uk.ac.man.bioinf.sequence.complex
Class AbstractComplexSequenceType

java.lang.Object
  |
  +--uk.ac.man.bioinf.sequence.types.AbstractSequenceType
        |
        +--uk.ac.man.bioinf.sequence.complex.AbstractComplexSequenceType
All Implemented Interfaces:
ComplexSequenceType, SequenceType

public abstract class AbstractComplexSequenceType
extends AbstractSequenceType
implements ComplexSequenceType

AbstractComplexSequenceType.java Created: Tue Feb 29 22:10:30 2000

Version:
$Id: AbstractComplexSequenceType.java,v 1.3 2001/04/11 17:04:43 lord Exp $
Author:
Phillip Lord

Field Summary
 
Fields inherited from class uk.ac.man.bioinf.sequence.types.AbstractSequenceType
elements
 
Constructor Summary
AbstractComplexSequenceType(Residue[] residues, Modification[] modifications, String name)
           
AbstractComplexSequenceType(Residue[] residues, Modification modification, String name)
           
 
Method Summary
 Modification[] getModifications()
          Gets all of the Modifications which are allowable in this sequence type.
 boolean isAllowableElement(ComplexElement elem)
          Is this given element allowable in this sequence type.
 boolean isModification(Modification mod)
          Is this modification one which is allowable in this sequence type.
 boolean isModification(Modification[] mod)
          Are these modifications allowable in this sequence type.
 
Methods inherited from class uk.ac.man.bioinf.sequence.types.AbstractSequenceType
getElements, getName, isElement, isElement, isElement, isElement, size
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 
Methods inherited from interface uk.ac.man.bioinf.sequence.SequenceType
getElementForInt, getElements, getIntForElement, getName, isElement, isElement, isElement, isElement, size
 

Constructor Detail

AbstractComplexSequenceType

public AbstractComplexSequenceType(Residue[] residues,
                                   Modification modification,
                                   String name)

AbstractComplexSequenceType

public AbstractComplexSequenceType(Residue[] residues,
                                   Modification[] modifications,
                                   String name)
Method Detail

getModifications

public Modification[] getModifications()
Description copied from interface: ComplexSequenceType
Gets all of the Modifications which are allowable in this sequence type. This should be immutable for a given instance of this.

Specified by:
getModifications in interface ComplexSequenceType
Returns:
the modifications

isModification

public boolean isModification(Modification mod)
Description copied from interface: ComplexSequenceType
Is this modification one which is allowable in this sequence type. This should be immutable for a given instance of this.

Specified by:
isModification in interface ComplexSequenceType
Parameters:
mod - the modification
Returns:
true if the modification is allowable

isModification

public boolean isModification(Modification[] mod)
Description copied from interface: ComplexSequenceType
Are these modifications allowable in this sequence type. This should be immutable.

Specified by:
isModification in interface ComplexSequenceType
Parameters:
mod - the modifications
Returns:
true if all the modifications are allowable

isAllowableElement

public boolean isAllowableElement(ComplexElement elem)
Description copied from interface: ComplexSequenceType
Is this given element allowable in this sequence type. A trivial implementation of this would simply check if the ComplexElement Residue is allowable, and all of the Modifications for this ComplexElement are allowable. However there are other possibilties if for instance not all Residues in a given sequence type are Modifiable by all the allowable modifications

Specified by:
isAllowableElement in interface ComplexSequenceType
Parameters:
elem -
Returns: