/** {@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; }
/** {@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; }