I will soon be adding a bunch of classes related to Alignments. I should have these ready today or tomorrow. I hate naming things so if anyone can come up with better names especially for ARAlignment I am open to suggestions.
Interface UnequalLengthAlignment (allows having sequences of different lengths) Interface ARAlignment (allows adding and removing sequences) Interface EditableAlignment (allows editing, and shifting bases) Class FlexibleAlignment (implements all 3 of the above) Interface AlignedElement (holds label, SymbolList, location) Class SimpleAlignedElement Abstract Class AbstractULAlignment Class IllegalAlignmentEditException Interface QualitativeAlignment (handles SymbolList that implement Qualitative) May I suggest a few other things Interface SequenceAlignment (extends Alignment) I think this could help in the recently discussed issues about SequencePanel. Anyone up for defining this one? In addition I REALLY think that we need an interface for a GappedSymbolList. Since this name is already taken I guess we could call it GappedList or something. This way GappedPhredSequence or other classes could implement this interface. I have some questions about how to best implement change support for EditableAlignment. Particularly how should changes that cascade be handled. Let me first define the function 'shift'. This will move bases in one direction or the other, filling in gaps on one side and adding gaps on the other. Of course shifting cannot delete bases only gaps. In the case of an UnequalLengthAlignment shifting bases that include the first or last base should not add gaps at the ends, rather it changes the location of the sequence withing the alignment. So there are two types of changes, adding removing gaps, and changing location. In addition if a sequence is shifted such that it extends the overall alignment, it will change the size of the alignment. Finally if a sequence at the begining of an alignment is sifted to the left, the whole alignment will shift so as to make the first base in the alignment = 1 again. In this cases all of the sequences in the alignment must be changed. The same is true if an sequence is added to the alignment that extends the alignment to the left. Now how should changes be signaled to listeners. Should each change be sent with a FirePreChangeEvent/FirePostChangeEvent. Or should I just come up with a global ChangeEvent, that holds all the information? If each change, gets sent individually, it seems that there is a possiblity (although it should not happen) that a one of the events gets vetoed, and I'd have to do a rollback. I know this sort of things has been discussed before but I don't know what the conclusion is. I would like to send ChangeEvents that will let the listeners know what sequences have been changed, and the overall range of the change so that, for instance, some Rendering object would know what it had to redraw without having to figure it all out for itself. Any suggestion would be appreciated David _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
