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: