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

Class DefaultProductIon

java.lang.Object

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

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

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

All Implemented Interfaces:

Comparable<ProductIon>, PeptideIon, ProductIon

public class DefaultProductIon
extends AbstractProductIon

Default implement of AbstractProductIon. In tandem mass spectrum, the level 1 mass generate precursor ions. For a special precursor ion, based on product ion type, cleavage position, product ion charge to generate a product ion.

Author:

Qingwei XU

Constructor Summary

Constructors

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

Method Summary

Methods

Modifier and Type	Method and Description
String	toString()

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

compareTo, getMass, getPosition, getPrecursorIon, getType

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

equals, getCharge, getMassOverCharge, getPeptide, hashCode

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

DefaultProductIon

public DefaultProductIon(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

toString

public String toString()

Overrides:

toString in class DefaultPeptideIon