de3bd15889
git-svn-id: https://yap.svn.sf.net/svnroot/yap/trunk@1389 b08c6af1-5177-4d33-ba66-4b1c6b8b522a
81 lines
1.6 KiB
Prolog
81 lines
1.6 KiB
Prolog
|
|
|
|
:- module(hmm, [init_hmm/0,
|
|
hmm_state/1,
|
|
emission/4]).
|
|
|
|
:- ensure_loaded(library(clpbn)).
|
|
|
|
:- use_module(library(lists),
|
|
[nth/3]).
|
|
|
|
:- meta_predicate hmm_state(:).
|
|
|
|
:- dynamic hmm_tabled/1.
|
|
|
|
:- attribute emission/1.
|
|
|
|
:- ensure_loaded(library('clpbn/viterbi')).
|
|
|
|
init_hmm :-
|
|
retractall(hmm_tabled(_)).
|
|
|
|
hmm_state(Mod:A) :- !, hmm_state(A,Mod).
|
|
hmm_state(A) :- prolog_flag(typein_module,Mod), hmm_state(A,Mod).
|
|
|
|
hmm_state(Mod:N/A,_) :- !,
|
|
hmm_state(N/A,Mod).
|
|
hmm_state((A,B),Mod) :- !,
|
|
hmm_state(A,Mod),
|
|
hmm_state(B,Mod).
|
|
hmm_state(N/A,Mod) :-
|
|
atom_codes(N,[TC|_]),
|
|
atom_codes(T,[TC]),
|
|
build_args(A,LArgs,KArgs,Last),
|
|
Key =.. [T|KArgs],
|
|
Head =.. [N|LArgs],
|
|
asserta_static( Mod:(Head :-
|
|
(
|
|
hmm:hmm_tabled(Key)
|
|
->
|
|
% leave work for solver!
|
|
%
|
|
%format(' ~w~n',[Key]),
|
|
Last = Key, !
|
|
% clpbn:put_atts(Last,[key(Key)]), !
|
|
;
|
|
% first time we saw this entry
|
|
%format('+~w~n',[Key]),
|
|
%write(Key),nl,
|
|
%(Key = d(30,46) -> start_low_level_trace ; stop_low_level_trace),
|
|
assert(hmm:hmm_tabled(Key)), fail
|
|
)
|
|
)
|
|
).
|
|
|
|
build_args(3,[A,B,C],[A,B],C).
|
|
build_args(2,[A,B],[A],B).
|
|
|
|
find_var(Key,Last) :-
|
|
array_element(hmm_tree,1,Tree),
|
|
lookup(Key, Tree, Last).
|
|
|
|
|
|
emission(Vals,CPT,Ev,V) :-
|
|
cvt_vals(Vals,LVals),
|
|
once(nth(Nth, LVals, Ev)),
|
|
find_probs(CPT,Nth,Prob),
|
|
put_atts(V,[emission(Prob)]).
|
|
|
|
cvt_vals(aminoacids,[a, c, d, e, f, g, h, i, k, l, m, n, p, q, r, s, t, v, w, y]).
|
|
cvt_vals(bool,[t,f]).
|
|
cvt_vals(bases,[a,c,g,t]).
|
|
cvt_vals([A|B],[A|B]).
|
|
|
|
% first, try standard representation
|
|
find_probs(Logs,Nth,Log) :-
|
|
arg(Nth,Logs,Log).
|
|
|
|
|
|
|