org.expasy.mzjava.core.ms.spectrum

Class AnnotatedPeak<A extends PeakAnnotation>

java.lang.Object

org.expasy.mzjava.core.ms.peaklist.Peak

org.expasy.mzjava.core.ms.spectrum.AnnotatedPeak<A>

All Implemented Interfaces:

Comparable<Peak>, Copyable<Peak>

public class AnnotatedPeak<A extends PeakAnnotation>
extends Peak

A peak that has a list of peak annotations.

Version:

1.0

Author:

Oliver Horlacher

Constructor Summary

Constructors

Constructor and Description
AnnotatedPeak() Default constructor.
AnnotatedPeak(AnnotatedPeak<A> src) Copy constructor.
AnnotatedPeak(double mz, double intensity, int charge, A... annotations) Constructs a AnnotatedPeak.

Method Summary

Methods

Modifier and Type	Method and Description
boolean	add(A annotation) Add annotation to this AnnotatedPeak
AnnotatedPeak<A>	copy() Creates and returns a copy of this object.
boolean	equals(Object o)
A	getAnnotation(int index) Returns the annotation at the specified position in this peak.
int	getAnnotationCount() Returns the number of annotations in this peak.
List<A>	getAnnotations() Returns an unmodifiable list containing this peaks annotations
boolean	hasAnnotations() Returns true this peak has annotations, false otherwise.
int	hashCode()
boolean	remove(A annotation) Remove annotation from this AnnotatedPeak
A	remove(int index) Removes the annotation at the specified position in this peak.
void	sortAnnotations(Comparator<A> comparator) Use the comparator to sort this peaks annotations
String	toString()

Methods inherited from class org.expasy.mzjava.core.ms.peaklist.Peak

compareTo, getCharge, getChargeList, getIntensity, getMass, getMz, getPolarity, noIntensity, setIntensity, setMzAndCharge, setValues

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Constructor Detail

AnnotatedPeak

public AnnotatedPeak()

Default constructor. Default values are:

     mz = 0.0
     intensity = 0.0
     charge = 0
     annotations = empty list
 

AnnotatedPeak

public AnnotatedPeak(double mz,
             double intensity,
             int charge,
             A... annotations)

Constructs a AnnotatedPeak.

Parameters:

mz - the peak m/z

intensity - the peak

charge - the peak charge

annotations - the annotations

AnnotatedPeak

public AnnotatedPeak(AnnotatedPeak<A> src)

Copy constructor.

Parameters:

src - the AnnotatedPeak to copy

Method Detail

add

public boolean add(A annotation)

Add annotation to this AnnotatedPeak

Parameters:

annotation - the annotation to add

Returns:

true if the annotation was added, false otherwise

remove

public boolean remove(A annotation)

Remove annotation from this AnnotatedPeak

Parameters:

annotation - the annotation to remove

Returns:

true if the annotation was removed, false otherwise

remove

public A remove(int index)

Removes the annotation at the specified position in this peak. Returns the annotation that was removed.

Parameters:

index - the index of the annotation to be removed

Returns:

the annotation previously at the specified position *

Throws:

IndexOutOfBoundsException - if the index is out of range (index < 0 || index >= getAnnotationCount())

getAnnotation

public A getAnnotation(int index)

Returns the annotation at the specified position in this peak.

Parameters:

index - index of the annotation to return

Returns:

the annotation at the specified position in this peak

Throws:

IndexOutOfBoundsException - if the index is out of range (index < 0 || index >= getAnnotationCount())

getAnnotationCount

public int getAnnotationCount()

Returns the number of annotations in this peak. If this peak contains more than Integer.MAX_VALUE annotation, returns Integer.MAX_VALUE.

Returns:

the number of annotations in this list

hasAnnotations

public boolean hasAnnotations()

Returns true this peak has annotations, false otherwise.

Returns:

true this peak has annotations, false otherwise

getAnnotations

public List<A> getAnnotations()

Returns an unmodifiable list containing this peaks annotations

Returns:

an unmodifiable list containing this peaks annotations

sortAnnotations

public void sortAnnotations(Comparator<A> comparator)

Use the comparator to sort this peaks annotations

Parameters:

comparator - the comparator that is used to sort the annotations

copy

public AnnotatedPeak<A> copy()

Description copied from interface: Copyable

Creates and returns a copy of this object. The precise meaning of "copy" may depend on the class of the object. The general intent is that, for any object x, the expression:

 x.copy() != x

will be true, and that the expression:

 x.copy().getClass() == x.getClass()

will be true, but these are not absolute requirements. While it is typically the case that:

 x.copy().equals(x)

will be true, this is not an absolute requirement.

Specified by:

copy in interface Copyable<Peak>

Overrides:

copy in class Peak

Returns:

a copy of this instance.

toString

public String toString()

Overrides:

toString in class Peak

equals

public boolean equals(Object o)

Overrides:

equals in class Peak

hashCode

public int hashCode()

Overrides:

hashCode in class Peak