[Treebase-guts] [ treebase-Bugs-2783200 ] Merge Algorithm classes and expand algorithm choices

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Bugs item #2783200, was opened at 2009-04-28 16:59
Message generated for change (Comment added) made by mjdominus
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Category: None
Group: None
Status: Open
Priority: 5
Private: No
Submitted By: Mark Dominus (mjdominus)
Assigned to: Nobody/Anonymous (nobody)
>Summary: Merge Algorithm classes and expand algorithm choices

Initial Comment:
Algorithm is an abstract class from which ParsimonyAlgorithm, DistanceAlgorithm, LikelihoodAlgorithm, and OtherAlgorithm are derived.  ParsimonyAlgorithm uses three other classes (GapMode, UserType, and PolyTCount) that are not used anywhere else.

These should be merged into a single class with a flag and some sort of associated string data; the GapMode, UserType, and PolyTCount tables should be eliminated.

Regarding this design, Jin Ruan, the original designer, says:

(04:48:42 PM) Jin Ruan: The algorithm design is not well reviewed. What is there was the first pass I had to model different algorithms into the system. The reason for different subclasses was to enable more interactions/relationships between generated trees with a particular algorithm. However we never actually design/ implment any use case to use that design in treebase2. That is why we have this first pass design but it is largely not used. Please feel free to redesign it. For example, as a starting point using a string instead of different subclasses. 

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>Comment By: Mark Dominus (mjdominus)
Date: 2009-04-28 17:03

Message:
Bill also says that the UI for the algorithm for an analysis step should
include the following items:


• Under analysis step entry, the "algorithm" lists the following in to
popup: maximum likelihood, parsimony, distance, and other. Please change it
to the following:

bayesian inference
maximum likelihood
minimum evolution
neighbor joining
parsimony
UPGMA
other


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