/** {@inheritDoc} */ @Override public double[] getMzValues(double array[]) { return spectrum.getMzValues(array); }
/** {@inheritDoc} */ @Override public float[] getIntensityValues(float array[]) { return spectrum.getIntensityValues(array); }
/** {@inheritDoc} */ @Override public Float getTIC() { return spectrum.getTIC(); }
/** * <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 Integer getNumberOfDataPoints() { return spectrum.getNumberOfDataPoints(); }
/** {@inheritDoc} */ @Override public FeatureTable execute() throws MSDKException { // Total features totalFeatures = featureTable.getRows().size(); /* * TODO: Write method */ processedFeatures = totalFeatures; // Return the new feature table return result; }
/** * <p>Constructor for AlignStructMol.</p> * * @param row1 a {@link io.github.msdk.datamodel.FeatureTableRow} object. * @param row2 a {@link io.github.msdk.datamodel.FeatureTableRow} object. */ public AlignStructMol(FeatureTableRow row1, FeatureTableRow row2) { this.row1 = row1; this.row2 = row2; RT = row1.getRT(); RT2 = row2.getRT(); }
/** {@inheritDoc} */ @Override public Feature getFeature(Integer index) { assert featureTable != null; synchronized (features) { List<Sample> samples = featureTable.getSamples(); return getFeature(samples.get(index)); } }
/** {@inheritDoc} */ @Override public @Nonnull float[] getIntensityValues() { return getIntensityValues(null); }
/** {@inheritDoc} */ @Override public @Nonnull float[] getRetentionTimes() { return getRetentionTimes(null); }
/** {@inheritDoc} */ @Override public Range<Double> getMzRange() { return spectrum.getMzRange(); }
/** * <p> * getMzValues. * </p> * * @return an array of double. */ @Nullable default double[] getMzValues() { return getMzValues(null); }
/** * <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 double[] getMzValues(double array[]) { return spectrum.getMzValues(array); }
/** {@inheritDoc} */ @Override public float[] getIntensityValues(float array[]) { return spectrum.getIntensityValues(array); }
/** {@inheritDoc} */ @Override public Integer getNumberOfDataPoints() { return spectrum.getNumberOfDataPoints(); }
/** * <p>Constructor for AlignStructMol.</p> * * @param row1 a {@link io.github.msdk.datamodel.FeatureTableRow} object. * @param row2 a {@link io.github.msdk.datamodel.FeatureTableRow} object. */ public AlignStructMol(FeatureTableRow row1, FeatureTableRow row2) { this.row1 = row1; this.row2 = row2; RT = row1.getRT(); RT2 = row2.getRT(); }
/** {@inheritDoc} */ @Override public Feature getFeature(Integer index) { assert featureTable != null; synchronized (features) { List<Sample> samples = featureTable.getSamples(); return getFeature(samples.get(index)); } }
/** {@inheritDoc} */ @Override public Float getTIC() { return spectrum.getTIC(); }
/** {@inheritDoc} */ @Override public Range<Double> getMzRange() { return spectrum.getMzRange(); }