/** {@inheritDoc} */ @Override public RawDataFile execute() throws MSDKException { try { logger.info("Started parsing file " + sourceFile); // Create the XMLBasedRawDataFile object newRawDataFile = new SimpleRawDataFile(sourceFile.getName(), Optional.of(sourceFile), fileType); // Use the default (non-validating) parser SAXParserFactory factory = SAXParserFactory.newInstance(); dataTypeFactory = DatatypeFactory.newInstance(); SAXParser saxParser = factory.newSAXParser(); saxParser.parse(sourceFile, handler); logger.info("Finished parsing " + sourceFile + ", parsed " + parsedScans + " scans"); return newRawDataFile; } catch (Throwable e) { // We may already have set the status to CANCELED. In that case the // caught exception simply indicates end of SAX parsing. if (canceled) return null; else throw new MSDKException(e); } }
/** {@inheritDoc} */ @Override public void dispose() { try { inputFile.close(); } catch (IOException e) { new MSDKRuntimeException(e); } super.dispose(); }
/** {@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; }
newRawDataFile.addScan(buildingScan); parsedScans++; return;
&& (newRawFile.getRawDataFileType() == FileType.THERMO_RAW) && (!Strings.isNullOrEmpty(scanId))) { if (scanId.startsWith("-")) if ((precursorMz == 0.0) && (newRawFile.getRawDataFileType() == FileType.THERMO_RAW) && (!Strings.isNullOrEmpty(scanId))) { Pattern precursorPattern = Pattern.compile(".* ms\\d+ (\\d+\\.\\d+)[@ ]"); if ((newRawFile.getRawDataFileType() == FileType.THERMO_RAW) && (!Strings.isNullOrEmpty(scanId))) { newRawFile.addScan(newScan); parsedScans++;
/** {@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; }
newRawDataFile.addScan(buildingScan); parsedScans++; return;
/** {@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; }
buildingScan.parseScan(); newRawFile.addScan(buildingScan); parsedScans++;
/** {@inheritDoc} */ @Override public RawDataFile execute() throws MSDKException { try { logger.info("Started parsing file " + sourceFile); // Create the XMLBasedRawDataFile object newRawDataFile = new SimpleRawDataFile(sourceFile.getName(), Optional.of(sourceFile), fileType); // Use the default (non-validating) parser SAXParserFactory factory = SAXParserFactory.newInstance(); dataTypeFactory = DatatypeFactory.newInstance(); SAXParser saxParser = factory.newSAXParser(); saxParser.parse(sourceFile, handler); logger.info("Finished parsing " + sourceFile + ", parsed " + parsedScans + " scans"); return newRawDataFile; } catch (Throwable e) { // We may already have set the status to CANCELED. In that case the // caught exception simply indicates end of SAX parsing. if (canceled) return null; else throw new MSDKException(e); } }
newRawFile.addScan(newScan); parsedScans++;
/** {@inheritDoc} */ @Override public RawDataFile execute() throws MSDKException { logger.info("Started parsing file " + sourceFile); String fileName = sourceFile.getName(); newRawFile = new SimpleRawDataFile(fileName, Optional.of(sourceFile), FileType.MZDATA); saxHandler = new MzDataSaxHandler(newRawFile); SAXParserFactory factory = SAXParserFactory.newInstance(); try { SAXParser saxParser = factory.newSAXParser(); saxParser.parse(sourceFile, saxHandler); } catch (Exception e) { if (canceled) return null; else throw new MSDKException(e); } logger.info("Finished parsing " + sourceFile); return newRawFile; }
newRawFile.addScan(newScan); parsedScans++;
/** {@inheritDoc} */ @Override public RawDataFile execute() throws MSDKException { logger.info("Started parsing file " + sourceFile); String fileName = sourceFile.getName(); newRawFile = new SimpleRawDataFile(fileName, Optional.of(sourceFile), FileType.MZDATA); saxHandler = new MzDataSaxHandler(newRawFile); SAXParserFactory factory = SAXParserFactory.newInstance(); try { SAXParser saxParser = factory.newSAXParser(); saxParser.parse(sourceFile, saxHandler); } catch (Exception e) { if (canceled) return null; else throw new MSDKException(e); } logger.info("Finished parsing " + sourceFile); return newRawFile; }
newRawFile = new SimpleRawDataFile(fileName, Optional.of(sourceFile), FileType.THERMO_RAW);
newRawFile = new SimpleRawDataFile(fileName, Optional.of(sourceFile), FileType.WATERS_RAW);