uk.ac.ebi.pride.utilities.iongen.impl

Class AbstractProductIon

java.lang.Object

uk.ac.ebi.pride.utilities.iongen.impl.DefaultPeptideIon

uk.ac.ebi.pride.utilities.iongen.impl.AbstractProductIon

All Implemented Interfaces:

Comparable<ProductIon>, PeptideIon, ProductIon

Direct Known Subclasses:

DefaultProductIon

public abstract class AbstractProductIon
extends DefaultPeptideIon
implements ProductIon, Comparable<ProductIon>

Implement most of methods of ProductIon interface. This class implements Comparable interface, which can be storage into sorted collections based on cleavage position ascending order. This class Extends DefaultPeptideIon which inherit peptide ion methods: such as DefaultPeptideIon.getMass(), DefaultPeptideIon.getMassOverCharge(), and so on.

Version:

0.1-SNAPSHOT

Author:

Qingwei XU

Constructor Summary

Constructors

Constructor and Description
AbstractProductIon(PrecursorIon precursorIon, ProductIonType type, int position, Peptide peptide, int charge) Create product ion instance.

Method Summary

Methods

Modifier and Type	Method and Description
int	compareTo(ProductIon o) Based on ascending order of product ion cleavage position.
double	getMass()
int	getPosition()
PrecursorIon	getPrecursorIon()
ProductIonType	getType()

Methods inherited from class uk.ac.ebi.pride.utilities.iongen.impl.DefaultPeptideIon

equals, getCharge, getMassOverCharge, getPeptide, hashCode, toString

Methods inherited from class java.lang.Object

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

Methods inherited from interface uk.ac.ebi.pride.utilities.iongen.model.ProductIon

getCharge

Methods inherited from interface uk.ac.ebi.pride.utilities.iongen.model.PeptideIon

getMassOverCharge, getPeptide

Constructor Detail

AbstractProductIon

public AbstractProductIon(PrecursorIon precursorIon,
                  ProductIonType type,
                  int position,
                  Peptide peptide,
                  int charge)

Create product ion instance. There are some constraints among the PrecursorIon, ProductIonType, cleavage position, and the ProductIon.

Notice: Not suggest user to create a instance by calling construct method directly.

Reference AbstractPrecursorIon.getProductIon(uk.ac.ebi.pride.utilities.mol.ProductIonType, int, int) see how to generate the product ion.

Parameters:

precursorIon - should not set null! Otherwise throw NullPointerException.

type - should not set null! Otherwise throw NullPointerException.

position - from [1..precursor.peptide.length-1]

peptide - product ion peptide. should not set null! Otherwise throw NullPointerException.

charge - from [1..3], should not great than precursor ion charges.

Method Detail

getType

public ProductIonType getType()

Specified by:

getType in interface ProductIon

Returns:

ProductIonType

getPrecursorIon

public PrecursorIon getPrecursorIon()

Specified by:

getPrecursorIon in interface ProductIon

Returns:

PrecursorIon

getPosition

public int getPosition()

Specified by:

getPosition in interface ProductIon

Returns:

the cleavage position of product ion.

compareTo

public int compareTo(ProductIon o)

Based on ascending order of product ion cleavage position.

Specified by:

compareTo in interface Comparable<ProductIon>

getMass

public double getMass()

Specified by:

getMass in interface PeptideIon

Overrides:

getMass in class DefaultPeptideIon

Returns:

the mass value of ion.