More whitespace cleanups

packages/CLPBN/clpbn.yap

@@ -221,14 +221,14 @@ set_em_solver(Solver) :-
 %
 % we use a mutable variable to avoid unnecessary trailing.
 %
-store_var(El) :- 
+store_var(El) :-
-	nb_current(clpbn_qvars, Mutable), 
+	nb_current(clpbn_qvars, Mutable),
 	nonvar(Mutable), !,
 	get_mutable(Tail, Mutable),
 	update_mutable(El.Tail, Mutable).
-store_var(El) :- 
+store_var(El) :-
 	init_clpbn_vars(El).
-	
+
 init_clpbn_vars(El) :-
 	create_mutable(El, Mutable),
 	b_setval(clpbn_qvars, Mutable).
@@ -278,7 +278,7 @@ project_attributes(GVars0, _AVars0) :-
 	b_setval(clpbn_query_variables, f(GVars0,Evidence)),
 	simplify_query(GVars0, GVars),
 	(
-	  GKeys = [] 
+	  GKeys = []
 	->
 	  GVars0 = [V|_],
 	  clpbn_display:put_atts(V, [posterior([],[],[],[])])
@@ -378,7 +378,7 @@ call_ground_solver(cbp, GVars, GoalKeys, Keys, Factors, Evidence) :- !,
 call_ground_solver(Solver, GVars, _GoalKeys, Keys, Factors, Evidence) :-
 	% fall back to traditional solver
 	b_hash_new(Hash0),
-	foldl(gvar_in_hash, GVars, Hash0, HashI), 
+	foldl(gvar_in_hash, GVars, Hash0, HashI),
 	foldl(key_to_var, Keys, AllVars, HashI, Hash1),
 	foldl(evidence_to_v, Evidence, _EVars, Hash1, Hash),
 	%writeln(Keys:AllVars),
@@ -432,7 +432,7 @@ write_out(Solver, _, _, _) :-
 %
 gvar_in_hash(V, Hash0, Hash) :-
 	get_atts(V, [key(K)]),
-	b_hash_insert(Hash0, K, V, Hash). 
+	b_hash_insert(Hash0, K, V, Hash).
 
 key_to_var(K, V, Hash0, Hash0) :-
 	b_hash_lookup(K, V, Hash0), !.
@@ -496,12 +496,12 @@ process_vars([V|Vs], [K|Ks]) :-
 	process_var(V, K),
 	process_vars(Vs, Ks).
 
-process_var(V, K) :- get_atts(V, [key(K)]), !. 
+process_var(V, K) :- get_atts(V, [key(K)]), !.
 % oops: this variable has no attributes.
 process_var(V, _) :- throw(error(instantiation_error,clpbn(attribute_goal(V)))).
 
 %
-% unify a CLPBN variable with something. 
+% unify a CLPBN variable with something.
 %
 verify_attributes(Var, T, Goal) :-
 	get_atts(Var, [key(Key),dist(Dist,Parents)]), !,
@@ -641,7 +641,7 @@ clpbn_init_solver(pcg, LVs, Vs0, VarsWithUnboundKeys, State) :-
 %
 % LVs is the list of lists of variables to marginalise
 % Vs is the full graph
-% Ps are the probabilities on LVs. 
+% Ps are the probabilities on LVs.
 %
 clpbn_run_solver(LVs, LPs, State) :-
 	solver(Solver),
@@ -708,7 +708,7 @@ pfl_run_solver(LVs, LPs, State) :-
 
 pfl_run_solver(LVs, LPs, State, ve) :- !,
 	run_ve_ground_solver(LVs, LPs, State).
-	
+
 pfl_run_solver(LVs, LPs, State, hve) :- !,
 	run_horus_ground_solver(LVs, LPs, State).
 
@@ -732,7 +732,7 @@ add_keys(Key1+V1,_Key2,Key1+V1).
 
 probability(Goal, Prob) :-
 	findall(Prob, do_probability(Goal, [], Prob), [Prob]).
-	
+
 conditional_probability(Goal, ListOfGoals, Prob) :-
 	\+ ground(Goal),
 	throw(error(ground(Goal),conditional_probability(Goal, ListOfGoals, Prob))).
@@ -766,7 +766,7 @@ evidence_to_var(Goal, C, VItem, V) :-
 	Goal =.. [L|Args],
 	variabilise_last(Args, C, NArgs, V),
 	VItem =.. [L|NArgs].
-	
+
 variabilise_last([Arg], Arg, [V], V).
 variabilise_last([Arg1,Arg2|Args], Arg, Arg1.NArgs, V) :-
 	variabilise_last(Arg2.Args, Arg, NArgs, V).

packages/CLPBN/clpbn/aggregates.yap

@@ -96,11 +96,11 @@ find_ev(_Evs, Key, RemKeys, [Key|RemKeys], Ev, Ev).
 % +final CPT
 % - New Parents
 % + - list of new keys
-% 
+%
 avg_table(Vars, OVars, Domain, Key, TotEvidence, Softness, Vars, Vs, Vs, Id) :-
 	length(Domain, SDomain),
 	int_power(Vars, SDomain, 1, TabSize),
-	TabSize =< 256, 
+	TabSize =< 256,
 	/* case gmp is not there !! */
 	TabSize > 0, !,
 	average_cpt(Vars, OVars, Domain, TotEvidence,  Softness, CPT),
@@ -170,7 +170,7 @@ cpt_min([_|Vars], Key, Els0, CPT, Vs, NewVs) :-
 build_avg_table(Vars, OVars, Domain, _, TotEvidence, Softness, CPT, Vars, Vs, Vs) :-
 	length(Domain, SDomain),
 	int_power(Vars, SDomain, 1, TabSize),
-	TabSize =< 256, 
+	TabSize =< 256,
 	/* case gmp is not there !! */
 	TabSize > 0, !,
 	average_cpt(Vars, OVars, Domain, TotEvidence,  Softness, CPT).
@@ -304,7 +304,7 @@ get_ds_lengths([],[]).
 get_ds_lengths([V|Vs],[Sz|Lengs]) :-
 	get_vdist_size(V, Sz),
 	get_ds_lengths(Vs,Lengs).
-	
+
 fill_in_average(Lengs, N, Base, MCPT) :-
 	generate(Lengs, Case),
 	average(Case, N, Base, Val),

packages/CLPBN/clpbn/bdd.yap

@@ -9,12 +9,12 @@ V = v(Va, Vb, Vc)
 
 The generic formula is
 
-V <- X, Y 
+V <- X, Y
 
 Va <- P*X1*Y1 + Q*X2*Y2 + ...
 
 
- 
+
 **************************************************/
 
 :- module(clpbn_bdd,
@@ -80,8 +80,8 @@ bdds(bdd).
 
 %
 % QVars: all query variables?
-% 
+%
-% 
+%
 init_bdd_ground_solver(QueryKeys, AllKeys, Factors, Evidence, bdd(QueryKeys, AllKeys, Factors, Evidence)).
 
 %
@@ -161,7 +161,7 @@ sort_keys(AllFs, AllVars, Leaves) :-
 	dgraph_top_sort(Graph, AllVars).
 
 add_node(f([K|Parents],_,_,_), Graph0, Graph) :-
-	dgraph_add_vertex(Graph0, K, Graph1), 
+	dgraph_add_vertex(Graph0, K, Graph1),
 	foldl(add_edge(K), Parents, Graph1, Graph).
 
 add_edge(K, K0, Graph0, Graph) :-
@@ -176,7 +176,7 @@ sort_vars(AllVars0, AllVars, Leaves) :-
 build_graph([], Graph, Graph).
 build_graph([V|AllVars0], Graph0, Graph) :-
 	clpbn:get_atts(V, [dist(_DistId, Parents)]), !,
-	dgraph_add_vertex(Graph0, V, Graph1), 
+	dgraph_add_vertex(Graph0, V, Graph1),
 	add_parents(Parents, V, Graph1, GraphI),
 	build_graph(AllVars0, GraphI, Graph).
 build_graph(_V.AllVars0, Graph0, Graph) :-
@@ -184,7 +184,7 @@ build_graph(_V.AllVars0, Graph0, Graph) :-
 
 add_parents([], _V, Graph, Graph).
 add_parents([V0|Parents], V, Graph0, GraphF) :-
-	dgraph_add_edge(Graph0, V0, V, GraphI), 
+	dgraph_add_edge(Graph0, V0, V, GraphI),
 	add_parents(Parents, V, GraphI, GraphF).
 
 get_keys_info([], _, _, _, Vs, Vs, Ps, Ps, _, _) --> [].
@@ -378,7 +378,7 @@ avg_tree([Vals|PVars], P, Max, Im, IM, Size, O, H0, HF) :-
 	MaxI is Max-(Size-1),
 	avg_exp(Vals, PVars, 0, P, MaxI, Size, Im, IM, HI, HF, Exp),
 	simplify_exp(Exp, Simp).
-	
+
 avg_exp([], _, _, _P, _Max, _Size, _Im, _IM, H, H, 0).
 avg_exp([Val|Vals], PVars, I0, P0, Max, Size, Im, IM, HI, HF, O) :-
 	(Vals = [] -> O=O1 ; O = Val*O1+not(Val)*O2 ),
@@ -434,7 +434,7 @@ bup_avg(V, Size, Domain, Parents0, Vs, Vs2, Lvs, Outs, DIST) :-
 bin_sums(Vs, Sums, F) :-
 	 vs_to_sums(Vs, Sums0),
 	 bin_sums(Sums0, Sums, F, []).
-	
+
 vs_to_sums([], []).
 vs_to_sums([V|Vs], [Sum|Sums0]) :-
 	Sum =.. [sum|V],
@@ -536,7 +536,7 @@ sum_all([_V|Vs], Pos, I, Max0, Sums, List) :-
 
 gen_arg(J, Sums, Max, S0) :-
 	gen_arg(0, Max, J, Sums, S0).
-	
+
 gen_arg(Max, Max, J, Sums, S0) :- !,
 	I is Max+1,
 	arg(I, Sums, A),
@@ -647,19 +647,19 @@ copy(N, [], [], Ms, Parms0, Parms, ParmVars) :-!,
 	copy(N, Ms, NewMs, NewMs, Parms0, Parms, ParmVars).
 copy(N, D.Ds, ND.NDs, New, El.Parms0, NEl.Parms, V.ParmVars) :-
 	N1 is N-1,
-	(El == 0.0 -> 
+	(El == 0.0 ->
 	    NEl = 0,
 	    V = NEl,
 	    ND = D
-	;El == 1.0 -> 
+	;El == 1.0 ->
 	    NEl = 1,
 	    V = NEl,
 	    ND = 0.0
-	;El == 0 -> 
+	;El == 0 ->
 	    NEl = 0,
 	    V = NEl,
 	    ND = D
-	;El =:= 1 -> 
+	;El =:= 1 ->
 	    NEl = 1,
 	    V = NEl,
 	    ND = 0.0,
@@ -818,7 +818,7 @@ get_key_evidence(V, Evs, _, Tree, Ev, F0, F, Leaves, Finals) :-
 %% 	deterministic(V, DistId),
 %% 	!,
 %% 	one_list(Ev),
-%% 	eval_outs(F0).	
+%% 	eval_outs(F0).
 %% no evidence !!!
 get_key_evidence(V, _, _, Tree, _Values, F0, F1, Leaves, Finals) :-
 	insert_output(Leaves, V, Finals, Tree, Outs, SendOut),
@@ -836,14 +836,14 @@ get_evidence(V, _Tree, Ev, F0, [], _Leaves, _Finals) :-
 	( Name = 'AVG' ; Name = 'MAX' ; Name = 'MIN' ),
 	!,
 	one_list(Ev),
-	eval_outs(F0).	
+	eval_outs(F0).
 %% no evidence !!!
 get_evidence(V, Tree, _Values, F0, F1, Leaves, Finals) :-
 	insert_output(Leaves, V, Finals, Tree, Outs, SendOut),
 	get_outs(F0, F1, SendOut, Outs).
 
 zero_pos(_, _Pos, []).
-zero_pos(Pos, Pos, [1|Values]) :- !, 
+zero_pos(Pos, Pos, [1|Values]) :- !,
 	I is Pos+1,
 	zero_pos(I, Pos, Values).
 zero_pos(I0, Pos, [0|Values]) :-
@@ -855,7 +855,7 @@ one_list(1.Ev) :-
 	one_list(Ev).
 
 %
-% insert a node with the disj of all alternatives, this is only done if node ends up to be in the output 
+% insert a node with the disj of all alternatives, this is only done if node ends up to be in the output
 %
 insert_output([], _V, [], _Out, _Outs, []).
 insert_output(V._Leaves, V0, [Top|_], Top, Outs, [Top = Outs]) :- V == V0, !.
@@ -1057,7 +1057,7 @@ generate_exclusions([V0|SeenVs], V) -->
 
 build_cnf(CNF, IVs, Indics, AllParms, AllParmValues, Val) :-
 %(numbervars(CNF,1,_), writeln(cnf_to_ddnnf(CNF, Vars, IVs, [], F)), fail ; true ),
-	cnf_to_ddnnf(CNF, AllParms, F), 
+	cnf_to_ddnnf(CNF, AllParms, F),
 	AllParms = AllParmValues,
 	IVs = Indics,
 	term_variables(CNF, Extra),

packages/CLPBN/clpbn/bnt.yap

@@ -101,7 +101,7 @@ do_bnt(QueryVars, AllVars, AllDiffs)  :-
 	add_evidence(SortedVertices, Size, NumberedVertices),
 	marginalize(QueryVars, SortedVertices, NumberedVertices, Ps),
 	clpbn_bind_vals(QueryVars, Ps, AllDiffs).
-	
+
 create_bnt_graph(AllVars, Representatives) :-
 	create_bnt_graph(AllVars, Representatives, _, _, _).
 
@@ -320,7 +320,7 @@ get_sizes_and_ids([V|Parents],[Id-V|Ids]) :-
 extract_vars([], L, L).
 extract_vars([_-V|NIds], NParents, Vs) :-
 	extract_vars(NIds, [V|NParents], Vs).
-	
+
 mkcpt(BayesNet, I, Tab) :-
 	(BayesNet.'CPD'({I})) <-- tabular_CPD(BayesNet,I,Tab).
 
@@ -336,7 +336,7 @@ create_class_vector([], [], [],[]).
 create_class_vector([V|Graph], [I|Is],  [Id|Classes], [Id-v(V,I,Parents)|Sets]) :-
 	clpbn:get_atts(V, [dist(Id,Parents)]),
 	create_class_vector(Graph, Is,Classes,Sets).
-	
+
 representatives([],[]).
 representatives([Class-Rep|Reps1],[Class-Rep|Reps]) :-
 	nonrepresentatives(Reps1, Class, Reps2),
@@ -390,7 +390,7 @@ mk_evidence([V|L], [I|Is], [ar(1,I,EvVal1)|LN]) :-
 	mk_evidence(L, Is, LN).
 mk_evidence([_|L], [_|Is], LN) :-
 	mk_evidence(L, Is, LN).
-	
+
 evidence_val(Ev,Val,[Ev|_],Val) :- !.
 evidence_val(Ev,I0,[_|Domain],Val) :-
 	I1 is I0+1,

packages/CLPBN/clpbn/discrete_utils.yap

@@ -24,7 +24,7 @@ propagate_evidence(V, Evs) :-
 	clpbn:get_atts(V, [evidence(Ev),dist(Id,_)]), !,
 	get_dist_domain(Id, Out),
 	generate_szs_with_evidence(Out,Ev,0,Evs,Found),
-	(var(Found) -> 
+	(var(Found) ->
 	  clpbn:get_atts(V, [key(K)]),
 	  throw(clpbn(evidence_does_not_match,K,Ev,[Out]))
 	;

packages/CLPBN/clpbn/display.yap

@@ -78,7 +78,7 @@ clpbn_bind_vals([Vs|MoreVs],[Ps|MorePs],AllDiffs) :-
 
 clpbn_bind_vals2([],_,_) :- !.
 % simple case, we want a distribution on a single variable.
-clpbn_bind_vals2([V],Ps,AllDiffs) :- 
+clpbn_bind_vals2([V],Ps,AllDiffs) :-
 	use_parfactors(on), !,
 	clpbn:get_atts(V, [key(K)]),
 	pfl:skolem(K,Vals),

packages/CLPBN/clpbn/dists.yap

@@ -90,7 +90,7 @@ where Id is the id,
     dna for [a,c,g,t]
     rna for [a,c,g,u]
     reals
-	
+
 
 ********************************************/
 

packages/CLPBN/clpbn/evidence.yap

@@ -31,7 +31,7 @@
 :- dynamic node/3, edge/2, evidence/2.
 
 %
-% new evidence storage algorithm. The idea is that instead of 
+% new evidence storage algorithm. The idea is that instead of
 % redoing all the evidence every time we query the network, we shall
 % keep a precompiled version around.
 %
@@ -51,9 +51,9 @@ compute_evidence(_,PreviousSolver) :-
 	set_clpbn_flag(solver, PreviousSolver).
 
 get_clpbn_vars(G, Vars) :-
-%	attributes:all_attvars(Vars0),	
+%	attributes:all_attvars(Vars0),
 	once(G),
-	attributes:all_attvars(Vars).	
+	attributes:all_attvars(Vars).
 
 evidence_error(Ball,PreviousSolver) :-
 	set_clpbn_flag(solver,PreviousSolver),

packages/CLPBN/clpbn/gibbs.yap

@@ -137,7 +137,7 @@ graph_representation([V|Vs], Graph, I0, Keys, [I-IParents|TGraph]) :-
 	graph_representation(Vs, Graph, I, Keys, TGraph).
 
 write_pars([]).
-write_pars([V|Parents]) :- 
+write_pars([V|Parents]) :-
 	clpbn:get_atts(V, [key(K),dist(I,_)]),write(K:I),nl,
 	write_pars(Parents).
 
@@ -149,7 +149,7 @@ get_sizes([V|Parents], [Sz|Szs]) :-
 
 parent_indices([], _, []).
 parent_indices([V|Parents], Keys, [I|IParents]) :-
-	rb_lookup(V, I, Keys),	
+	rb_lookup(V, I, Keys),
 	parent_indices(Parents, Keys, IParents).
 
 
@@ -174,7 +174,7 @@ propagate2parents([V|NewParents], Table, Variables, Graph, Keys) :-
 	propagate2parents(NewParents,Table, Variables, Graph, Keys).
 
 add2graph(V, Vals, Table, IParents, Graph, Keys) :-
-	rb_lookup(V, Index, Keys),	
+	rb_lookup(V, Index, Keys),
 	(var(Vals) -> true ; length(Vals,Sz)),
 	arg(Index, Graph, var(V,Index,_,Vals,Sz,VarSlot,_,_,_)),
 	member(tabular(Table,Index,IParents), VarSlot), !.
@@ -239,7 +239,7 @@ mult_list([Sz|Sizes],Mult0,Mult) :-
 	MultI is Sz*Mult0,
 	mult_list(Sizes,MultI,Mult).
 
-% compile node as set of facts, faster execution 
+% compile node as set of facts, faster execution
 compile_var(TotSize,I,_Vals,Sz,CPTs,Parents,_Sizes,Graph) :-
 	TotSize < 1024*64, TotSize > 0, !,
 	multiply_all(I,Parents,CPTs,Sz,Graph).
@@ -367,8 +367,8 @@ generate_est_mults([], [], _, [], 1).
 generate_est_mults([V|Vs], [I|Is], Graph, [M0|Mults], M) :-
 	arg(V,Graph,var(_,I,_,_,Sz,_,_,_,_)),
 	generate_est_mults(Vs, Is, Graph, Mults, M0),
-	M is M0*Sz.	
+	M is M0*Sz.
-	
+
 gen_e0(0,[]) :- !.
 gen_e0(Sz,[0|E0L]) :-
 	Sz1 is Sz-1,
@@ -531,7 +531,7 @@ add_up_mes(Counts,[me(_,_,Cs)|Chains], Add) :-
 	sum_lists(Counts, Cs, NCounts),
 	add_up_mes(NCounts, Chains, Add).
 
-sum_lists([],[],[]).	
+sum_lists([],[],[]).
 sum_lists([Count|Counts], [C|Cs], [NC|NCounts]) :-
 	NC is Count+C,
 	sum_lists(Counts, Cs, NCounts).

packages/CLPBN/clpbn/graphviz.yap

@@ -50,7 +50,7 @@ output_parents1(Stream,[V|L]) :-
 	put_code(Stream, 0' ), %'
 	output_parents1(Stream,L).
 
-output_v(V,Stream) :- 
+output_v(V,Stream) :-
 	clpbn:get_atts(V,[key(Key)]),
 	output_key(Stream,Key).
 

packages/CLPBN/clpbn/horus.yap

@@ -1,7 +1,7 @@
 /*******************************************************
 
  Horus Interface
- 
+
 ********************************************************/
 
 :- module(clpbn_horus,

packages/CLPBN/clpbn/horus_ground.yap

@@ -4,7 +4,7 @@
 	- Variable Elimination
 	- Belief Propagation
 	- Counting Belief Propagation
- 
+
 ********************************************************/
 
 :- module(clpbn_horus_ground,

packages/CLPBN/clpbn/jt.yap

@@ -98,7 +98,7 @@ jt(LLVs,Vs0,AllDiffs) :-
 
 
 init_jt_solver(LLVs, Vs0, _, State) :-
-	check_for_agg_vars(Vs0, Vs1), 
+	check_for_agg_vars(Vs0, Vs1),
 	init_influences(Vs1, G, RG),
 	maplist(init_jt_solver_for_question(G, RG), LLVs, State).
 
@@ -163,7 +163,7 @@ initial_graph(_,Parents, CPTs) :-
 	% from the very beginning.
 	dgraph_transpose(V1, V2),
 	dgraph_to_ugraph(V2, Parents).
-	
+
 
 problem_graph([], []).
 problem_graph([V|BNet], GraphF) :-

packages/CLPBN/clpbn/matrix_cpt_utils.yap

@@ -87,7 +87,7 @@ evidence(V, Pos) :-
 	clpbn:get_atts(V, [evidence(Pos)]).
 
 vnth([V1|Deps], N, V, N, Deps) :-
-	V == V1, !.	
+	V == V1, !.
 vnth([V1|Deps], N0, V, N, [V1|NDeps]) :-
 	N1 is N0+1,
 	vnth(Deps, N1, V, N, NDeps).
@@ -207,9 +207,9 @@ generate_map([V|DimsNew], [V0|Dims0], [0|Map]) :- V == V0, !,
 	generate_map(DimsNew, Dims0, Map).
 generate_map([V|DimsNew], Dims0, [Sz|Map]) :-
 	clpbn:get_atts(V, [dist(Id,_)]),
-	clpbn_dist:get_dist_domain_size(Id, Sz),	
+	clpbn_dist:get_dist_domain_size(Id, Sz),
 	generate_map(DimsNew, Dims0, Map).
-	
+
 unit_CPT(V,CPT) :-
 	clpbn:get_atts(V, [dist(Id,_)]),
 	clpbn_dist:get_dist_domain_size(Id, Sz),
@@ -287,7 +287,7 @@ uniform_CPT(Dims, M) :-
 	normalise_possibly_deterministic_CPT(M1, M).
 
 normalise_CPT_on_lines(MAT0, MAT2, L1) :-
-	matrix_agg_cols(MAT0, +, MAT1), 
+	matrix_agg_cols(MAT0, +, MAT1),
 	matrix_sum(MAT1, SUM),
 	matrix_op_to_all(MAT1, /, SUM, MAT2),
 	matrix:matrix_to_list(MAT2,L1).

packages/CLPBN/clpbn/numbers.yap

@@ -1,7 +1,7 @@
 
 :- module(clpbn_numbers,
-		[keys_to_numbers/7, 
+		[keys_to_numbers/7,
-		 keys_to_numbers/9, 
+		 keys_to_numbers/9,
 		 lists_of_keys_to_ids/6
 		]).
 

packages/CLPBN/clpbn/pgrammar.yap

@@ -176,7 +176,7 @@ get_internal(S, InternalS, Arg) :-
 
 extract_probability(p(Id,Goals), P) :-
 	id(Id,_,P0,_),
-	LogP0 is log(P0),	
+	LogP0 is log(P0),
 	extract_logprobability(Goals, LogP0, LogP),
 	P is exp(LogP).
 

packages/CLPBN/clpbn/table.yap

@@ -37,11 +37,11 @@
 	clpbn_tabled_clause_ref(:.?,?),
 	clpbn_tabled_retract(:),
 	clpbn_tabled_abolish(:),
-	clpbn_tabled_asserta(:), 
+	clpbn_tabled_asserta(:),
-	clpbn_tabled_assertz(:), 
+	clpbn_tabled_assertz(:),
-	clpbn_tabled_asserta(:,-), 
+	clpbn_tabled_asserta(:,-),
-	clpbn_tabled_assertz(:,-), 
+	clpbn_tabled_assertz(:,-),
-	clpbn_tabled_number_of_clauses(:,-), 
+	clpbn_tabled_number_of_clauses(:,-),
 	clpbn_is_tabled(:).
 
 :- use_module(library(terms),

packages/CLPBN/clpbn/utils.yap

@@ -66,7 +66,7 @@ merge_same_key([K1-V1,K2-V2|Vs], SortedAVars, Ks, UnifiableVars) :-
 	attributes:fast_unify_attributed(V1,V2),
 	merge_same_key([K1-V1|Vs], SortedAVars, Ks, UnifiableVars).
 merge_same_key([K1-V1,K2-V2|Vs], [V1|SortedAVars], Ks, [K1|UnifiableVars]) :-
-	(in_keys(K1, Ks) ; \+ \+ K1 == K2), !, 
+	(in_keys(K1, Ks) ; \+ \+ K1 == K2), !,
 	add_to_keys(K1, Ks, NKs),
 	merge_same_key([K2-V2|Vs], SortedAVars, NKs, UnifiableVars).
 merge_same_key([K-V|Vs], [V|SortedAVars], Ks, UnifiableVars) :-
@@ -74,7 +74,7 @@ merge_same_key([K-V|Vs], [V|SortedAVars], Ks, UnifiableVars) :-
 	merge_same_key(Vs, SortedAVars, NKs, UnifiableVars).
 
 in_keys(K1,[K|_]) :- \+ \+ K1 = K, !.
-in_keys(K1,[_|Ks]) :- 
+in_keys(K1,[_|Ks]) :-
 	in_keys(K1,Ks).
 
 add_to_keys(K1, Ks, Ks) :- ground(K1), !.

packages/CLPBN/clpbn/ve.yap

@@ -11,7 +11,7 @@
       all tables they connect to;
       multiply their size
       order by size
-  
+
 *********************************/
 
 :- module(clpbn_ve,
@@ -134,7 +134,7 @@ evtotree(K=V,Ev0,Ev) :-
 factor_to_graph( f(Nodes, Sizes, _Pars0, Id), Factors0, Factors, Edges0, Edges, I0, I) :-
 	I is I0+1,
 	pfl:get_pfl_parameters(Id, Pars0),
-	init_CPT(Pars0, Sizes, CPT0), 
+	init_CPT(Pars0, Sizes, CPT0),
 	reorder_CPT(Nodes, CPT0, FIPs, CPT, _),
 	F = f(I0, FIPs, CPT),
 	rb_insert(Factors0, I0, F, Factors),
@@ -196,7 +196,7 @@ id_to_factor(VMap, V-I, IF0, IF, Fs0, Fs, Evs0, Evs) :-
 	get_dist_params(D, Pars0),
 	get_dist_domain_size(D, DS),
 	maplist(parent_to_id(VMap), Ps, Sizes, IPs),
-	init_CPT(Pars0, [DS|Sizes], CPT0), 
+	init_CPT(Pars0, [DS|Sizes], CPT0),
 	reorder_CPT([I|IPs], CPT0, FIPs, CPT, _),
 	rb_insert(Fs0, IF0, f(IF0, FIPs, CPT), Fs),
 	IF is IF0+1.
@@ -261,7 +261,7 @@ solve([_|LQVs], FIds, Bigraph, Ev, LPs) :-
 
 do_solve(IQVs, IVs, bigraph(OldVs, IF, _Fs), Ev, Ps) :-
 	% get only what is relevant to query,
-	project_to_query_related(IVs, OldVs, SVs, Fs1), 
+	project_to_query_related(IVs, OldVs, SVs, Fs1),
 	% and also prune using evidence
 	rb_visit(Ev, EvL),
 	foldl2(clean_v_ev, EvL, Fs1, Fs2, SVs, EVs),
@@ -300,9 +300,9 @@ run_ve_solver(_, LLPs, state(LQVs, LVs, _VMap,  Bigraph, Ev)) :-
 %
 solve_ve([IQVs|_], [IVs|_], bigraph(OldVs, IF, _Fs), Ev, Ps) :-
 	% get only what is relevant to query,
-	project_to_query_related(IVs, OldVs, SVs, Fs1), 
+	project_to_query_related(IVs, OldVs, SVs, Fs1),
 	% and also prune using evidence
-	foldl2(clean_v_ev, Ev, Fs1, Fs2, SVs, EVs), 
+	foldl2(clean_v_ev, Ev, Fs1, Fs2, SVs, EVs),
 	% eliminate
 	eliminate(IQVs, digraph(EVs, IF, Fs2), Dist),
 % writeln(m:Dist),matrix:matrix_to_list(Dist,LD),writeln(LD),
@@ -319,7 +319,7 @@ solve_ve([_|MoreLVs], [_|MoreLVis], Digraph, Ev, Ps) :-
 project_to_query_related(IVs0, OldVs, NVs, NFs) :-
 	sort(IVs0, IVs),
 	rb_new(Vs0),
-	foldl(cp_to_vs, IVs, Vs0, AuxVs), 
+	foldl(cp_to_vs, IVs, Vs0, AuxVs),
 	rb_new(NFs0),
 	foldl(simplify_graph_node(OldVs, AuxVs), IVs, VFs, NFs0, NFs),
 	list_to_rbtree(VFs, NVs).
@@ -343,14 +343,14 @@ simplify_graph_node(OldVs, NVs, V, V-RemFs, NFs0, NFs) :-
 %
 % Two cases: first time factor comes up: all its vars must be in subgraph
 % second case: second time it comes up, it must be already in graph
-% 
+%
-% args: +Factor F, +current V (int), +rbtree with all Vs, 
+% args: +Factor F, +current V (int), +rbtree with all Vs,
 %       -Factors in new Graph, +factors in current graph, -rbtree of factors
 %
 %
 check_factor(V, NVs, F, NFs0, NFs, RemFs, NewRemFs) :-
 	F = f(IF, [V|More], _), !,
-	( 
+	(
 	  checklist(check_v(NVs), More)
 	->
 	  rb_insert(NFs0, IF, F, NFs),
@@ -361,7 +361,7 @@ check_factor(V, NVs, F, NFs0, NFs, RemFs, NewRemFs) :-
 	).
 check_factor(_V, _NVs, F, NFs, NFs, RemFs, NewRemFs) :-
 	F = f(Id, _, _),
-	( 
+	(
 	  rb_lookup(Id, F, NFs)
 	->
 	  NewRemFs = [F|RemFs]

packages/CLPBN/clpbn/vmap.yap

@@ -12,7 +12,7 @@
 :- use_module(library(maplist)).
 
 %
-% vmap: map V->I 
+% vmap: map V->I
 % contiguous Vs to contiguous integers
 %
 init_vmap(vmap(0,Empty)) :-

packages/CLPBN/examples/School/parlearn.yap

@@ -41,4 +41,4 @@ write_cpts([CPT|CPTs]) :-
 	matrix_to_list(CPT,L),
 	format('CPT=~w~n',[L]),
 	write_cpts(CPTs).
-	
+

packages/CLPBN/examples/School/parschema.pfl

@@ -55,7 +55,7 @@ professor_popularity(P,A) :- pop(P,A).
 course_difficulty(P,A) :- diff(P,A).
 
 student_intelligence(P,A) :- int(P,A).
-	
+
 course_rating(C,X) :- rat(C,X).
 
 registration_grade(R,A) :-

packages/CLPBN/examples/city.pfl

@@ -75,17 +75,17 @@ hair_color_table(
 /*               high  low  */
 /* dark     */ [ 0.05, 0.1,
 /* bright   */   0.95, 0.9 ]).
-    
+
 car_color_table(
 /*               dark bright */
 /* dark     */ [ 0.9, 0.2,
 /* bright   */   0.1, 0.8 ]).
-	
+
 height_table(
 /*               male female */
 /* tall     */ [ 0.6, 0.4,
 /* short    */   0.4, 0.6 ]).
-	
+
 shoe_size_table(
 /*               tall short */
 /* big      */ [ 0.9, 0.1,
@@ -99,7 +99,7 @@ descn_table(
 /*               car_color(P), hair_color(P), height(P), guilty(P) */
 /* fits     */ [ 0.99, 0.5,  0.23, 0.88, 0.41, 0.3,  0.76, 0.87,
 /* fits     */   0.44, 0.43, 0.29, 0.72, 0.23, 0.91, 0.95, 0.92,
-/* dont_fit */   0.01, 0.5,  0.77, 0.12, 0.59, 0.7,  0.24, 0.13, 
+/* dont_fit */   0.01, 0.5,  0.77, 0.12, 0.59, 0.7,  0.24, 0.13,
 /* dont_fit */   0.56, 0.57, 0.71, 0.28, 0.77, 0.09, 0.05, 0.08 ]).
 
 witness_table(

packages/CLPBN/horus/BayesBall.h

@@ -4,7 +4,6 @@
 #include <vector>
 #include <queue>
 #include <list>
-#include <map>
 
 #include "FactorGraph.h"
 #include "BayesBallGraph.h"
@@ -15,8 +14,8 @@ using namespace std;
 
 struct ScheduleInfo
 {
-  ScheduleInfo (BBNode* n, bool vfp, bool vfc) : 
+  ScheduleInfo (BBNode* n, bool vfp, bool vfc)
-      node(n), visitedFromParent(vfp), visitedFromChild(vfc) { }
+      : node(n), visitedFromParent(vfp), visitedFromChild(vfc) { }
 
   BBNode*  node;
   bool     visitedFromParent;
@@ -30,7 +29,7 @@ typedef queue<ScheduleInfo, list<ScheduleInfo>> Scheduling;
 class BayesBall
 {
   public:
-    BayesBall (FactorGraph& fg) 
+    BayesBall (FactorGraph& fg)
         : fg_(fg) , dag_(fg.getStructure())
     {
       dag_.clear();
@@ -63,7 +62,7 @@ inline void
 BayesBall::scheduleParents (const BBNode* n, Scheduling& sch) const
 {
   const vector<BBNode*>& ps = n->parents();
-  for (vector<BBNode*>::const_iterator it = ps.begin(); 
+  for (vector<BBNode*>::const_iterator it = ps.begin();
       it != ps.end(); ++it) {
     sch.push (ScheduleInfo (*it, false, true));
   }

packages/CLPBN/horus/BayesBallGraph.h

@@ -30,15 +30,15 @@ class BBNode : public Var
     void addChild (BBNode* c) { childs_.push_back (c); }
 
     bool isVisited (void) const { return visited_; }
- 
+
     void setAsVisited (void) { visited_ = true; }
 
     bool isMarkedOnTop (void) const { return markedOnTop_; }
- 
+
     void markOnTop (void) { markedOnTop_ = true; }
 
     bool isMarkedOnBottom (void) const { return markedOnBottom_; }
- 
+
     void markOnBottom (void) { markedOnBottom_ = true; }
 
     void clear (void) { visited_ = markedOnTop_ = markedOnBottom_ = false; }

packages/CLPBN/horus/BeliefProp.cpp

@@ -146,7 +146,7 @@ BeliefProp::getFactorJoint (
   if (Globals::logDomain) {
     Util::exp (jointDist);
   }
-  return jointDist; 
+  return jointDist;
 }
 
 
@@ -185,7 +185,7 @@ BeliefProp::runSolver (void)
   }
   if (Globals::verbosity > 0) {
     if (nIters_ < BpOptions::maxIter) {
-      cout << "Belief propagation converged in " ; 
+      cout << "Belief propagation converged in " ;
       cout << nIters_ << " iterations" << endl;
     } else {
       cout << "The maximum number of iterations was hit, terminating..." ;
@@ -459,7 +459,7 @@ void
 BeliefProp::printLinkInformation (void) const
 {
   for (size_t i = 0; i < links_.size(); i++) {
-    BpLink* l = links_[i]; 
+    BpLink* l = links_[i];
     cout << l->toString() << ":" << endl;
     cout << "    curr msg = " ;
     cout << l->message() << endl;

packages/CLPBN/horus/BeliefProp.h

@@ -17,7 +17,7 @@ class BpLink
 {
   public:
     BpLink (FacNode* fn, VarNode* vn)
-    { 
+    {
       fac_ = fn;
       var_ = vn;
       v1_.resize (vn->range(), LogAware::log (1.0 / vn->range()));
@@ -46,7 +46,7 @@ class BpLink
       residual_ = LogAware::getMaxNorm (v1_,v2_);
     }
 
-    virtual void updateMessage (void) 
+    virtual void updateMessage (void)
     {
       swap (currMsg_, nextMsg_);
     }

packages/CLPBN/horus/ConstraintTree.cpp

@@ -190,7 +190,7 @@ ConstraintTree::ConstraintTree (
 ConstraintTree::ConstraintTree (vector<vector<string>> names)
 {
   assert (names.empty() == false);
-  assert (names.front().empty() == false);  
+  assert (names.front().empty() == false);
   unsigned nrLvs = names[0].size();
   for (size_t i = 0; i < nrLvs; i++) {
     logVars_.push_back (LogVar (i));
@@ -201,7 +201,7 @@ ConstraintTree::ConstraintTree (vector<vector<string>> names)
     Tuple t;
     for (size_t j = 0; j < names[i].size(); j++) {
       assert (names[i].size() == nrLvs);
-      t.push_back (LiftedUtils::getSymbol (names[i][j]));	
+      t.push_back (LiftedUtils::getSymbol (names[i][j]));
     }
     addTuple (t);
   }
@@ -266,7 +266,7 @@ ConstraintTree::moveToTop (const LogVars& lvs)
     assert (pos != logVars_.size());
     for (size_t j = pos; j-- > i; ) {
       swapLogVar (logVars_[j]);
-    }                                 
+    }
   }
 }
 
@@ -318,7 +318,7 @@ ConstraintTree::join (ConstraintTree* ct, bool oneTwoOne)
   } else {
     moveToTop (intersect.elements());
     ct->moveToTop (intersect.elements());
-    
+
     Tuples tuples;
     CTNodes appendNodes;
     getTuples (ct->root(), Tuples(), intersect.size(),
@@ -455,7 +455,7 @@ ConstraintTree::singletons (void)
     if (isSingleton (logVars_[i])) {
       singletons.insert (logVars_[i]);
     }
-  }  
+  }
   return singletons;
 }
 
@@ -585,13 +585,13 @@ ConstraintTree::isCountNormalized (const LogVarSet& Ys)
     if (countTuples (*it) != count) {
       return false;
     }
-  }  
+  }
   return true;
 }
 
 
 
-unsigned 
+unsigned
 ConstraintTree::getConditionalCount (const LogVarSet& Ys)
 {
   assert (isCountNormalized (Ys));
@@ -792,7 +792,7 @@ ConstraintTree::jointCountNormalize (
   }
 
   for (size_t i = 0; i < normCts1.size(); i++) {
-    unsigned j; 
+    unsigned j;
     for (j = 0; counts1[i] + counts2[j] != N; j++) ;
     // cout << "joint-count(" << counts1[i] ;
     // cout <<  "," << counts2[j] << ")" << endl;
@@ -947,7 +947,7 @@ ConstraintTree::getNodesBelow (CTNode* fromHere) const
 
 
 CTNodes
-ConstraintTree::getNodesAtLevel (unsigned level) const 
+ConstraintTree::getNodesAtLevel (unsigned level) const
 {
   assert (level <= logVars_.size());
   if (level == 0) {
@@ -1057,7 +1057,7 @@ ConstraintTree::join (
     } else {
       tupleFounded = join (*it, tuple, currIdx + 1, appendNode);
     }
-  } 
+  }
   return tupleFounded;
 }
 
@@ -1065,7 +1065,7 @@ ConstraintTree::join (
 
 void
 ConstraintTree::getTuples (
-    CTNode* n, 
+    CTNode* n,
     Tuples currTuples,
     unsigned stopLevel,
     Tuples& tuplesCollected,
@@ -1147,7 +1147,7 @@ ConstraintTree::split (
     CTNode* n2,
     CTChilds& commChilds,
     CTChilds& exclChilds,
-    unsigned stopLevel) 
+    unsigned stopLevel)
 {
   CTChilds& childs1 = n1->childs();
   for (CTChilds::const_iterator chIt1 = childs1.begin();

packages/CLPBN/horus/CountingBp.cpp

@@ -47,8 +47,7 @@ CountingBp::printSolverFlags (void) const
   ss << ",max_iter=" << BpOptions::maxIter;
   ss << ",accuracy=" << BpOptions::accuracy;
   ss << ",log_domain=" << Util::toString (Globals::logDomain);
-  ss << ",chkif=" << 
+  ss << ",chkif=" << Util::toString (CountingBp::checkForIdenticalFactors);
-      Util::toString (CountingBp::checkForIdenticalFactors);
   ss << "]" ;
   cout << ss.str() << endl;
 }
@@ -139,7 +138,7 @@ CountingBp::setInitialColors (void)
     VarColorMap::iterator it = colorMap.find (range);
     if (it == colorMap.end()) {
       it = colorMap.insert (make_pair (
-          range, Colors (range + 1, -1))).first; 
+          range, Colors (range + 1, -1))).first;
     }
     unsigned idx = varNodes[i]->hasEvidence()
                  ? varNodes[i]->getEvidence()

packages/CLPBN/horus/ElimGraph.cpp

@@ -28,7 +28,7 @@ ElimGraph::ElimGraph (const vector<Factor*>& factors)
         }
         if (neighbors (n1, n2) == false) {
           addEdge (n1, n2);
-        } 
+        }
       }
     }
     if (vids.size() == 1) {
@@ -86,7 +86,7 @@ ElimGraph::print (void) const
       cout << "  " << neighs[j]->label();
     }
     cout << endl;
-  }  
+  }
 }
 
 
@@ -142,7 +142,7 @@ ElimGraph::getEliminationOrder (
     Factors::const_iterator first = factors.begin();
     Factors::const_iterator end   = factors.end();
     for (; first != end; ++first) {
-      Util::addToVector (allVids, (*first)->arguments());      
+      Util::addToVector (allVids, (*first)->arguments());
     }
     TinySet<VarId> elimOrder (allVids);
     elimOrder -= TinySet<VarId> (excludedVids);

packages/CLPBN/horus/Factor.h

@@ -143,7 +143,7 @@ class TFactor
       assert (idx != args_.size());
       assert (obsIdx < ranges_[idx]);
       Params newps;
-      newps.reserve (params_.size() / ranges_[idx]); 
+      newps.reserve (params_.size() / ranges_[idx]);
       Indexer indexer (ranges_);
       for (unsigned i = 0; i < obsIdx; ++i) {
         indexer.incrementDimension (idx);
@@ -285,7 +285,7 @@ class Factor : public TFactor<VarId>
     void sumOutLastVariable (void);
 
     void sumOutArgs (const vector<bool>& mask);
-   
+
     void clone (const Factor& f);
 
 };

packages/CLPBN/horus/FactorGraph.cpp

@@ -171,7 +171,7 @@ FactorGraph::readFromLibDaiFormat (const char* fileName)
     std::reverse (vids.begin(), vids.end());
     Factor f (vids, ranges, params);
     std::reverse (vids.begin(), vids.end());
-    f.reorderArguments (vids); 
+    f.reorderArguments (vids);
     addFactor (f);
   }
   is.close();
@@ -188,7 +188,7 @@ FactorGraph::addFactor (const Factor& factor)
   for (size_t i = 0; i < vids.size(); i++) {
     VarMap::const_iterator it = varMap_.find (vids[i]);
     if (it != varMap_.end()) {
-      addEdge (it->second, fn);      
+      addEdge (it->second, fn);
     } else {
       VarNode* vn = new VarNode (vids[i], fn->factor().range (i));
       addVarNode (vn);
@@ -293,7 +293,7 @@ FactorGraph::exportToGraphViz (const char* fileName) const
   }
   for (size_t i = 0; i < facNodes_.size(); i++) {
     out << '"' << facNodes_[i]->getLabel() << '"' ;
-    out << " [label=\"" << facNodes_[i]->getLabel(); 
+    out << " [label=\"" << facNodes_[i]->getLabel();
     out << "\"" << ", shape=box]" << endl;
   }
   for (size_t i = 0; i < facNodes_.size(); i++) {

packages/CLPBN/horus/FactorGraph.h

@@ -76,7 +76,7 @@ class FactorGraph
     const FacNodes& facNodes (void) const { return facNodes_; }
 
     void setFactorsAsBayesian (void) { bayesFactors_ = true; }
- 
+
     bool bayesianFactors (void) const { return bayesFactors_; }
 
     size_t nrVarNodes (void) const { return varNodes_.size(); }

packages/CLPBN/horus/Histogram.cpp

@@ -59,10 +59,10 @@ HistogramSet::reset (void)
 
 
 
-vector<Histogram> 
+vector<Histogram>
 HistogramSet::getHistograms (unsigned N, unsigned R)
 {
-  HistogramSet hs (N, R);  
+  HistogramSet hs (N, R);
   unsigned H = hs.nrHistograms();
   vector<Histogram> histograms;
   histograms.reserve (H);
@@ -135,7 +135,7 @@ HistogramSet::maxCount (size_t idx) const
   }
   return size_ - sum;
 }
-  
+
 
 
 void

packages/CLPBN/horus/HorusCli.cpp

@@ -77,7 +77,7 @@ readFactorGraph (FactorGraph& fg, const char* s)
   } else if (extension == "fg") {
     fg.readFromLibDaiFormat (fileName.c_str());
   } else {
-    cerr << "Error: the probabilistic graphical model must be " ; 
+    cerr << "Error: the probabilistic graphical model must be " ;
     cerr << "defined either in a UAI or libDAI file." << endl;
     exit (EXIT_FAILURE);
   }

packages/CLPBN/horus/HorusYap.cpp

@@ -57,7 +57,7 @@ createLiftedNetwork (void)
   }
 
   ParfactorList* pfList = new ParfactorList (parfactors);
-  
+
   if (Globals::verbosity > 2) {
     Util::printHeader ("SHATTERED PARFACTORS");
     pfList->print();
@@ -91,7 +91,7 @@ createGroundNetwork (void)
     // read the ranges
     Ranges ranges = readUnsignedList (YAP_ArgOfTerm (2, factor));
     // read the parameters
-    Params params = readParameters (YAP_ArgOfTerm (3, factor)); 
+    Params params = readParameters (YAP_ArgOfTerm (3, factor));
     // read dist id
     unsigned distId = (unsigned) YAP_IntOfTerm (YAP_ArgOfTerm (4, factor));
     fg->addFactor (Factor (varIds, ranges, params, distId));
@@ -126,7 +126,7 @@ runLiftedSolver (void)
   LiftedNetwork* network = (LiftedNetwork*) YAP_IntOfTerm (YAP_ARG1);
   ParfactorList pfListCopy (*network->first);
   LiftedOperations::absorveEvidence (pfListCopy, *network->second);
-  
+
   LiftedSolver* solver = 0;
   switch (Globals::liftedSolver) {
     case LiftedSolverType::LVE:  solver = new LiftedVe (pfListCopy); break;
@@ -181,7 +181,7 @@ int
 runGroundSolver (void)
 {
   FactorGraph* fg = (FactorGraph*) YAP_IntOfTerm (YAP_ARG1);
-  
+
   vector<VarIds> tasks;
   YAP_Term taskList = YAP_ARG2;
   while (taskList != YAP_TermNil()) {
@@ -407,7 +407,7 @@ readParfactor (YAP_Term pfTerm)
   }
 
   // read the parameters
-  const Params& params = readParameters (YAP_ArgOfTerm (4, pfTerm)); 
+  const Params& params = readParameters (YAP_ArgOfTerm (4, pfTerm));
 
   // read the constraint
   Tuples tuples;
@@ -478,7 +478,7 @@ readLiftedEvidence (
       obsFormulas.push_back (ObservedFormula (functor, evidence, args));
     }
     observedList = YAP_TailOfTerm (observedList);
-  } 
+  }
 }
 
 

packages/CLPBN/horus/Indexer.h

@@ -167,7 +167,7 @@ class MapIndexer
         }
       }
     }
-    
+
    template <typename T>
    MapIndexer (
         const vector<T>& allArgs,

packages/CLPBN/horus/LiftedKc.cpp

@@ -128,7 +128,7 @@ double
 LeafNode::weight (void) const
 {
   assert (clause_->isUnit());
-  if (clause_->posCountedLogVars().empty() == false 
+  if (clause_->posCountedLogVars().empty() == false
     || clause_->negCountedLogVars().empty() == false) {
     if (SetOrNode::isSet() == false) {
       // return a NaN if we have a SetOrNode

packages/CLPBN/horus/LiftedOperations.cpp

@@ -60,7 +60,7 @@ LiftedOperations::runWeakBayesBall (
     const Grounds& query)
 {
   queue<PrvGroup> todo; // groups to process
-  set<PrvGroup> done;   // processed or in queue 
+  set<PrvGroup> done;   // processed or in queue
   for (size_t i = 0; i < query.size(); i++) {
     ParfactorList::iterator it = pfList.begin();
     while (it != pfList.end()) {
@@ -225,7 +225,7 @@ LiftedOperations::absorve (
           absorvedPfs.push_back (0);
         }
         break;
-      } 
+      }
 
       g->constr()->moveToTop (formulas[i].logVars());
       std::pair<ConstraintTree*, ConstraintTree*> res;

packages/CLPBN/horus/LiftedOperations.h

@@ -10,7 +10,7 @@ class LiftedOperations
         ParfactorList& pfList, const Grounds& query);
 
     static void runWeakBayesBall (
-        ParfactorList& pfList, const Grounds&); 
+        ParfactorList& pfList, const Grounds&);
 
     static void absorveEvidence (
         ParfactorList& pfList, ObservedFormulas& obsFormulas);

packages/CLPBN/horus/LiftedUtils.cpp

@@ -61,7 +61,7 @@ ostream& operator<< (ostream &os, const Symbol& s)
 ostream& operator<< (ostream &os, const LogVar& X)
 {
   const string labels[] = {
-      "A", "B", "C", "D", "E", "F", 
+      "A", "B", "C", "D", "E", "F",
       "G", "H", "I", "J", "K", "M"  };
   (X >= 12) ? os << "X_" << X.id_ : os << labels[X];
   return os;

packages/CLPBN/horus/LiftedUtils.h

@@ -51,7 +51,7 @@ class LogVar
     }
 
     bool valid (void) const
-    { 
+    {
       return id_ != Util::maxUnsigned();
     }
 
@@ -145,7 +145,7 @@ class Substitution
       return X;
     }
 
-    bool containsReplacementFor (LogVar X) const 
+    bool containsReplacementFor (LogVar X) const
     {
       return Util::contains (subs_, X);
     }

packages/CLPBN/horus/LiftedVe.cpp

@@ -133,7 +133,7 @@ ProductOperator::toString (void)
   stringstream ss;
   ss << "just multiplicate " ;
   ss << (*g1_)->getAllGroups();
-  ss << " x " ; 
+  ss << " x " ;
   ss << (*g2_)->getAllGroups();
   ss << " [cost=" << std::exp (getLogCost()) << "]" << endl;
   return ss.str();
@@ -155,7 +155,7 @@ ProductOperator::validOp (Parfactor* g1, Parfactor* g2)
       }
       size_t idx1 = g1->indexOfGroup (intersect[i]);
       size_t idx2 = g2->indexOfGroup (intersect[i]);
-      if (g1->range (idx1) != g2->range (idx2)) { 
+      if (g1->range (idx1) != g2->range (idx2)) {
         return false;
       }
     }
@@ -713,7 +713,7 @@ LiftedVe::getBestOperation (const Grounds& query)
     if ((bestOp == 0) || (cost < bestCost)) {
       bestOp   = validOps[i];
       bestCost = cost;
-    } 
+    }
   }
   if (bestCost > largestCost_) {
     largestCost_ = bestCost;

packages/CLPBN/horus/LiftedVe.h

@@ -9,7 +9,7 @@ class LiftedOperator
 {
   public:
     virtual ~LiftedOperator (void) { }
-  
+
     virtual double getLogCost (void) = 0;
 
     virtual void apply (void) = 0;
@@ -55,7 +55,7 @@ class ProductOperator : public LiftedOperator
 class SumOutOperator : public LiftedOperator
 {
   public:
-    SumOutOperator (PrvGroup group, ParfactorList& pfList) 
+    SumOutOperator (PrvGroup group, ParfactorList& pfList)
         : group_(group), pfList_(pfList) { }
 
     double getLogCost (void);

packages/CLPBN/horus/LiftedWCNF.cpp

@@ -195,7 +195,7 @@ Clause::isPositiveCountedLogVar (LogVar X) const
   assert (constr_.logVarSet().contains (X));
   return posCountedLvs_.contains (X);
 }
-  
+
 
 
 bool
@@ -235,7 +235,7 @@ Clause::ipgCandidates (void) const
   LogVarSet allLvs = constr_.logVarSet();
   allLvs -= ipgLvs_;
   allLvs -= posCountedLvs_;
-  allLvs -= negCountedLvs_;  
+  allLvs -= negCountedLvs_;
   for (size_t i = 0; i < allLvs.size(); i++) {
     bool valid = true;
     for (size_t j = 0; j < literals_.size(); j++) {
@@ -262,7 +262,7 @@ Clause::logVarTypes (size_t litIdx) const
     if (posCountedLvs_.contains (lvs[i])) {
       types.push_back (LogVarType::POS_LV);
     } else if (negCountedLvs_.contains (lvs[i])) {
-      types.push_back (LogVarType::NEG_LV);    
+      types.push_back (LogVarType::NEG_LV);
     } else {
       types.push_back (LogVarType::FULL_LV);
     }
@@ -391,7 +391,7 @@ LiftedWCNF::LiftedWCNF (const ParfactorList& pfList)
 {
   addIndicatorClauses (pfList);
   addParameterClauses (pfList);
-  
+
   /*
   // INCLUSION-EXCLUSION TEST
   clauses_.clear();
@@ -579,7 +579,7 @@ LiftedWCNF::addParameterClauses (const ParfactorList& pfList)
       // ¬θxi|u1,...,un v λu2           -> tempClause
       double posWeight = (**it)[indexer];
       addWeight (paramVarLid, posWeight, LogAware::one());
-      
+
       Clause* clause1 = new Clause (*(*it)->constr());
 
       for (unsigned i = 0; i < groups.size(); i++) {
@@ -593,7 +593,7 @@ LiftedWCNF::addParameterClauses (const ParfactorList& pfList)
         tempClause->addLiteralComplemented (Literal (
             paramVarLid, (*it)->constr()->logVars()));
         tempClause->addLiteral (Literal (lid, (*it)->argument(i).logVars()));
-        clauses_.push_back (tempClause);        
+        clauses_.push_back (tempClause);
       }
       clause1->addLiteral (Literal (paramVarLid, (*it)->constr()->logVars()));
       clauses_.push_back (clause1);

packages/CLPBN/horus/Parfactor.cpp

@@ -8,7 +8,7 @@
 
 Parfactor::Parfactor (
     const ProbFormulas& formulas,
-    const Params& params, 
+    const Params& params,
     const Tuples& tuples,
     unsigned distId)
 {
@@ -221,7 +221,7 @@ Parfactor::countConvert (LogVar X)
   assert (constr_->isCountNormalized (X));
   assert (constr_->getConditionalCount (X) > 1);
   assert (canCountConvert (X));
- 
+
   unsigned N = constr_->getConditionalCount (X);
   unsigned R = ranges_[fIdx];
   unsigned H = HistogramSet::nrHistograms (N, R);
@@ -336,7 +336,7 @@ Parfactor::fullExpand (LogVar X)
     sumIndexes.push_back (HistogramSet::findIndex (hist, originHists));
     ++ indexer;
   }
-  
+
   expandPotential (fIdx, std::pow (R, N), sumIndexes);
 
   ProbFormula f = args_[fIdx];
@@ -360,7 +360,7 @@ Parfactor::reorderAccordingGrounds (const Grounds& grounds)
   ProbFormulas newFormulas;
   for (size_t i = 0; i < grounds.size(); i++) {
     for (size_t j = 0; j < args_.size(); j++) {
-      if (grounds[i].functor() == args_[j].functor() && 
+      if (grounds[i].functor() == args_[j].functor() &&
           grounds[i].arity()   == args_[j].arity()) {
         constr_->moveToTop (args_[j].logVars());
         if (constr_->containsTuple (grounds[i].args())) {
@@ -424,7 +424,7 @@ Parfactor::indexOfGround (const Ground& ground) const
 {
   size_t idx = args_.size();
   for (size_t i = 0; i < args_.size(); i++) {
-    if (args_[i].functor() == ground.functor() && 
+    if (args_[i].functor() == ground.functor() &&
         args_[i].arity()   == ground.arity()) {
       constr_->moveToTop (args_[i].logVars());
       if (constr_->containsTuple (ground.args())) {
@@ -806,7 +806,7 @@ Parfactor::simplifyParfactor (size_t fIdx1, size_t fIdx2)
   while (indexer.valid()) {
     if (indexer[fIdx1] == indexer[fIdx2]) {
       params_.push_back (backup[indexer]);
-    }     
+    }
     ++ indexer;
   }
   for (size_t i = 0; i < args_[fIdx2].logVars().size(); i++) {
@@ -829,7 +829,7 @@ Parfactor::getAlignLogVars (Parfactor* g1, Parfactor* g2)
   TinySet<size_t> matchedI;
   TinySet<size_t> matchedJ;
   ProbFormulas& formulas1 = g1->arguments();
-  ProbFormulas& formulas2 = g2->arguments(); 
+  ProbFormulas& formulas2 = g2->arguments();
   for (size_t i = 0; i < formulas1.size(); i++) {
     for (size_t j = 0; j < formulas2.size(); j++) {
       if (formulas1[i].group() == formulas2[j].group() &&
@@ -882,7 +882,7 @@ Parfactor::alignLogicalVars (Parfactor* g1, Parfactor* g2)
   LogVar freeLogVar (0);
   Substitution theta1, theta2;
   for (size_t i = 0; i < alignLvs1.size(); i++) {
-    bool b1 = theta1.containsReplacementFor (alignLvs1[i]); 
+    bool b1 = theta1.containsReplacementFor (alignLvs1[i]);
     bool b2 = theta2.containsReplacementFor (alignLvs2[i]);
     if (b1 == false && b2 == false) {
       theta1.add (alignLvs1[i], freeLogVar);
@@ -911,11 +911,11 @@ Parfactor::alignLogicalVars (Parfactor* g1, Parfactor* g2)
   }
 
   // handle this type of situation:
-  // g1 = p(X), q(X) ;  X    in {(p1),(p2)} 
+  // g1 = p(X), q(X) ;  X    in {(p1),(p2)}
   // g2 = p(X), q(Y) ; (X,Y) in {(p1,p2),(p2,p1)}
   LogVars discardedLvs1 = theta1.getDiscardedLogVars();
   for (size_t i = 0; i < discardedLvs1.size(); i++) {
-    if (g1->constr()->isSingleton (discardedLvs1[i]) && 
+    if (g1->constr()->isSingleton (discardedLvs1[i]) &&
         g1->nrFormulas (discardedLvs1[i]) == 1) {
       g1->constr()->remove (discardedLvs1[i]);
     } else {

packages/CLPBN/horus/Parfactor.h

@@ -115,7 +115,7 @@ class Parfactor : public TFactor<ProbFormula>
     static void alignLogicalVars (Parfactor*, Parfactor*);
 
     ConstraintTree*  constr_;
- 
+
 };
 
 

packages/CLPBN/horus/ParfactorList.cpp

@@ -9,7 +9,7 @@ ParfactorList::ParfactorList (const ParfactorList& pfList)
   while (it != pfList.end()) {
     addShattered (new Parfactor (**it));
     ++ it;
-  } 
+  }
 }
 
 
@@ -74,7 +74,7 @@ ParfactorList::insertShattered (
 
 
 list<Parfactor*>::iterator
-ParfactorList::remove (list<Parfactor*>::iterator it) 
+ParfactorList::remove (list<Parfactor*>::iterator it)
 {
   return pfList_.erase (it);
 }
@@ -418,7 +418,7 @@ ParfactorList::shatter (Parfactor* g1, Parfactor* g2)
       if (formulas1[i].sameSkeletonAs (formulas2[j])) {
         std::pair<Parfactors, Parfactors> res;
         res = shatter (i, g1, j, g2);
-        if (res.first.empty()  == false || 
+        if (res.first.empty()  == false ||
             res.second.empty() == false) {
           return res;
         }
@@ -470,7 +470,7 @@ ParfactorList::shatter (
   ConstraintTree* exclCt1 = split1.second;
 
   if (commCt1->empty()) {
-    // disjoint 
+    // disjoint
     delete commCt1;
     delete exclCt1;
     return { };
@@ -549,11 +549,11 @@ ParfactorList::shatter (
       Parfactor* newPf = new Parfactor (g, cts[i]);
       if (cts[i]->nrLogVars() == g->constr()->nrLogVars() + 1) {
         newPf->expand (f.countedLogVar(), X_new1, X_new2);
-        assert (g->constr()->getConditionalCount (f.countedLogVar()) == 
+        assert (g->constr()->getConditionalCount (f.countedLogVar()) ==
             cts[i]->getConditionalCount (X_new1) +
             cts[i]->getConditionalCount (X_new2));
       } else {
-        assert (g->constr()->getConditionalCount (f.countedLogVar()) == 
+        assert (g->constr()->getConditionalCount (f.countedLogVar()) ==
             cts[i]->getConditionalCount (f.countedLogVar()));
       }
       newPf->setNewGroups();

packages/CLPBN/horus/ProbFormula.cpp

@@ -61,7 +61,7 @@ ProbFormula::countedLogVar (void) const
 }
 
 
-    
+
 void
 ProbFormula::setCountedLogVar (LogVar lv)
 {
@@ -92,9 +92,10 @@ ProbFormula::rename (LogVar oldName, LogVar newName)
 }
 
 
+
 bool operator== (const ProbFormula& f1, const ProbFormula& f2)
-{ 
+{
-  return f1.group_   == f2.group_ && 
+  return f1.group_   == f2.group_ &&
          f1.logVars_ == f2.logVars_;
 }
 

packages/CLPBN/horus/ProbFormula.h

@@ -12,11 +12,11 @@ typedef unsigned long PrvGroup;
 class ProbFormula
 {
   public:
-    ProbFormula (Symbol f, const LogVars& lvs, unsigned range) 
+    ProbFormula (Symbol f, const LogVars& lvs, unsigned range)
         : functor_(f), logVars_(lvs), range_(range),
           countedLogVar_(), group_(numeric_limits<PrvGroup>::max()) { }
 
-    ProbFormula (Symbol f, unsigned r) 
+    ProbFormula (Symbol f, unsigned r)
         : functor_(f), range_(r), group_(numeric_limits<PrvGroup>::max()) { }
 
     Symbol functor (void) const { return functor_; }
@@ -76,10 +76,10 @@ typedef vector<ProbFormula> ProbFormulas;
 class ObservedFormula
 {
   public:
-    ObservedFormula (Symbol f, unsigned a, unsigned ev) 
+    ObservedFormula (Symbol f, unsigned a, unsigned ev)
         : functor_(f), arity_(a), evidence_(ev), constr_(a) { }
 
-    ObservedFormula (Symbol f, unsigned ev, const Tuple& tuple) 
+    ObservedFormula (Symbol f, unsigned ev, const Tuple& tuple)
         : functor_(f), arity_(tuple.size()), evidence_(ev), constr_(arity_)
     {
       constr_.addTuple (tuple);

packages/CLPBN/horus/TinySet.h

@@ -21,7 +21,7 @@ class TinySet
     TinySet (const Compare& cmp = Compare())
         : vec_(), cmp_(cmp) { }
 
-    TinySet (const T& t, const Compare& cmp = Compare()) 
+    TinySet (const T& t, const Compare& cmp = Compare())
         : vec_(1, t), cmp_(cmp) { }
 
     TinySet (const vector<T>& elements, const Compare& cmp = Compare())
@@ -153,12 +153,12 @@ class TinySet
     {
       return vec_[i];
     }
-    
+
     T& operator[] (typename vector<T>::size_type i)
     {
       return vec_[i];
     }
-  
+
     T front (void) const
     {
       return vec_.front();
@@ -219,7 +219,7 @@ class TinySet
       return ! (s1.vec_ == s2.vec_);
     }
 
