Package com.compomics.util.experiment.io.mass_spectrometry.cms

Class CmsFileReader

java.lang.Object
com.compomics.util.experiment.io.mass_spectrometry.cms.CmsFileReader
All Implemented Interfaces:
SpectrumProvider, AutoCloseable
public class CmsFileReader extends Object implements SpectrumProvider
Reader for Compomics Mass Spectrometry (cms) files.
Author:
Marc Vaudel, Harald Barsnes

  • Field Details

    • titles

      public final String[] titles
      The titles of the spectra.

  • Constructor Details

  • Method Details

    • getSpectrum

      public Spectrum getSpectrum(String spectrumTitle)
      Returns the spectrum with the given title.
      Parameters:
      spectrumTitle - title of the spectrum
      Returns:
      the spectrum

    • getPrecursor

      public Precursor getPrecursor(String spectrumTitle)
      Returns the precursor of the spectrum with the given title.
      Parameters:
      spectrumTitle - title of the spectrum
      Returns:
      the precursor of the spectrum

    • getPrecursorMz

      public double getPrecursorMz(String spectrumTitle)
      Returns the m/z of the precursor of the spectrum with the given title.
      Parameters:
      spectrumTitle - the title of the spectrum
      Returns:
      the precursor m/z of the spectrum

    • getPrecursorRt

      public double getPrecursorRt(String spectrumTitle)
      Returns the RT of the precursor of the spectrum with the given title.
      Parameters:
      spectrumTitle - the title of the spectrum
      Returns:
      the precursor RT of the spectrum

    • getSpectrumLevel

      public int getSpectrumLevel(String spectrumTitle)
      Returns the spectrum level of the spectrum with the given title.
      Parameters:
      spectrumTitle - the title of the spectrum
      Returns:
      the spectrum level of the spectrum

    • getPeaks

      public double[][] getPeaks(String spectrumTitle)
      Returns the peaks of the spectrum with the given title.
      Parameters:
      spectrumTitle - the title of the spectrum
      Returns:
      the peaks of the spectrum

    • uncompress

      public static byte[] uncompress(byte[] compressedByteArray, int uncompressedLength)
      Uncompresses the given byte array.
      Parameters:
      compressedByteArray - the compressed byte array
      uncompressedLength - the uncompressed length
      Returns:
      the uncompressed array

    • getSpectrum

      public Spectrum getSpectrum(String fileName, String spectrumTitle)
      Description copied from interface: SpectrumProvider
      Returns the spectrum with the given title in the given file.
      Specified by:
      getSpectrum in interface SpectrumProvider
      Parameters:
      fileName - The name of the spectrum file without file extension.
      spectrumTitle - The title of the spectrum.
      Returns:
      The spectrum with the given title in the given file.

    • getPrecursor

      public Precursor getPrecursor(String fileName, String spectrumTitle)
      Description copied from interface: SpectrumProvider
      Returns the precursor. Null if none.
      Specified by:
      getPrecursor in interface SpectrumProvider
      Parameters:
      fileName - The name of the spectrum file without file extension.
      spectrumTitle - The title of the spectrum.
      Returns:
      The precursor.

    • getPrecursorMz

      public double getPrecursorMz(String fileName, String spectrumTitle)
      Description copied from interface: SpectrumProvider
      Returns the measured precursor m/z. NaN if none.
      Specified by:
      getPrecursorMz in interface SpectrumProvider
      Parameters:
      fileName - The name of the spectrum file without file extension.
      spectrumTitle - The title of the spectrum.
      Returns:
      The measured precursor m/z.

    • getPrecursorRt

      public double getPrecursorRt(String fileName, String spectrumTitle)
      Description copied from interface: SpectrumProvider
      Returns the precursor RT window. NaN if none.
      Specified by:
      getPrecursorRt in interface SpectrumProvider
      Parameters:
      fileName - The name of the spectrum file without file extension.
      spectrumTitle - The title of the spectrum.
      Returns:
      The precursor RT.

    • getSpectrumLevel

      public int getSpectrumLevel(String fileName, String spectrumTitle)
      Description copied from interface: SpectrumProvider
      Returns the spectrum level.
      Specified by:
      getSpectrumLevel in interface SpectrumProvider
      Parameters:
      fileName - The name of the spectrum file without file extension.
      spectrumTitle - The title of the spectrum.
      Returns:
      The spectrum level.

    • getPeaks

      public double[][] getPeaks(String fileName, String spectrumTitle)
      Description copied from interface: SpectrumProvider
      Returns the spectrum peaks.
      Specified by:
      getPeaks in interface SpectrumProvider
      Parameters:
      fileName - The name of the spectrum file without file extension.
      spectrumTitle - The title of the spectrum.
      Returns:
      The peaks.

    • getMinPrecMz

      public double getMinPrecMz(String fileName)
      Description copied from interface: SpectrumProvider
      Returns the minimum precursor m/z in a given file.
      Specified by:
      getMinPrecMz in interface SpectrumProvider
      Parameters:
      fileName - The name of the spectrum file without file extension.
      Returns:
      The minimum precursor m/z in a given file.

    • getMaxPrecMz

      public double getMaxPrecMz(String fileName)
      Description copied from interface: SpectrumProvider
      Returns the maximum precursor m/z in a given file.
      Specified by:
      getMaxPrecMz in interface SpectrumProvider
      Parameters:
      fileName - The name of the spectrum file without file extension.
      Returns:
      The maximum precursor m/z in a given file.

    • getMaxPrecInt

      public double getMaxPrecInt(String fileName)
      Description copied from interface: SpectrumProvider
      Returns the maximum precursor intensity in a given file.
      Specified by:
      getMaxPrecInt in interface SpectrumProvider
      Parameters:
      fileName - The name of the spectrum file without file extension.
      Returns:
      The maximum precursor intensity in a given file.

    • getMaxPrecRT

      public double getMaxPrecRT(String fileName)
      Description copied from interface: SpectrumProvider
      Returns the maximum precursor RT in a given file.
      Specified by:
      getMaxPrecRT in interface SpectrumProvider
      Parameters:
      fileName - The name of the spectrum file without file extension.
      Returns:
      The maximum precursor RT in a given file.

    • getMinPrecMz

      public double getMinPrecMz()
      Description copied from interface: SpectrumProvider
      Returns the minimum precursor m/z among all files.
      Specified by:
      getMinPrecMz in interface SpectrumProvider
      Returns:
      The minimum precursor m/z among all files.

    • getMaxPrecMz

      public double getMaxPrecMz()
      Description copied from interface: SpectrumProvider
      Returns the maximum precursor m/z among all files.
      Specified by:
      getMaxPrecMz in interface SpectrumProvider
      Returns:
      The maximum precursor m/z among all files.

    • getMaxPrecInt

      public double getMaxPrecInt()
      Description copied from interface: SpectrumProvider
      Returns the maximum precursor intensity among all files.
      Specified by:
      getMaxPrecInt in interface SpectrumProvider
      Returns:
      The maximum precursor intensity among all files.

    • getMaxPrecRT

      public double getMaxPrecRT()
      Description copied from interface: SpectrumProvider
      Returns the maximum precursor RT among all files.
      Specified by:
      getMaxPrecRT in interface SpectrumProvider
      Returns:
      The maximum precursor RT among all files.

    • getOrderedFileNamesWithoutExtensions

      public String[] getOrderedFileNamesWithoutExtensions()
      Description copied from interface: SpectrumProvider
      Returns the spectrum file names without file extensions.
      Specified by:
      getOrderedFileNamesWithoutExtensions in interface SpectrumProvider
      Returns:
      The spectrum file names without file extensions.

    • getFilePaths

      public HashMap<String,String> getFilePaths()
      Description copied from interface: SpectrumProvider
      Returns the absolute path to the original mass spec file containing the spectra in a map indexed by file name without file extension.
      Specified by:
      getFilePaths in interface SpectrumProvider
      Returns:
      The absolute path to the original mass spec file containing the spectra in a map indexed by file name.

    • getCmsFilePaths

      public HashMap<String,String> getCmsFilePaths()
      Description copied from interface: SpectrumProvider
      Returns the absolute path to the cms file indexed by ms file name without file extension. Null if none.
      Specified by:
      getCmsFilePaths in interface SpectrumProvider
      Returns:
      The absolute path to the cms file indexed by ms file name.

    • close

      public void close()
      Specified by:
      close in interface AutoCloseable
      Specified by:
      close in interface SpectrumProvider

    • getSpectrumTitles

      public String[] getSpectrumTitles(String fileName)
      Description copied from interface: SpectrumProvider
      Returns the spectrum titles for the given mass spectrometry file name.
      Specified by:
      getSpectrumTitles in interface SpectrumProvider
      Parameters:
      fileName - The mass spectrometry file name without file extension.
      Returns:
      The spectrum titles as array.

    • getPostcursorSpectrumTitles

      public ArrayList<String> getPostcursorSpectrumTitles(String fileNameWithoutExtension, String spectrumTitle)
      Description copied from interface: SpectrumProvider
      Returns the postcursor spectrum titles. Null if none.
      Specified by:
      getPostcursorSpectrumTitles in interface SpectrumProvider
      Parameters:
      fileNameWithoutExtension - The name of the spectrum file without file extension.
      spectrumTitle - The title of the spectrum.
      Returns:
      The postcursor spectrum titles. Null if none.