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## uk.ac.man.bioinf.sequence.complex
Class DefaultComplexSequence

    java.lang.Object
      |
      +--uk.ac.man.bioinf.sequence.AbstractSequence
            |
            +--uk.ac.man.bioinf.sequence.AbstractMutableSequence
                  |
                  +--uk.ac.man.bioinf.sequence.complex.AbstractComplexSequence
                        |
                        +--uk.ac.man.bioinf.sequence.complex.DefaultComplexSequence

All Implemented Interfaces:
  ComplexSequence, Identifiable, MutableSequence, Sequence, SequenceEventProvider

public class DefaultComplexSequence
extends AbstractComplexSequence

DefaultComplexSequence.java Created: Fri Nov 24 14:08:23 2000

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

Constructor Summary
`DefaultComplexSequence(ComplexElement[] elements, ComplexSequenceType type, Identifier identifier)`
`DefaultComplexSequence(Residue[] elements, ComplexSequenceType type, Identifier identifier)`

Method Summary
`ComplexElement` | `getComplexElementAt(int index)`
`Element` | `getElementAt(int index)` Returns an element at a given location.
`Identifier` | `getIdentifier()`
`int` | `getLength()` Returns the length of the sequence.
`ComplexElement[]` | `getSequenceAsComplexElements()`
`Element[]` | `getSequenceAsElements()` Returns the sequence as an array of elements.
`protected ComplexElement` | `setElementAtQuietly(ComplexElement elem, int index)`

Methods inherited from class uk.ac.man.bioinf.sequence.complex.AbstractComplexSequence
`addModificationAt, checkComplexSequenceType, checkComplexSequenceType, checkSequenceType, checkSequenceType, getComplexElementAtAsChar, getComplexSequenceAsChars, getComplexSequenceTypeException, getComplexType, removeModificationAt`

Methods inherited from class uk.ac.man.bioinf.sequence.AbstractMutableSequence
`addSequenceListener, addVetoableSequenceListener, fireSequenceEvent, fireVetoableSequenceEvent, hasListeners, removeSequenceListener, removeVetoableSequenceListener`

Methods inherited from class uk.ac.man.bioinf.sequence.AbstractSequence
`checkRange, getElementAtAsChar, getSequenceAsChars, getSequenceIndexException, getSequenceType, getSequenceTypeException, getSubSequence`

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.Sequence
`getElementAtAsChar, getSequenceAsChars, getSequenceType, getSubSequence`

Constructor Detail

### DefaultComplexSequence

    public DefaultComplexSequence(Residue[] elements,
                                  ComplexSequenceType type,
                                  Identifier identifier)

### DefaultComplexSequence

    public DefaultComplexSequence(ComplexElement[] elements,
                                  ComplexSequenceType type,
                                  Identifier identifier)

Method Detail

### getIdentifier

    public Identifier getIdentifier()

### getElementAt

    public Element getElementAt(int index)

  Description copied from interface: `Sequence`
  Returns an element at a given location.

  Parameters:
    `index` - the location of the target element
  Returns:
    the element

### getComplexElementAt

    public ComplexElement getComplexElementAt(int index)

### getLength

    public int getLength()

  Description copied from interface: `Sequence`
  Returns the length of the sequence.

  Returns:
    the length of the sequence

### getSequenceAsComplexElements

    public ComplexElement[] getSequenceAsComplexElements()

### getSequenceAsElements

    public Element[] getSequenceAsElements()

  Description copied from interface: `Sequence`
  Returns the sequence as an array of elements.

  Returns:
    the sequence

### setElementAtQuietly

    protected ComplexElement setElementAtQuietly(ComplexElement elem,
                                                 int index)

  Specified by:
    `setElementAtQuietly` in class `AbstractComplexSequence`

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