Package uk.ac.man.bioinf.sequence.alignment

Interface Summary

GappedSequence	GappedSequence.java Created: Wed Mar 1 18:28:44 2000
SequenceAlignment	SequenceAlignment.java This interface is designed to mimic a biological sequence alignment.

Class Summary

AbstractGappedSequence	AbstractGappedSequence.java Created: Sat Mar 4 12:17:02 2000
AbstractSequenceAlignment	AbstractSequenceAlignment.java An abstract class to extend for the basic definition of a multiple sequence alignment.
AlignmentColumn	AlignmentColumn.java The Sequence and SequenceAlignment classes have been created to be fail-fast.
DefaultGappedSequence	DefaultGappedSequence.java Created: Sat Mar 4 12:28:57 2000
DefaultSequenceAlignment	DefaultSequenceAlignment.java A class to model the multiple sequence alignment.
EmptyGappedSequence	EmptyGappedSequence.java Created: Tue Nov 7 18:15:06 2000
EmptySequenceAlignment	EmptySequenceAlignment.java Created: Wed Apr 19 17:23:30 2000
Gap	Gap.java Created: Wed Mar 1 19:35:57 2000
SingleSequenceAlignment	SingleSequenceAlignment.java This class is for those stick occasions when you want a SequenceAlignment but all you have is a Sequence.

Exception Summary

NoGapAtThisPositionException	NoGapAtThisPositionException.java Created: Sat Mar 4 14:04:07 2000
NoSuchSequenceException	NoSuchSequenceException.java Alerts to an invalid sequence index within a sequence alignment.