-    friend std::ostream& operator << (std::ostream& out, const TinySet& s)
+    friend std::ostream& operator<< (std::ostream& out, const TinySet& s)
     {
       out << "{" ;
       typename vector<T>::size_type i;

packages/CLPBN/horus/Util.cpp

@@ -140,7 +140,7 @@ nrDigits (int num)
 {
   unsigned count = 1;
   while (num >= 10) {
-    num /= 10; 
+    num /= 10;
     count ++;
   }
   return count;
@@ -166,7 +166,7 @@ parametersToString (const Params& v, unsigned precision)
 {
   stringstream ss;
   ss.precision (precision);
-  ss << "[" ; 
+  ss << "[" ;
   for (size_t i = 0; i < v.size(); i++) {
     if (i != 0) ss << ", " ;
     ss << v[i];

packages/CLPBN/horus/Util.h

@@ -373,8 +373,8 @@ void operator^=(std::vector<T>& v, int iexp)
 
 
 
-template <typename T> 
+template <typename T>
-std::ostream& operator << (std::ostream& os, const vector<T>& v)
+std::ostream& operator<< (std::ostream& os, const vector<T>& v)
 {
   os << "[" ;
   os << Util::elementsToString (v, ", ");

packages/CLPBN/horus/Var.cpp

@@ -49,7 +49,7 @@ Var::isValidState (const string& stateName)
 
 
 void
-Var::setEvidence (int ev) 
+Var::setEvidence (int ev)
 {
   assert (ev < (int) range_);
   evidence_ = ev;
@@ -58,8 +58,8 @@ Var::setEvidence (int ev)
 
 
 void
-Var::setEvidence (const string& ev) 
+Var::setEvidence (const string& ev)
-{ 
+{
   States states = Var::getVarInfo (varId_).states;
   for (size_t i = 0; i < states.size(); i++) {
     if (states[i] == ev) {

packages/CLPBN/horus/VarElim.cpp

@@ -70,7 +70,7 @@ VarElim::createFactorList (void)
     factorList_.push_back (new Factor (facNodes[i]->factor()));
     const VarNodes& neighs = facNodes[i]->neighbors();
     for (size_t j = 0; j < neighs.size(); j++) {
-      unordered_map<VarId, vector<size_t>>::iterator it 
+      unordered_map<VarId, vector<size_t>>::iterator it
           = varFactors_.find (neighs[j]->varId());
       if (it == varFactors_.end()) {
         it = varFactors_.insert (make_pair (

packages/CLPBN/horus/WeightedBp.cpp

@@ -132,7 +132,7 @@ WeightedBp::maxResidualSchedule (void)
       }
     }
     // in counting bp, the message that a variable X sends to
-    // to a factor F depends on the message that F sent to the X 
+    // to a factor F depends on the message that F sent to the X
     const BpLinks& links = ninf(link->facNode())->getLinks();
     for (size_t i = 0; i < links.size(); i++) {
       if (links[i]->varNode() != link->varNode()) {
@@ -258,7 +258,7 @@ WeightedBp::getVarToFactorMsg (const BpLink* _link) const
       if ( ! (l->facNode() == dst && l->index() == link->index())) {
         msg *= l->powMessage();
         if (Constants::SHOW_BP_CALCS) {
-          cout << " x " << l->nextMessage() << "^" << link->weight(); 
+          cout << " x " << l->nextMessage() << "^" << link->weight();
         }
       }
     }

packages/CLPBN/horus/WeightedBp.h

@@ -6,7 +6,7 @@
 class WeightedLink : public BpLink
 {
   public:
-    WeightedLink (FacNode* fn, VarNode* vn, size_t idx, unsigned weight) 
+    WeightedLink (FacNode* fn, VarNode* vn, size_t idx, unsigned weight)
         : BpLink (fn, vn), index_(idx), weight_(weight),
           pwdMsg_(vn->range(), LogAware::one()) { }
 
@@ -16,7 +16,7 @@ class WeightedLink : public BpLink
 
     const Params& powMessage (void) const { return pwdMsg_; }
 
-    void updateMessage (void) 
+    void updateMessage (void)
     {
       pwdMsg_ = *nextMsg_;
       swap (currMsg_, nextMsg_);

packages/CLPBN/learning/aleph_params.yap

@@ -50,7 +50,7 @@
 %
 % Tell Aleph not to use default solver during saturation
 %
-% all work will be done by EM 
+% all work will be done by EM
 %:- set_clpbn_flag(solver,none).
 
 %
@@ -123,7 +123,7 @@ add_new_clause(_,(H :- B),_,_) :-
 	  asserta(user:(H :- IB))
 	),
 	user:setting(verbosity,V),
-	( V >= 1 -> 
+	( V >= 1 ->
 	  user:p_message('CLP(BN) Theory'),
 	  functor(H,N,Ar), listing(user:N/Ar)
 	;
@@ -138,7 +138,7 @@ update_tabled_theory(H) :-
 	clpbn_tabled_assertz((user:(H:-NB))),
 	fail.
 update_tabled_theory(_).
-	
+
 update_theory(H) :-
 	clause(user:H,B,Ref),
 	add_correct_cpt(B,NB),
@@ -161,7 +161,7 @@ correct_tab(p(Vs,_,Ps),K,p(Vs,TDist,Ps)) :-
 	get_dist_key(Id, K),
 	get_dist_params(Id, TDist).
 
-% user-defined cost function, Aleph knows about this (and only about this). 
+% user-defined cost function, Aleph knows about this (and only about this).
 user:cost((H :- B),Inf,Score) :-
 	domain(H, K, V, D),
 	check_info(Inf),
@@ -261,7 +261,7 @@ rewrite_body((A,B), (user:NA,NB), [V|Vs], [D|Ds], Tail) :-
 	rewrite_body(B, NB, Vs, Ds, Tail).
 rewrite_body((A,B), (user:A,NB), Vs, Ds, Tail) :- !,
 	rewrite_body(B,NB, Vs, Ds, Tail).
-rewrite_body(A,(user:NA,Tail), [V], [D], Tail) :- 
+rewrite_body(A,(user:NA,Tail), [V], [D], Tail) :-
 	rewrite_goal(A, V, D, NA), !.
 rewrite_body(A, (user:A,Tail), [], [], Tail).
 

packages/CLPBN/learning/em.yap

@@ -33,7 +33,7 @@
 		[generate_network/5,
 		 f/3
 		]).
-	
+
 :- use_module(library('clpbn/utils'),
 		[check_for_hidden_vars/3,
 		 sort_vars_by_key/3
@@ -46,7 +46,7 @@
 		 compute_likelihood/3,
 		 soften_sample/2
 		]).
-	
+
 :- use_module(library(bhash),
 		[b_hash_new/1,
 		 b_hash_lookup/3,
@@ -198,7 +198,7 @@ ltables([Id-T|Tables], [Key-LTable|FTables]) :-
 
 
 generate_dists(Factors, EList, AllDists, AllInfo, MargVars) :-
-	b_hash_new(Ev0), 
+	b_hash_new(Ev0),
 	foldl(elist_to_hash, EList, Ev0, Ev),
 	maplist(process_factor(Ev), Factors, Dists0),
 	sort(Dists0, Dists1),
@@ -220,7 +220,7 @@ fetch_evidence(_Ev, K, Ns, NonEvs, [K|NonEvs]) :-
 
 domain_to_number(_, I0, I0, I) :-
 	I is I0+1.
-	
+
 
 % collect the different dists we are going to learn next.
 different_dists(AllVars, AllDists, AllInfo, MargVars) :-
@@ -232,9 +232,9 @@ different_dists(AllVars, AllDists, AllInfo, MargVars) :-
 %
 % V -> to Id defining V. We get:
 % the random variables that are parents
-% the cases that can happen, eg if we have A <- B, C 
+% the cases that can happen, eg if we have A <- B, C
 % A and B are boolean w/o evidence, and C is f, the cases could be
-% [0,0,1], [0,1,1], [1,0,0], [1,1,0], 
+% [0,0,1], [0,1,1], [1,0,0], [1,1,0],
 % Hiddens will be C
 %
 all_dists([], _, []).

packages/CLPBN/learning/mle.yap

@@ -57,7 +57,7 @@ mk_sample(AllVars, SortedSample) :-
 	msort(Sample, SortedSample).
 
 %
-% assumes we have full data, meaning evidence for every variable 
+% assumes we have full data, meaning evidence for every variable
 %
 add2sample([],  []).
 add2sample([V|Vs],[val(Id,[Ev|EParents])|Vals]) :-

packages/CLPBN/pfl.yap

@@ -50,7 +50,7 @@
 		 append/3,
 		 member/2
 		]).
-	 
+
 :- dynamic factor/6, skolem_in/2, skolem/2, preprocess/3, evidence/2, id/1.
 
 user:term_expansion( bayes((Formula ; Phi ; Constraints)), pfl:factor(bayes,Id,FList,FV,Phi,Constraints)) :-
@@ -178,7 +178,7 @@ add_evidence(Sk,Var) :-
 	clpbn:put_atts(_V,[key(Sk),evidence(E)]).
 
 
-%% get_pfl_cpt(Id, Keys, Ev, NewKeys, Out) :- 
+%% get_pfl_cpt(Id, Keys, Ev, NewKeys, Out) :-
 %% 	factor(_Type,Id,[Key|_],_FV,avg,_Constraints), !,
 %% 	Keys = [Key|Parents],
 %% 	writeln(Key:Parents),