/** {@inheritDoc} */ @Override public float[] getIntensityValues(float array[]) { return spectrum.getIntensityValues(array); }
/** {@inheritDoc} */ @Override public float[] getIntensityValues(float array[]) { return spectrum.getIntensityValues(array); }
/** * <p> * Returns the intensity values of this spectrum. * * Note: this method may need to read data from disk, therefore it may be quite slow. * </p> * * @return an array of float. */ @Nonnull default float[] getIntensityValues() { return getIntensityValues(null); }
/** * <p> * Returns the intensity values of this spectrum. * * Note: this method may need to read data from disk, therefore it may be quite slow. * </p> * * @return an array of float. */ @Nonnull default float[] getIntensityValues() { return getIntensityValues(null); }
/** * <p> * Export a spectrum to a writer. * </p> * * @param spectrum a {@link io.github.msdk.datamodel.MsSpectrum} object. * @param writer a {@link java.io.Writer} object. * @param delimiter a {@link java.lang.String object}. * @throws java.io.IOException if any. */ public static void spectrumToWriter(@Nonnull MsSpectrum spectrum, @Nonnull Writer writer, @Nonnull String delimiter) throws IOException { double mzValues[] = spectrum.getMzValues(); float intensityValues[] = spectrum.getIntensityValues(); int numOfDataPoints = spectrum.getNumberOfDataPoints(); for (int i = 0; i < numOfDataPoints; i++) { // Write data point row writer.write(mzValues[i] + delimiter + intensityValues[i]); writer.write(System.lineSeparator()); } }
/** * calculates our spectral hash * * @param spectrum a {@link io.github.msdk.datamodel.MsSpectrum} object. * @return a {@link java.lang.String} object. */ public static @Nonnull String calculateSplash(@Nonnull MsSpectrum spectrum) { return calculateSplash(spectrum.getMzValues(), spectrum.getIntensityValues(), spectrum.getNumberOfDataPoints()); }
/** * <p> * Export a spectrum to a writer. * </p> * * @param spectrum a {@link io.github.msdk.datamodel.MsSpectrum} object. * @param writer a {@link java.io.Writer} object. * @param delimiter a {@link java.lang.String object}. * @throws java.io.IOException if any. */ public static void spectrumToWriter(@Nonnull MsSpectrum spectrum, @Nonnull Writer writer, @Nonnull String delimiter) throws IOException { double mzValues[] = spectrum.getMzValues(); float intensityValues[] = spectrum.getIntensityValues(); int numOfDataPoints = spectrum.getNumberOfDataPoints(); for (int i = 0; i < numOfDataPoints; i++) { // Write data point row writer.write(mzValues[i] + delimiter + intensityValues[i]); writer.write(System.lineSeparator()); } }
/** * calculates our spectral hash * * @param spectrum a {@link io.github.msdk.datamodel.MsSpectrum} object. * @return a {@link java.lang.String} object. */ public static @Nonnull String calculateSplash(@Nonnull MsSpectrum spectrum) { return calculateSplash(spectrum.getMzValues(), spectrum.getIntensityValues(), spectrum.getNumberOfDataPoints()); }
for (float temp : ms.getIntensityValues()) { if (temp > biggest) biggest = temp;
/** * <p> * msSpectrumToString. * </p> * * @param spectrum a {@link io.github.msdk.datamodel.MsSpectrum} object. * @return a {@link java.lang.String} object. */ public static @Nonnull String msSpectrumToString(MsSpectrum spectrum) { return msSpectrumToString(spectrum.getMzValues(), spectrum.getIntensityValues(), spectrum.getNumberOfDataPoints()); }
/** * <p> Method for transformation of MsSpectrum into Spectrum<Peak></p> * Method transforms MSDK object into Sirius object * @param msdkSpectrum - non-null MsSpectrum object. * @return new Spectrum<Peak> */ private Spectrum<Peak> transformSpectrum(@Nonnull MsSpectrum msdkSpectrum) { double mz[], intensity[]; mz = msdkSpectrum.getMzValues(); intensity = LocalArrayUtil.convertToDoubles(msdkSpectrum.getIntensityValues()); return sirius.wrapSpectrum(mz, intensity); }
for (float temp : ms.getIntensityValues()) { if (temp > biggest) biggest = temp;
/** * <p> Method for transformation of MsSpectrum into Spectrum<Peak></p> * Method transforms MSDK object into Sirius object * @param msdkSpectrum - non-null MsSpectrum object. * @return new Spectrum<Peak> */ private Spectrum<Peak> transformSpectrum(@Nonnull MsSpectrum msdkSpectrum) { double mz[], intensity[]; mz = msdkSpectrum.getMzValues(); intensity = LocalArrayUtil.convertToDoubles(msdkSpectrum.getIntensityValues()); return sirius.wrapSpectrum(mz, intensity); }
/** * <p> * msSpectrumToString. * </p> * * @param spectrum a {@link io.github.msdk.datamodel.MsSpectrum} object. * @return a {@link java.lang.String} object. */ public static @Nonnull String msSpectrumToString(MsSpectrum spectrum) { return msSpectrumToString(spectrum.getMzValues(), spectrum.getIntensityValues(), spectrum.getNumberOfDataPoints()); }
/** * <p> * detectSpectrumType. * </p> * * @param msSpectrum a {@link io.github.msdk.datamodel.MsSpectrum} object. * @return a {@link io.github.msdk.datamodel.MsSpectrumType} object. */ public static MsSpectrumType detectSpectrumType(@Nonnull MsSpectrum msSpectrum) { double mzValues[] = msSpectrum.getMzValues(); float intensityValues[] = msSpectrum.getIntensityValues(); Integer size = msSpectrum.getNumberOfDataPoints(); return detectSpectrumType(mzValues, intensityValues, size); }
/** * <p> * detectSpectrumType. * </p> * * @param msSpectrum a {@link io.github.msdk.datamodel.MsSpectrum} object. * @return a {@link io.github.msdk.datamodel.MsSpectrumType} object. */ public static MsSpectrumType detectSpectrumType(@Nonnull MsSpectrum msSpectrum) { double mzValues[] = msSpectrum.getMzValues(); float intensityValues[] = msSpectrum.getIntensityValues(); Integer size = msSpectrum.getNumberOfDataPoints(); return detectSpectrumType(mzValues, intensityValues, size); }
intensityValues = spectrum.getIntensityValues(); numOfDataPoints = spectrum.getNumberOfDataPoints();
intensityValues = spectrum.getIntensityValues(); numOfDataPoints = spectrum.getNumberOfDataPoints();
float intensity[] = ms.getIntensityValues(); if (mz.length <= pairsLimit) return ms;
float intensity[] = ms.getIntensityValues(); if (mz.length <= pairsLimit) return ms;