mainbranch fixes to:

- fix quoted characters output
- fix line position in read_term and friends
- make messages look a bit better
- CLP(BN) EM improvements.

CLPBN/learning/em.yap

@@ -16,6 +16,9 @@
 	       empty_dist/2,
 	       dist_new_table/2]).
 
+:- use_module(library('clpbn/connected'),
+	      [clpbn_subgraphs/2]).
+
 :- use_module(library('clpbn/learning/learn_utils'),
 	      [run_all/1,
 	       clpbn_vars/2,
@@ -29,8 +32,10 @@
 	      [matrix_add/3,
 	       matrix_to_list/2]).
 
-:- use_module(library('clpbn/utils'), [
-	check_for_hidden_vars/3]).
+:- use_module(library('clpbn/utils'),
+	      [
+	       check_for_hidden_vars/3,
+	       sort_vars_by_key/3]).
 
 :- meta_predicate em(:,+,+,-,-), init_em(:,-).
 
@@ -50,8 +55,9 @@ em(Items, MaxError, MaxIts, Tables, Likelihood) :-
 init_em(Items, state(AllVars, AllDists, AllDistInstances, MargVars)) :-
 	run_all(Items),
 	attributes:all_attvars(AllVars0),
+	sort_vars_by_key(AllVars0,AllVars1,[]),
 	% remove variables that do not have to do with this query.
-	check_for_hidden_vars(AllVars0, AllVars0, AllVars),
+	check_for_hidden_vars(AllVars1, AllVars1, AllVars),
 	different_dists(AllVars, AllDists, AllDistInstances, MargVars),
 	clpbn_init_solver(MargVars, AllVars, _).
 
@@ -59,6 +65,8 @@ init_em(Items, state(AllVars, AllDists, AllDistInstances, MargVars)) :-
 em_loop(Its, Likelihood0, State, MaxError, MaxIts, LikelihoodF, FTables) :-
 	estimate(State, LPs),
 	maximise(State, Tables, LPs, Likelihood),
+	(recorded(clpbn_dist_db, DB, _), writeln(DB), fail ; true),
+	writeln(Likelihood:Tables),
 	(
 	    (
 	     (Likelihood - Likelihood0)/Likelihood < MaxError

CLPBN/learning/example/school_params.yap

@@ -28,7 +28,5 @@ goal(student_intelligence(P,V)) :-
 goal(course_difficulty(P,V)) :-
         pos:course_difficulty(P,V1),
         ( random > 0.1 -> V = V1 ; true).
-/*
 goal(registration_satisfaction(P,V)) :-
         pos:registration_satisfaction(P,V).
-*/

CLPBN/learning/learn_utils.yap

@@ -54,8 +54,6 @@ normalise_counts(MAT,NMAT) :-
 	matrix_op_to_lines(MAT, Sum, /, NMAT).
 
 compute_likelihood(Table0, NewTable, DeltaLik) :-
-	matrix:matrix_to_list(Table0,L0), writeln(L0),
-	matrix:matrix_to_list(NewTable,L1), writeln(L1),
 	matrix_to_logs(NewTable, Logs),
 	matrix_op(Table0, Logs, *, Logs),
 	matrix_sum(Logs, DeltaLik).