/** {@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; }
/** * <p> * getNextChromatogramNumber. * </p> * * @param rawDataFile a {@link io.github.msdk.datamodel.RawDataFile} object. * @return a {@link java.lang.Integer} object. */ @Nonnull static public Integer getNextChromatogramNumber(RawDataFile rawDataFile) { int chromatogramNumber = 1; List<Chromatogram> chromatograms = rawDataFile.getChromatograms(); for (Chromatogram chromatogram : chromatograms) { int currentChromatogramNumber = chromatogram.getChromatogramNumber(); if (currentChromatogramNumber > chromatogramNumber) chromatogramNumber = currentChromatogramNumber; } return chromatogramNumber; } }
/** * {@inheritDoc} * * @param scan a {@link io.github.msdk.datamodel.MsScan} object. * @return a {@link java.lang.String} object. */ public String msScanToString(@Nonnull MsScan scan) { StringBuilder buf = new StringBuilder(); buf.append("Scan "); final RawDataFile rawDataFile2 = scan.getRawDataFile(); if (rawDataFile2 != null && rawDataFile2.getOriginalFile() != null) { buf.append(rawDataFile2.getOriginalFilename()); buf.append(" "); } if (scan.getMsFunction() != null) { buf.append(scan.getMsFunction()); buf.append(" "); } buf.append("#"); buf.append(scan.getScanNumber()); return buf.toString(); }
public List<Chromatogram> execute() throws MSDKException { logger.info("Started SRM chromatogram builder on file " + rawDataFile.getName()); List<Chromatogram> chromatograms = rawDataFile.getChromatograms(); total += chromatograms.size(); List<MsScan> scans = rawDataFile.getScans(); total += scans.size();
/** * <p> * Constructor for ChromatogramBuilderMethod. This version uses the same MzTolerance for every * scan that does not provide its own MzTolerance. * </p> * * @param inputFile a {@link io.github.msdk.datamodel.RawDataFile} object. * @param minimumTimeSpan a {@link java.lang.Double} object. * @param minimumHeight a {@link java.lang.Double} object. * @param mzTolerance an object that implements the MZTolerance interface. * @param noiseLevel a {@link java.lang.Float} object. */ public ChromatogramBuilderMethod(RawDataFile inputFile, double noiseLevel, double minimumTimeSpan, double minimumHeight, MzTolerance mzTolerance) { this(inputFile, inputFile.getScans(), noiseLevel, minimumTimeSpan, minimumHeight, mzTolerance); }
/** {@inheritDoc} */ @Override public void cancel() { logger.info("Cancelling ADAP3D feature detection on file " + rawFile.getName()); canceled = true; if (objPeakDetection != null) { objPeakDetection.cancel(); } } }
public List<Chromatogram> execute() throws MSDKException { logger.info("Started SRM chromatogram builder on file " + rawDataFile.getName()); List<Chromatogram> chromatograms = rawDataFile.getChromatograms(); total += chromatograms.size(); List<MsScan> scans = rawDataFile.getScans(); total += scans.size();
/** * <p> * Constructor for ChromatogramBuilderMethod. This version uses the same MzTolerance for every * scan that does not provide its own MzTolerance. * </p> * * @param inputFile a {@link io.github.msdk.datamodel.RawDataFile} object. * @param minimumTimeSpan a {@link java.lang.Double} object. * @param minimumHeight a {@link java.lang.Double} object. * @param mzTolerance an object that implements the MZTolerance interface. * @param noiseLevel a {@link java.lang.Float} object. */ public ChromatogramBuilderMethod(RawDataFile inputFile, double noiseLevel, double minimumTimeSpan, double minimumHeight, MzTolerance mzTolerance) { this(inputFile, inputFile.getScans(), noiseLevel, minimumTimeSpan, minimumHeight, mzTolerance); }
/** {@inheritDoc} */ @Override public void cancel() { logger.info("Cancelling ADAP3D feature detection on file " + rawFile.getName()); canceled = true; if (objPeakDetection != null) { objPeakDetection.cancel(); } } }
/** * {@inheritDoc} * * @param scan a {@link io.github.msdk.datamodel.MsScan} object. * @return a {@link java.lang.String} object. */ public String msScanToString(@Nonnull MsScan scan) { StringBuilder buf = new StringBuilder(); buf.append("Scan "); final RawDataFile rawDataFile2 = scan.getRawDataFile(); if (rawDataFile2 != null && rawDataFile2.getOriginalFile() != null) { buf.append(rawDataFile2.getOriginalFilename()); buf.append(" "); } if (scan.getMsFunction() != null) { buf.append(scan.getMsFunction()); buf.append(" "); } buf.append("#"); buf.append(scan.getScanNumber()); return buf.toString(); }
public Void execute() throws MSDKException { logger.info("Started export of " + rawDataFile.getName() + " to " + target); List<MsScan> scans = rawDataFile.getScans(); List<Chromatogram> chromatograms = rawDataFile.getChromatograms(); totalScans = scans.size(); totalChromatograms = chromatograms.size(); 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
/** {@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; }
/** * <p> * getScans. * </p> * * @param rawDataFile a {@link io.github.msdk.datamodel.RawDataFile} object. * @param msFunction a {@link io.github.msdk.datamodel.rawdata.MsFunction} object. * @return a {@link java.util.List} object. */ @Nonnull static public List<MsScan> getScans(RawDataFile rawDataFile, String msFunction) { ArrayList<MsScan> msScanList = new ArrayList<MsScan>(); List<MsScan> scans = rawDataFile.getScans(); synchronized (scans) { for (MsScan scan : scans) { String scanMsFunction = scan.getMsFunction(); if (scanMsFunction == null) continue; if (scanMsFunction.equals(msFunction)) msScanList.add(scan); } } return msScanList; }
/** * <p> * getNextChromatogramNumber. * </p> * * @param rawDataFile a {@link io.github.msdk.datamodel.RawDataFile} object. * @return a {@link java.lang.Integer} object. */ @Nonnull static public Integer getNextChromatogramNumber(RawDataFile rawDataFile) { int chromatogramNumber = 1; List<Chromatogram> chromatograms = rawDataFile.getChromatograms(); for (Chromatogram chromatogram : chromatograms) { int currentChromatogramNumber = chromatogram.getChromatogramNumber(); if (currentChromatogramNumber > chromatogramNumber) chromatogramNumber = currentChromatogramNumber; } return chromatogramNumber; } }
public Void execute() throws MSDKException { logger.info("Started export of " + rawDataFile.getName() + " to " + target); List<MsScan> scans = rawDataFile.getScans(); List<Chromatogram> chromatograms = rawDataFile.getChromatograms(); totalScans = scans.size(); totalChromatograms = chromatograms.size(); 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
/** {@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; }