uk.ac.man.bioinf.sequence.group
Class DefaultGappedSequenceGroup

java.lang.Object
  |
  +--uk.ac.man.bioinf.sequence.group.AbstractGappedSequenceGroup
        |
        +--uk.ac.man.bioinf.sequence.group.DefaultGappedSequenceGroup
All Implemented Interfaces:
GappedSequenceGroup, SequenceGroup

public class DefaultGappedSequenceGroup
extends AbstractGappedSequenceGroup

DefaultGappedSequenceGroup.java Created: Thu Jun 1 18:33:14 2000

Version:
$Id: DefaultGappedSequenceGroup.java,v 1.5 2001/04/11 17:04:43 lord Exp $
Author:
Phillip Lord

Constructor Summary
DefaultGappedSequenceGroup()
           
 
Method Summary
 void addSequenceToGroup(Sequence seq)
          Adds a sequence to this group
 void clearSequences()
          Empty the group of sequences
 boolean containsSequence(Sequence seq)
          Does this group contain the sequence
 GappedSequence getGappedSequenceAt(int index)
           
 int getNumberSequences()
          Return the number of sequences in this group.
 Sequence getSequenceAt(int index)
           
 Sequence[] getSequences()
          Get all the sequences in this group.
 Iterator iterator()
          Returns an iterator of all the sequences.
 void removeSequenceFromGroup(Sequence seq)
          Removes a sequence from this group
 
Methods inherited from class uk.ac.man.bioinf.sequence.group.AbstractGappedSequenceGroup
getGappedSequences
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

DefaultGappedSequenceGroup

public DefaultGappedSequenceGroup()
Method Detail

addSequenceToGroup

public void addSequenceToGroup(Sequence seq)
Description copied from interface: SequenceGroup
Adds a sequence to this group

Parameters:
seq - the sequence

removeSequenceFromGroup

public void removeSequenceFromGroup(Sequence seq)
Description copied from interface: SequenceGroup
Removes a sequence from this group

Parameters:
seq - the sequence

containsSequence

public boolean containsSequence(Sequence seq)
Description copied from interface: SequenceGroup
Does this group contain the sequence

Parameters:
seq - the sequence
Returns:
true if containined

getSequences

public Sequence[] getSequences()
Description copied from interface: SequenceGroup
Get all the sequences in this group.

Returns:

clearSequences

public void clearSequences()
Description copied from interface: SequenceGroup
Empty the group of sequences


getNumberSequences

public int getNumberSequences()
Description copied from interface: SequenceGroup
Return the number of sequences in this group.

Returns:
the number

getSequenceAt

public Sequence getSequenceAt(int index)

getGappedSequenceAt

public GappedSequence getGappedSequenceAt(int index)

iterator

public Iterator iterator()
Description copied from interface: SequenceGroup
Returns an iterator of all the sequences. This should be fail fast if the group is modified whilst the iterator is being used.

Returns: