82 lines
1.7 KiB
Prolog
82 lines
1.7 KiB
Prolog
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:- module(hmm,
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[init_hmm/0,
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hmm_state/1,
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emission/1
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]).
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:- ensure_loaded(library(clpbn)).
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:- use_module(library(atts)).
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:- use_module(library(lists),
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[nth/3]).
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:- use_module(library(bhash),
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[b_hash_new/2,
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b_hash_lookup/3,
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b_hash_insert/3
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]).
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:- ensure_loaded(library(tries)).
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:- meta_predicate hmm_state(:).
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:- dynamic hmm_tabled/1.
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:- attribute emission/1.
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:- ensure_loaded(library('clpbn/viterbi')).
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init_hmm :-
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% retractall(hmm_tabled(_)).
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% eraseall(hmm_tabled).
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% nb_hash_new(hmm_table, 1000000).
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trie_open(Trie), nb_setval(trie,Trie).
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hmm_state(Mod:A) :- !, hmm_state(A,Mod).
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hmm_state(A) :- prolog_flag(typein_module,Mod), hmm_state(A,Mod).
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hmm_state(Mod:N/A,_) :- !,
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hmm_state(N/A,Mod).
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hmm_state((A,B),Mod) :- !,
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hmm_state(A,Mod),
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hmm_state(B,Mod).
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hmm_state(N/A,Mod) :-
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atom_codes(N,[TC|_]),
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atom_codes(T,[TC]),
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build_args(A,LArgs,KArgs,First,Last),
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Key =.. [T|KArgs],
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Head =.. [N|LArgs],
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asserta_static( (Mod:Head :-
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(First > 2 ->
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Last = Key, !
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;
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nb_getval(trie, Trie), trie_check_entry(Trie, Key, _) ->
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% leave work for solver!
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Last = Key, !
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;
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% first time we saw this entry
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nb_getval(trie, Trie), trie_put_entry(Trie, Key, _),
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fail
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)
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)).
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build_args(4,[A,B,C,D],[A,B,C],A,D).
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build_args(3, [A,B,C], [A,B],A,C).
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build_args(2, [A,B], [A],A,B).
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emission(V) :-
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put_atts(V,[emission(Prob)]).
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cvt_vals(aminoacids,[a, c, d, e, f, g, h, i, k, l, m, n, p, q, r, s, t, v, w, y]).
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cvt_vals(bool,[t,f]).
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cvt_vals(dna,[a,c,g,t]).
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cvt_vals(rna,[a,c,g,u]).
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cvt_vals([A|B],[A|B]).
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% first, try standard representation
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find_probs(Logs,Nth,Log) :-
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arg(Nth,Logs,Log).
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