getIntensityValues(); int numOfDataPoints = scan.getNumberOfDataPoints();
mzBuffer = inputScan.getMzValues(); intensityBuffer = inputScan.getIntensityValues(); final int numOfDataPoints = inputScan.getNumberOfDataPoints();
mzBuffer = inputScan.getMzValues(); intensityBuffer = inputScan.getIntensityValues(); final int numOfDataPoints = inputScan.getNumberOfDataPoints();
/** * <p> * clone. * </p> * * @param scan a {@link io.github.msdk.datamodel.MsScan} object. * @param copyDataPoints a {@link java.lang.Boolean} object. * @return a {@link io.github.msdk.datamodel.MsScan} object. */ @Nonnull static public SimpleMsScan clone(@Nonnull MsScan scan, @Nonnull Boolean copyDataPoints) { Preconditions.checkNotNull(scan); Preconditions.checkNotNull(copyDataPoints); SimpleMsScan newScan = new SimpleMsScan(scan.getScanNumber(), scan.getMsFunction()); newScan.setPolarity(scan.getPolarity()); newScan.setMsScanType(scan.getMsScanType()); newScan.setScanningRange(scan.getScanningRange()); newScan.setRetentionTime(scan.getRetentionTime()); newScan.setMsLevel(scan.getMsLevel()); newScan.setSourceInducedFragmentation(scan.getSourceInducedFragmentation()); newScan.getIsolations().addAll(scan.getIsolations()); if (copyDataPoints) { double mzValues[] = scan.getMzValues(); float intensityValues[] = scan.getIntensityValues(); newScan.setDataPoints(mzValues, intensityValues, scan.getNumberOfDataPoints()); } return newScan; }
/** * <p> * clone. * </p> * * @param scan a {@link io.github.msdk.datamodel.MsScan} object. * @param copyDataPoints a {@link java.lang.Boolean} object. * @return a {@link io.github.msdk.datamodel.MsScan} object. */ @Nonnull static public SimpleMsScan clone(@Nonnull MsScan scan, @Nonnull Boolean copyDataPoints) { Preconditions.checkNotNull(scan); Preconditions.checkNotNull(copyDataPoints); SimpleMsScan newScan = new SimpleMsScan(scan.getScanNumber(), scan.getMsFunction()); newScan.setPolarity(scan.getPolarity()); newScan.setMsScanType(scan.getMsScanType()); newScan.setScanningRange(scan.getScanningRange()); newScan.setRetentionTime(scan.getRetentionTime()); newScan.setMsLevel(scan.getMsLevel()); newScan.setSourceInducedFragmentation(scan.getSourceInducedFragmentation()); newScan.getIsolations().addAll(scan.getIsolations()); if (copyDataPoints) { double mzValues[] = scan.getMzValues(); float intensityValues[] = scan.getIntensityValues(); newScan.setDataPoints(mzValues, intensityValues, scan.getNumberOfDataPoints()); } return newScan; }
mzBuffer = scan.getMzValues(); intensityBuffer = scan.getIntensityValues(); numOfDataPoints = scan.getNumberOfDataPoints();
float intensityValues[] = new float[10000]; for (MsScan scan : scans) { mzValues = scan.getMzValues(mzValues); intensityValues = scan.getIntensityValues(intensityValues);