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.