/** {@inheritDoc} */ @Override public void cancel() { logger.info("Cancelling ADAP3D feature detection on file " + rawFile.getName()); canceled = true; if (objPeakDetection != null) { objPeakDetection.cancel(); } } }
/** {@inheritDoc} */ @Override public void cancel() { logger.info("Cancelling ADAP3D feature detection on file " + rawFile.getName()); canceled = true; if (objPeakDetection != null) { objPeakDetection.cancel(); } } }
/** {@inheritDoc} */ @Override public RawDataFile execute() throws MSDKException { logger.info("Started centroiding file " + rawDataFile.getName()); // Create a new raw data file result = new SimpleRawDataFile(rawDataFile.getName(), rawDataFile.getOriginalFile(), rawDataFile.getRawDataFileType()); List<MsScan> scans = rawDataFile.getScans(); totalScans = scans.size(); for (MsScan scan : scans) { if (canceled) return null; MsScan newScan = centroidingAlgorithm.centroidScan(scan); // Add the new scan to the created raw data file if (newScan != null) result.addScan(newScan); processedScans++; } logger.info("Finished centroiding file " + rawDataFile.getName()); return result; }
/** {@inheritDoc} */ @Override public RawDataFile execute() throws MSDKException { logger.info("Started centroiding file " + rawDataFile.getName()); // Create a new raw data file result = new SimpleRawDataFile(rawDataFile.getName(), rawDataFile.getOriginalFile(), rawDataFile.getRawDataFileType()); List<MsScan> scans = rawDataFile.getScans(); totalScans = scans.size(); for (MsScan scan : scans) { if (canceled) return null; MsScan newScan = centroidingAlgorithm.centroidScan(scan); // Add the new scan to the created raw data file if (newScan != null) result.addScan(newScan); processedScans++; } logger.info("Finished centroiding file " + rawDataFile.getName()); return result; }
/** {@inheritDoc} */ @Override public RawDataFile execute() throws MSDKException { logger.info("Started filter " + filteringAlgorithm.getClass().getName() + " on raw data file " + rawDataFile.getName()); // Create a new raw data file result = new SimpleRawDataFile(rawDataFile.getName(), rawDataFile.getOriginalFile(), rawDataFile.getRawDataFileType()); List<MsScan> scans = rawDataFile.getScans(); totalScans = scans.size(); for (MsScan scan : scans) { if (canceled) return null; if (scan == null) continue; MsScan newScan = filteringAlgorithm.performFilter(scan); // Add the new scan to the created raw data file if (newScan != null) result.addScan(newScan); processedScans++; } logger.info("Finished filter " + filteringAlgorithm.getClass().getName() + " on raw data file " + rawDataFile.getName()); return result; }
public List<Chromatogram> execute() throws MSDKException { logger.info("Started SRM chromatogram builder on file " + rawDataFile.getName());
public List<Chromatogram> execute() throws MSDKException { logger.info("Started SRM chromatogram builder on file " + rawDataFile.getName());
newSample = new SimpleSample(rawDataFile.getName(), rawDataFile);
newSample = new SimpleSample(rawDataFile.getName(), rawDataFile);
public Void execute() throws MSDKException { logger.info("Started export of " + rawDataFile.getName() + " to " + target);
public Void execute() throws MSDKException { logger.info("Started export of " + rawDataFile.getName() + " to " + target); xmlStreamWriter.writeAttribute(XML_SCHEMA_INSTANCE, MzMLTags.ATTR_SCHEME_LOCATION, XML_SCHEMA_LOCATION); xmlStreamWriter.writeAttribute(MzMLTags.ATTR_ID, rawDataFile.getName()); xmlStreamWriter.writeAttribute(MzMLTags.ATTR_VERSION, DEFAULT_VERSION); xmlStreamWriter.writeAttribute(MzMLTags.ATTR_ID, rawDataFile.getName()); xmlStreamWriter.writeAttribute(MzMLTags.ATTR_DEFAULT_INSTRUMENT_CONFIGURATION_REF, rawDataFile instanceof MzMLRawDataFile
public Void execute() throws MSDKException { logger.info("Started export of " + rawDataFile.getName() + " to " + target); xmlStreamWriter.writeAttribute(XML_SCHEMA_INSTANCE, MzMLTags.ATTR_SCHEME_LOCATION, XML_SCHEMA_LOCATION); xmlStreamWriter.writeAttribute(MzMLTags.ATTR_ID, rawDataFile.getName()); xmlStreamWriter.writeAttribute(MzMLTags.ATTR_VERSION, DEFAULT_VERSION); xmlStreamWriter.writeAttribute(MzMLTags.ATTR_ID, rawDataFile.getName()); xmlStreamWriter.writeAttribute(MzMLTags.ATTR_DEFAULT_INSTRUMENT_CONFIGURATION_REF, rawDataFile instanceof MzMLRawDataFile