com.compomics.util.general

Class IsotopicDistributionSpectrum

java.lang.Object

com.compomics.util.general.IsotopicDistributionSpectrum

All Implemented Interfaces:

SpectrumFile, Comparable

public class IsotopicDistributionSpectrum
extends Object
implements SpectrumFile

This class is an implementation of the SpectrumFile specific for the isotopic distribution Created by IntelliJ IDEA. User: Niklaas Date: 16-Aug-2010 Time: 14:36:23

Constructor Summary

Constructors

Constructor and Description
IsotopicDistributionSpectrum()

Method Summary

Methods

Modifier and Type	Method and Description
int	compareTo(Object o) Method that compares an IsotopicDistributionSpectrum
int	getCharge() Getter for the charge
String	getFilename() Getter for the filename
double	getHighestIntensity() Method that find the intensity of the most intense peak
double	getIntensity() Getter for the precursor intensity (here always zero)
HashMap	getPeaks() Getter for the peaks
double	getPrecursorMZ() Getter for the precursor MZ
double	getTotalIntensity() Method calculates the total intensity of the peaks
void	setCharge(int aCharge) Setter for the charge
void	setFilename(String aFilename) Setter for the filename
void	setIntensity(double aIntensity) Setter for the intensity.
void	setPeaks(HashMap aPeaks) Setter for the peaks
void	setPrecursorMZ(double aPrecursorMZ) Setter for the precursor MZ
void	writeToFile(File aParentDir) Method to write to a given file
void	writeToStream(OutputStream aOut) Method to write to a givern stream

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

IsotopicDistributionSpectrum

public IsotopicDistributionSpectrum()

Method Detail

getCharge

public int getCharge()

Getter for the charge

Specified by:

getCharge in interface SpectrumFile

Returns:

int with the charge

setCharge

public void setCharge(int aCharge)

Setter for the charge

Specified by:

setCharge in interface SpectrumFile

Parameters:

aCharge - int with the charge of the precursor ion.

getFilename

public String getFilename()

Getter for the filename

Specified by:

getFilename in interface SpectrumFile

Returns:

String with "Isotopic distribution"

setFilename

public void setFilename(String aFilename)

Setter for the filename

Specified by:

setFilename in interface SpectrumFile

Parameters:

aFilename - String with the filename for the file.

getPeaks

public HashMap getPeaks()

Getter for the peaks

Specified by:

getPeaks in interface SpectrumFile

Returns:

HashMap with the peaks (key = mass, value = intensity)

setPeaks

public void setPeaks(HashMap aPeaks)

Setter for the peaks

Specified by:

setPeaks in interface SpectrumFile

Parameters:

aPeaks - HashMap with Doubles as keys (the masses) and Doubles as values (the intensities).

getPrecursorMZ

public double getPrecursorMZ()

Getter for the precursor MZ

Specified by:

getPrecursorMZ in interface SpectrumFile

Returns:

double with the precursor MZ

setPrecursorMZ

public void setPrecursorMZ(double aPrecursorMZ)

Setter for the precursor MZ

Specified by:

setPrecursorMZ in interface SpectrumFile

Parameters:

aPrecursorMZ - double with the precursor M/Z

getIntensity

public double getIntensity()

Getter for the precursor intensity (here always zero)

Specified by:

getIntensity in interface SpectrumFile

Returns:

zero

setIntensity

public void setIntensity(double aIntensity)

Setter for the intensity. Here this will do nothing since there is no precursor

Specified by:

setIntensity in interface SpectrumFile

Parameters:

aIntensity - double with the intensity of the precursor ion.

getTotalIntensity

public double getTotalIntensity()

Method calculates the total intensity of the peaks

Specified by:

getTotalIntensity in interface SpectrumFile

Returns:

double with the sum of all the peak intensities

getHighestIntensity

public double getHighestIntensity()

Method that find the intensity of the most intense peak

Specified by:

getHighestIntensity in interface SpectrumFile

Returns:

double with the intensity of the most intense peak

writeToStream

public void writeToStream(OutputStream aOut)
                   throws IOException

Method to write to a givern stream

Specified by:

writeToStream in interface SpectrumFile

Parameters:

aOut - OutputStream to write the file to. This Stream will NOT be closed by this method.

Throws:

IOException

writeToFile

public void writeToFile(File aParentDir)
                 throws IOException

Method to write to a given file

Specified by:

writeToFile in interface SpectrumFile

Parameters:

aParentDir - File with the parent directory to put the file in.

Throws:

IOException

compareTo

public int compareTo(Object o)

Method that compares an IsotopicDistributionSpectrum

Specified by:

compareTo in interface Comparable

Parameters:

o - Another IsotopicDistributionSpectrum

Returns:

int (always zero)