/** * <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); }
/** * <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); }
/** * <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> * getScans. * </p> * * @param rawDataFile a {@link io.github.msdk.datamodel.RawDataFile} object. * @param rtRange a {@link com.google.common.collect.Range} object. * @return a {@link java.util.List} object. */ @Nonnull static public List<MsScan> getScans(RawDataFile rawDataFile, Range<Float> rtRange) { ArrayList<MsScan> msScanList = new ArrayList<MsScan>(); List<MsScan> scans = rawDataFile.getScans(); synchronized (scans) { for (MsScan scan : scans) { Float scanRT = scan.getRetentionTime(); if (scanRT != null) { if (rtRange.contains(scanRT)) msScanList.add(scan); } } } return new ArrayList<MsScan>(); }
/** * <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> * getScans. * </p> * * @param rawDataFile a {@link io.github.msdk.datamodel.RawDataFile} object. * @param rtRange a {@link com.google.common.collect.Range} object. * @return a {@link java.util.List} object. */ @Nonnull static public List<MsScan> getScans(RawDataFile rawDataFile, Range<Float> rtRange) { ArrayList<MsScan> msScanList = new ArrayList<MsScan>(); List<MsScan> scans = rawDataFile.getScans(); synchronized (scans) { for (MsScan scan : scans) { Float scanRT = scan.getRetentionTime(); if (scanRT != null) { if (rtRange.contains(scanRT)) msScanList.add(scan); } } } return new ArrayList<MsScan>(); }
/** * <p> * getScans. * </p> * * @param rawDataFile a {@link io.github.msdk.datamodel.RawDataFile} object. * @param msFunction a {@link io.github.msdk.datamodel.rawdata.MsFunction} object. * @param rtRange a {@link com.google.common.collect.Range} object. * @return a {@link java.util.List} object. */ @Nonnull static public List<MsScan> getScans(RawDataFile rawDataFile, String msFunction, Range<Float> rtRange) { ArrayList<MsScan> msScanList = new ArrayList<MsScan>(); List<MsScan> scans = rawDataFile.getScans(); synchronized (scans) { for (MsScan scan : scans) { Float scanRT = scan.getRetentionTime(); String scanMsFunction = scan.getMsFunction(); if (scanRT == null || scanMsFunction == null) continue; if (scanMsFunction.equals(msFunction) && rtRange.contains(scanRT)) msScanList.add(scan); } } return new ArrayList<MsScan>(); }
/** * <p> * getScans. * </p> * * @param rawDataFile a {@link io.github.msdk.datamodel.RawDataFile} object. * @param msFunction a {@link io.github.msdk.datamodel.rawdata.MsFunction} object. * @param rtRange a {@link com.google.common.collect.Range} object. * @return a {@link java.util.List} object. */ @Nonnull static public List<MsScan> getScans(RawDataFile rawDataFile, String msFunction, Range<Float> rtRange) { ArrayList<MsScan> msScanList = new ArrayList<MsScan>(); List<MsScan> scans = rawDataFile.getScans(); synchronized (scans) { for (MsScan scan : scans) { Float scanRT = scan.getRetentionTime(); String scanMsFunction = scan.getMsFunction(); if (scanRT == null || scanMsFunction == null) continue; if (scanMsFunction.equals(msFunction) && rtRange.contains(scanRT)) msScanList.add(scan); } } return new ArrayList<MsScan>(); }
/** {@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; }
rawFile.getScans().stream().filter(msScanPredicate).collect(Collectors.<MsScan>toList()); List<Triplet> listOfTriplet = new ArrayList<Triplet>(); rtMap = new HashMap<Integer, Float>();
rawFile.getScans().stream().filter(msScanPredicate).collect(Collectors.<MsScan>toList()); List<Triplet> listOfTriplet = new ArrayList<Triplet>(); rtMap = new HashMap<Integer, Float>();
/** {@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; }
List<MsScan> scans = rawDataFile.getScans(); total += scans.size();
/** {@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; }
List<MsScan> scans = rawDataFile.getScans(); total += scans.size();
List<MsScan> scans = rawDataFile.getScans(); totalScans = scans.size();
List<MsScan> scans = rawDataFile.getScans(); totalScans = scans.size();
List<MsScan> allScans = rawDataFile.getScans(); List<MsScan> msScans = new ArrayList<MsScan>(); for (MsScan scan : allScans) {
List<MsScan> allScans = rawDataFile.getScans(); List<MsScan> msScans = new ArrayList<MsScan>(); for (MsScan scan : allScans) {
scans = rawDataFile.getScans(); totalScans = scans.size(); scanStartPositions = new int[totalScans + 1];