Package com.compomics.util.interfaces

Interface SpectrumFile

All Superinterfaces:
Comparable
All Known Implementing Classes:
IsotopicDistributionSpectrum
public interface SpectrumFile extends Comparable
This interface describes the behaviour for a spectrum file (ie., PKL file, Mascot Generic file, dat file, ...).
Version:
$Id: SpectrumFile.java,v 1.2 2009/06/22 09:10:18 lennart Exp $
Author:
Lennart Martens

  • Method Summary

    Modifier and Type
    Method
    Description
    int
    getCharge()
    This method reports on the charge of the precursor ion.
    String
    getFilename()
    This method reports on the filename for the file.
    double
    getHighestIntensity()
    This method returns the intensity of the highest intensity peak in this spectrum.
    double
    getIntensity()
    This method reports on the intensity of the precursor ion.
    HashMap<Double,Double>
    getPeaks()
    This method reports on the peaks in the spectrum, with the Doubles for the masses as keys in the HashMap, and the intensities for each peak as Double value for that mass key.
    double
    getPrecursorMZ()
    This method reports on the precursor M/Z
    double
    getTotalIntensity()
    This method returns the total intensity contributed by all the ions in this spectrum.
    void
    setCharge(int aCharge)
    This method sets the charge of the precursor ion.
    void
    setFilename(String aFilename)
    This method sets the filename for the file.
    void
    setIntensity(double aIntensity)
    This method sets the intensity of the precursor ion.
    void
    setPeaks(HashMap aPeaks)
    This method sets the peaks on the spectrum.
    void
    setPrecursorMZ(double aPrecursorMZ)
    This method sets the precursor M/Z on the file.
    void
    writeToFile(File aParentDir)
    This method allows the caller to write the spectrum file to the specified folder using its current filename.
    void
    writeToStream(OutputStream aOut)
    This method allows to write the spectrum file to the specified OutputStream.

    Methods inherited from interface java.lang.Comparable

    compareTo

  • Method Details

    • getCharge

      int getCharge()
      This method reports on the charge of the precursor ion. Note that when the charge could not be determined, this method will return '0'.
      Returns:
      int with the charge of the precursor, or '0' if no charge state is known.

    • setCharge

      void setCharge(int aCharge)
      This method sets the charge of the precursor ion. When the charge is not known, it should be set to '0'.
      Parameters:
      aCharge - int with the charge of the precursor ion.

    • getFilename

      String getFilename()
      This method reports on the filename for the file.
      Returns:
      String with the filename for the file.

    • setFilename

      void setFilename(String aFilename)
      This method sets the filename for the file.
      Parameters:
      aFilename - String with the filename for the file.

    • getPeaks

      HashMap<Double,Double> getPeaks()
      This method reports on the peaks in the spectrum, with the Doubles for the masses as keys in the HashMap, and the intensities for each peak as Double value for that mass key.
      Returns:
      HashMap with Doubles as keys (the masses) and Doubles as values (the intensities).

    • setPeaks

      void setPeaks(HashMap aPeaks)
      This method sets the peaks on the spectrum. Doubles for the masses as keys in the HashMap, and the intensities for each peak as Double value for that mass key.
      Parameters:
      aPeaks - HashMap with Doubles as keys (the masses) and Doubles as values (the intensities).

    • getPrecursorMZ

      double getPrecursorMZ()
      This method reports on the precursor M/Z
      Returns:
      double with the precursor M/Z

    • setPrecursorMZ

      void setPrecursorMZ(double aPrecursorMZ)
      This method sets the precursor M/Z on the file.
      Parameters:
      aPrecursorMZ - double with the precursor M/Z

    • getIntensity

      double getIntensity()
      This method reports on the intensity of the precursor ion.
      Returns:
      double with the intensity of the precursor ion.

    • setIntensity

      void setIntensity(double aIntensity)
      This method sets the intensity of the precursor ion.
      Parameters:
      aIntensity - double with the intensity of the precursor ion.

    • getTotalIntensity

      double getTotalIntensity()
      This method returns the total intensity contributed by all the ions in this spectrum.
      Returns:
      double with the total intensity.

    • getHighestIntensity

      double getHighestIntensity()
      This method returns the intensity of the highest intensity peak in this spectrum.
      Returns:
      double with the intensity of the highest intensity peak in this spectrum.

    • writeToStream

      void writeToStream(OutputStream aOut) throws IOException
      This method allows to write the spectrum file to the specified OutputStream.
      Parameters:
      aOut - OutputStream to write the file to. This Stream will NOT be closed by this method.
      Throws:
      IOException - when the write operation fails.

    • writeToFile

      void writeToFile(File aParentDir) throws IOException
      This method allows the caller to write the spectrum file to the specified folder using its current filename.
      Parameters:
      aParentDir - File with the parent directory to put the file in.
      Throws:
      IOException - whenever the write process failed.