Package org.biojava.nbio.protmod

Class Component

java.lang.Object

org.biojava.nbio.protmod.Component

public final class Component
extends Object

contains information about a certain Component. The Component class uses the extensible enum pattern. You can't instantiate Component directly, instead you have to use one of the register and of(java.lang.String) methods.

Since:

3.0

Author:

Jianjiong Gao

Method Summary

Modifier and Type	Method	Description
static Set<Component>	allComponents()
Set<String>	getPdbccIds()
boolean	isCTerminal()
boolean	isNTerminal()
static Component	of(String pdbccId)	Get a Component that does not have to occur at terminals.
static Component	of(String pdbccId, boolean isNTerminal, boolean isCTerminal)	Get or create a Component.
static Component	of(Set<String> pdbccIds)	Get a Component that does not have to occur at terminals.
static Component	of(Set<String> pdbccIds, boolean isNTerminal, boolean isCTerminal)	Get or create a Component.
String	toString()

Methods inherited from class java.lang.Object

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

Method Detail

getPdbccIds

public Set<String> getPdbccIds()

Returns:

Protein Data Bank ID.

isNTerminal

public boolean isNTerminal()

Returns:

true if occurring on N terminal; false, otherwise.

isCTerminal

public boolean isCTerminal()

Returns:

true if occurring on C terminal; false, other wise.

of

public static Component of(String pdbccId)

Get a Component that does not have to occur at terminals. If the corresponding component has already been registered, return that one.

Parameters:

pdbccIds - possible Protein Data Bank ID.

Returns:

a component.

Throws:

IllegalArgumentException - if pdbccId or type is null, or the pdbccId has been registered as a different type.

of

public static Component of(String pdbccId,
                           boolean isNTerminal,
                           boolean isCTerminal)

Get or create a Component.

Parameters:

pdbccId - Protein Data Bank ID.

isNTerminal - true if occurring at N-terminal. false, otherwise.

isCTerminal - true if occurring at C-terminal. false, otherwise.

Returns:

a component.

Throws:

IllegalArgumentException - if pdbccId or type is null, or the pdbccId has been registered as a different type, or terminal condition is indicated for non-amino-acid component, or both N-terminal and C-terminal are true.

of

public static Component of(Set<String> pdbccIds)

Get a Component that does not have to occur at terminals. If the corresponding component has already been registered, return that one.

Parameters:

pdbccIds - a set of possible Protein Data Bank ID.

Returns:

a component.

Throws:

IllegalArgumentException - if pdbccId or type is null, or the pdbccId has been registered as a different type.

of

public static Component of(Set<String> pdbccIds,
                           boolean isNTerminal,
                           boolean isCTerminal)

Get or create a Component.

Parameters:

pdbccIds - a set of possible Protein Data Bank ID.

isNTerminal - true if occurring at N-terminal. false, otherwise.

isCTerminal - true if occurring at C-terminal. false, otherwise.

Returns:

a component.

Throws:

IllegalArgumentException - if pdbccId or type is null, or the pdbccId has been registered as a different type, or terminal condition is indicated for non-amino-acid component, or both N-terminal and C-terminal are true.

allComponents

public static Set<Component> allComponents()

toString

public String toString()

Overrides:

toString in class Object

Returns:

informative description.