uk.ac.ebi.pride.utilities.mol

Class Group

java.lang.Object

uk.ac.ebi.pride.utilities.mol.Group

public class Group
extends Object

Chemical Group, which including at least one Element. User can get mass value of chemical group. This is a read only class, which implements hashCode() and equals(Object) methods.

Author:

Qingwei XU

See Also:

Element

Field Summary

Fields

Modifier and Type	Field and Description
static Group	CO CO group used in calcute the mass of a and x ion.
static Group	H
static Group	H2O Water group.
static Group	NH NH group used in calcute the mass of z ion.
static Group	NH3 Ammonia group
static Group	OH

Constructor Summary

Constructors

Constructor and Description
Group(Element... elementList) A chemical group maybe include more than one chemical elements.

Method Summary

Methods

Modifier and Type	Method and Description
boolean	equals(Object o)
List<Element>	getElements()
double	getMass()
String	getName() User can get the group name based on the elements name which are included in the chemical group.
int	hashCode()
String	toString()

Methods inherited from class java.lang.Object

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

Field Detail

H

public static Group H

See Also:

Peptide.n_terminal

OH

public static Group OH

See Also:

Peptide.c_terminal

CO

public static Group CO

CO group used in calcute the mass of a and x ion.

NH

public static Group NH

NH group used in calcute the mass of z ion.

H2O

public static Group H2O

Water group.

NH3

public static Group NH3

Ammonia group

Constructor Detail

Group

public Group(Element... elementList)

A chemical group maybe include more than one chemical elements. We overwrite the equals and hashCode method, thus, user can put object of Group class into the hash collection.

Notice that: Group.OH and Group.HO are not same group, although both of them mass value are same. If user set elementList is null, system will throw NullPointerException.

Parameters:

elementList - a var-arg @see uk.ac.ebi.pride.iongen.model.Element

Throws:

NullPointerException

Method Detail

getMass

public double getMass()

getElements

public List<Element> getElements()

getName

public String getName()

User can get the group name based on the elements name which are included in the chemical group. We comment user to call getName() method, to display chemical group in their visualization interface.

toString

public String toString()

Overrides:

toString in class Object

equals

public boolean equals(Object o)

Overrides:

equals in class Object

hashCode

public int hashCode()

Overrides:

hashCode in class Object