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TODO
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TODO
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1. rename SearchGuess to Placement
2. pull [BetaStrand] out of SearchStrategy and capture it in a closure
try
data Scored a = Scored a Score
(/+/) :: Score -> Scored a -> Scored a
x /+/ Scored a y = Scored a (x + y)
instance Functor Scored where
fmap f (Scored a x) = Scored (f a) x
scoremin :: [Scored a] -> Scored a
scoremax :: [Scored a] -> Scored a
Use fake inheritance in the search strategy modules
Memoize viterbi at top level
quick check
write wrapper functions around indexing and slicing functions
delaying viterbi until BETA scoring reaches some POINT
initial guess Psipred secondary structure prediction
since we are sensitive to initial conditions
what happens when the query sequence is shorter than the sum of all beta strands
tons of Main cleanup