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

Interface MsFileIterator

All Superinterfaces:
AutoCloseable
All Known Implementing Classes:
CmsFileIterator, MgfFileIterator, MzmlFileIterator
public interface MsFileIterator extends AutoCloseable
Interface for mass spectrometry file readers.
Author:
Marc Vaudel, Harald Barsnes

  • Method Summary

    Modifier and Type
    Method
    Description
    void
    close()
     
    static MsFileIterator
    getMsFileIterator(File file, WaitingHandler waitingHandler)
    Returns the file reader for the given mass spectrometry file based on its extension.
    Spectrum
    getSpectrum()
    Returns the spectrum corresponding to the title returned by the last call to the next() method.
    static String[]
    getSupportedExtensions()
    Returns the supported extensions.
    String
    next()
    Returns the title of the next spectrum, null if none.

  • Method Details

    • next

      String next()
      Returns the title of the next spectrum, null if none.
      Returns:
      The title of the next spectrum.

    • getSpectrum

      Spectrum getSpectrum()
      Returns the spectrum corresponding to the title returned by the last call to the next() method.
      Returns:
      The spectrum corresponding to the title returned by the last call to the next() method.

    • close

      void close()
      Specified by:
      close in interface AutoCloseable

    • getMsFileIterator

      static MsFileIterator getMsFileIterator(File file, WaitingHandler waitingHandler) throws IOException
      Returns the file reader for the given mass spectrometry file based on its extension.
      Parameters:
      file - The mass spectrometry file.
      waitingHandler - The waiting handler.
      Returns:
      The file reader.
      Throws:
      IOException - Exception thrown if an error occurred while reading the file.

    • getSupportedExtensions

      static String[] getSupportedExtensions()
      Returns the supported extensions.
      Returns:
      The supported extensions.