uk.ac.man.bioinf.sequence
Interface Sequence

All Superinterfaces:
Identifiable
All Known Subinterfaces:
ComplexEditableGappedSequence, ComplexSequence, ConsensusSequence, EditableSequence, GappedComplexSequence, GappedSequence, MutableSequence
All Known Implementing Classes:
AbstractComplexSequence, AbstractEditableSequence, AbstractGappedSequence, AbstractMutableSequence, AbstractSequence, DefaultConsensusSequence, DefaultEditableSequence, DefaultGappedComplexSequence, EmptyGappedSequence, EmptySequence

public interface Sequence
extends Identifiable

Sequence.java This interface is designed to model a biological sequence. It is non-specific in the manor in which a sequence may be implemented. The default implementation of this sequence will be imutable, and all sequence numbering will start at 1 NOT 0. This may be a set of rules worth following. For a mutable sequence, see the interface MutableSequence.

Version:
$Id: Sequence.java,v 1.5 2001/04/11 17:04:43 lord Exp $
Author:
J Selley
See Also:
Created: Fri Feb 25 19:21:55 2000

Method Summary
 Element getElementAt(int index)
          Returns an element at a given location.
 char getElementAtAsChar(int index)
          Returns the character of an target element.
 int getLength()
          Returns the length of the sequence.
 char[] getSequenceAsChars()
          Returns the sequence as an array of characters.
 Element[] getSequenceAsElements()
          Returns the sequence as an array of elements.
 SequenceType getSequenceType()
          Returns the type of sequence.
 Sequence getSubSequence(int from, int length)
          Returns a sub-sequence from the current sequence.
 
Methods inherited from interface uk.ac.man.bioinf.sequence.identifier.Identifiable
getIdentifier
 

Method Detail

getSubSequence

public Sequence getSubSequence(int from,
                               int length)
Returns a sub-sequence from the current sequence.

Parameters:
from - the initial index of the sub-sequence
Returns:
the sub-sequence

getSequenceAsChars

public char[] getSequenceAsChars()
Returns the sequence as an array of characters.

Returns:
the sequence

getSequenceAsElements

public Element[] getSequenceAsElements()
Returns the sequence as an array of elements.

Returns:
the sequence

getElementAtAsChar

public char getElementAtAsChar(int index)
Returns the character of an target element.

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

getElementAt

public Element getElementAt(int index)
Returns an element at a given location.

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

getSequenceType

public SequenceType getSequenceType()
Returns the type of sequence.

Returns:
the sequence type

getLength

public int getLength()
Returns the length of the sequence.

Returns:
the length of the sequence