Whitespace clean

packages/CLPBN/examples/HMMer/fasta.yap

@@ -5,7 +5,10 @@
 % support for a single sequence.
 %
 
-:- module(fasta, [fa2atoms/2,fa2atoms/3]).
+:- module(fasta,
+		[fa2atoms/2,
+		 fa2atoms/3
+		]).
 
 fa2atoms(F, L) :-
 	fa2atoms(F, L, []).
@@ -25,8 +28,8 @@ read_chars(10,S) --> !,
 read_chars(C,S) -->
 	[AC],
 	{
-	 cvt_c(C,AC),
-	 get0(S,MC)
+	  cvt_c(C,AC),
+	  get0(S,MC)
 	},
 	read_chars(MC, S).
 
@@ -44,4 +47,3 @@ skip_header(_,S) :-
 	skip_header(C,S).
 
 
-	

packages/CLPBN/examples/HMMer/globin.yap

@@ -32,9 +32,9 @@ g_f_cpt(-8455,1.0,0.00284964910984409).
 
 %Null state emission CPT.
 nule_cpt(
-     e(595,-1558,85,338,-294,453,-1158,197,249,902,-1085,-142,-21,-313,45,531,201,384,-1998,-644),
-     0.05,
-     e(0.0755236292781413,0.0169810785568618,0.0530343870684108,0.0632001549226403,0.0407818746669505,0.0684441906545919,0.0224066674892351,0.0573156092864189,0.0594191552528466,0.093432734688318,0.023569613397956,0.0453130969133667,0.0492774668469685,0.0402483068810561,0.051584158965068,0.0722465198961763,0.0574747424017338,0.0652477473844479,0.0125173406963917,0.0319968103461077)).
+    e(595,-1558,85,338,-294,453,-1158,197,249,902,-1085,-142,-21,-313,45,531,201,384,-1998,-644),
+    0.05,
+    e(0.0755236292781413,0.0169810785568618,0.0530343870684108,0.0632001549226403,0.0407818746669505,0.0684441906545919,0.0224066674892351,0.0573156092864189,0.0594191552528466,0.093432734688318,0.023569613397956,0.0453130969133667,0.0492774668469685,0.0402483068810561,0.051584158965068,0.0722465198961763,0.0574747424017338,0.0652477473844479,0.0125173406963917,0.0319968103461077)).
 
 %Reaching first D.
 b_d_cpt(-110,-3765,-110).

packages/CLPBN/examples/HMMer/scan.yap

@@ -14,7 +14,7 @@ stop(S,W,Info) :-
 	gen_program(W, Info).
 stop(_,_,_) :-
 	format(user_error,"Bad HMM~n", []).
-   
+
 parse_model(S,Info) :-
 	get_line(S, Line, Info),
 %	format('~s~n',[Line]),
@@ -45,7 +45,7 @@ match_field(hmmer(_,_,_,Alph,_,_,_,_),_) --> "ALPH", !, % aminos or bases
 match_field(_,_) --> "RF", !, scanner_skip.
 match_field(_,_) --> "CS", !, scanner_skip.
 match_field(hmmer(_,_,_,_,_,_,_,MAP),_) --> "MAP", !,
-        scanner_skip_blanks,
+	scanner_skip_blanks,
 	to_lower(Codes),
 	{ map_code(Codes,MAP) }.
 match_field(_,_) --> "COM", !, scanner_skip.
@@ -76,11 +76,11 @@ match_field(_,_) --> "EVD", !,
 match_field(Info,S) --> "HMM", !, 
 	scanner_skip,
 	{
-	 get_line(S,_,Info),
-	 Info = hmmer(_,_,NOfStates,Alph,_,_,model(BD,NBD,Transitions),MAP),
-	 nof_symbols(Alph,N),
-	 scan_model(S,NOfStates,N,BD,NBD,Transitions,MAP,Info),
-	 throw(done(Info))
+	  get_line(S,_,Info),
+	  Info = hmmer(_,_,NOfStates,Alph,_,_,model(BD,NBD,Transitions),MAP),
+	  nof_symbols(Alph,N),
+	  scan_model(S,NOfStates,N,BD,NBD,Transitions,MAP,Info),
+	  throw(done(Info))
 	}.
 
 scan_model(S,NOfStates,N,BD,NBD,Transitions,MAP,Info) :-
@@ -95,7 +95,7 @@ scan_states(NOfStates, N, Stream, MAP, [t(E,I,S)|Transitions], Info) :-
 	scan_states(NOfStates1, N, Stream, NMAP, Transitions, Info).
 
 scan_state(Stream, E,I,MAP,s(MM,MI,MD,IM,II,DM,DD,BM,ME), N, NMAP, Info) :-
-        get_line(Stream, ELine, Info),
+	get_line(Stream, ELine, Info),
 	get_line(Stream, ILine, Info),
 	get_line(Stream, SLine, Info),
 %	format('~s~n~s~n~s~n',[ELine,ILine,SLine]),
@@ -265,7 +265,7 @@ gen_model(W, model(BD,NBD,States),PsCPT) :-
 	format(W, '~n%Reaching first D.~n',[]),
 	format(W, 'b_d_cpt(~w,~w,~w).~n',[BD,NBD,BDCPT]),
 	gen_states(W, States,1,PsCPT).
-	
+
 gen_states(_, [],_,_).
 gen_states(W, [State|States],StateNo,PsCPT) :-
 	gen_state(W, State,StateNo,PsCPT),
@@ -327,4 +327,3 @@ max_index([_|L],I0,Max0,MaxIndex0,Max,MaxIndex) :-
 	I is I0+1,
 	max_index(L,I,Max0,MaxIndex0,Max,MaxIndex).
 
-

packages/CLPBN/examples/HMMer/score.yap

@@ -6,13 +6,12 @@
 :- ensure_loaded(library('clpbn/viterbi')).
 
 :- use_module(fasta,
-	      [fa2atoms/3]).
+		[fa2atoms/3]).
 
 :- use_module(library(lists),
-	      [
-	       nth/3,
-	       append/3
-	      ]).
+		[nth/3,
+		 append/3
+		]).
 
 :- [plan7].