/** * <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; }
SpectrumTypeDetectionAlgorithm.detectSpectrumType(mzBuffer, intensityBuffer, peaksCount); SimpleMsScan newScan = new SimpleMsScan(scanNumber); newScan.setMsLevel(msLevel); newScan.setDataPoints(mzBuffer, intensityBuffer, peaksCount); newScan.setSpectrumType(spectrumType); newScan.setPolarity(polarity); newScan.setRetentionTime(retentionTime); newScan.getIsolations().add(isolation);
buildingScan = new SimpleMsScan(scanNumber); buildingScan.setRawDataFile(newRawDataFile); buildingScan.setMsLevel(msLevel); buildingScan.setMsFunction(msFuncName); buildingScan.setMsScanType(MsScanType.UNKNOWN); String filterLine = attrs.getValue("filterLine"); buildingScan.setScanDefinition(filterLine); break; buildingScan.setPolarity(polarity); Duration dur = dataTypeFactory.newDuration(retentionTimeStr); final float rt = (float) (dur.getTimeInMillis(currentDate) / 1000.0); buildingScan.setRetentionTime(rt);
buildingScan = new SimpleMsScan(scanNumberInt); buildingScan.setRawDataFile(newRawFile); buildingScan.setMsLevel(msLevelInt); buildingScan.setMsFunction(msFuncName.toString()); buildingScan.setMsScanType(MsScanType.UNKNOWN); buildingScan.setScanDefinition(null); buildingScan.setPolarity(polarity); Duration dur = dataTypeFactory.newDuration(retentionTimeStr.toString()); final float rt = (float) (dur.getTimeInMillis(currentDate) / 1000.0); buildingScan.setRetentionTime(rt); buildingScan.setDataPoints(mzValues, intensityValues, vars.peaksCount); buildingScan.setSpectrumType(spectrumType); break; Range.singleton(xmlStreamReader.getText().toDouble()), null, xmlStreamReader.getText().toDouble(), vars.precursorCharge, null, vars.precursorScanNumber); buildingScan.getIsolations().add(newIsolation); break;
SimpleMsScan newScan = new SimpleMsScan(scanNumber); newScan.setMsFunction(msFunction); newScan.setMsLevel(msLevel); newScan.setRetentionTime(retentionTime); newScan.setDataPoints(mzValues, intensityValues, numOfDataPoints); newScan.setSpectrumType(spectrumType); newScan.setPolarity(polarity); newScan.setScanningRange(scanningMzRange); newScan.setScanDefinition(scanId); newScan.getIsolations().add(isolation);
newScan.setDataPoints(mzBuffer, intensityBuffer, 0); return newScan; firstIndex++; if (firstIndex == numOfDataPoints) { newScan.setDataPoints(mzBuffer, intensityBuffer, 0); return newScan; newScan.setDataPoints(mzBuffer, intensityBuffer, newNumOfDataPoints); return newScan;
IsolationInfo newIsolation = new SimpleIsolationInfo(Range.singleton(precursorMz), null, precursorMz, precursorCharge, null, precursorScanNumber); buildingScan.getIsolations().add(newIsolation); buildingScan.setDataPoints(mzValues, intensityValues, peaksCount); buildingScan.setSpectrumType(spectrumType);
float intensityList[] = eachSpectrumData.getIntensityList(); SimpleMsScan eachSimpleMsScan = new SimpleMsScan(scanNumber); eachSimpleMsScan.setDataPoints(mzList, intensityList, mzList.length);
buildingScan = new SimpleMsScan(scanNumberInt); buildingScan.setRawDataFile(newRawFile); buildingScan.setMsLevel(msLevelInt); buildingScan.setMsFunction(msFuncName.toString()); buildingScan.setMsScanType(MsScanType.UNKNOWN); buildingScan.setScanDefinition(null); buildingScan.setPolarity(polarity); Duration dur = dataTypeFactory.newDuration(retentionTimeStr.toString()); final float rt = (float) (dur.getTimeInMillis(currentDate) / 1000.0); buildingScan.setRetentionTime(rt); buildingScan.setDataPoints(mzValues, intensityValues, vars.peaksCount); buildingScan.setSpectrumType(spectrumType); break; Range.singleton(xmlStreamReader.getText().toDouble()), null, xmlStreamReader.getText().toDouble(), vars.precursorCharge, null, vars.precursorScanNumber); buildingScan.getIsolations().add(newIsolation); break;
/** {@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; }
IsolationInfo newIsolation = new SimpleIsolationInfo(Range.singleton(precursorMz), null, precursorMz, precursorCharge, null, precursorScanNumber); buildingScan.getIsolations().add(newIsolation); buildingScan.setDataPoints(mzValues, intensityValues, peaksCount); buildingScan.setSpectrumType(spectrumType);
float intensityList[] = eachSpectrumData.getIntensityList(); SimpleMsScan eachSimpleMsScan = new SimpleMsScan(scanNumber); eachSimpleMsScan.setDataPoints(mzList, intensityList, mzList.length);
/** * <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; }
SpectrumTypeDetectionAlgorithm.detectSpectrumType(mzBuffer, intensityBuffer, peaksCount); SimpleMsScan newScan = new SimpleMsScan(scanNumber); newScan.setMsLevel(msLevel); newScan.setDataPoints(mzBuffer, intensityBuffer, peaksCount); newScan.setSpectrumType(spectrumType); newScan.setPolarity(polarity); newScan.setRetentionTime(retentionTime); newScan.getIsolations().add(isolation);
buildingScan = new SimpleMsScan(scanNumber); buildingScan.setRawDataFile(newRawDataFile); buildingScan.setMsLevel(msLevel); buildingScan.setMsFunction(msFuncName); buildingScan.setMsScanType(MsScanType.UNKNOWN); String filterLine = attrs.getValue("filterLine"); buildingScan.setScanDefinition(filterLine); break; buildingScan.setPolarity(polarity); Duration dur = dataTypeFactory.newDuration(retentionTimeStr); final float rt = (float) (dur.getTimeInMillis(currentDate) / 1000.0); buildingScan.setRetentionTime(rt);
/** {@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; }
newScan.setDataPoints(mzBuffer, intensityBuffer, 0); return newScan; newScan.setDataPoints(mzBuffer, intensityBuffer, newNumOfDataPoints);
newScan.setDataPoints(mzBuffer, intensityBuffer, 0); return newScan; newScan.setDataPoints(mzBuffer, intensityBuffer, newNumOfDataPoints);
result.setDataPoints(mzBuffer, intensityBuffer, newNumOfDataPoints);
/** {@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; }