Reaction graphs

doc.pl

@@ -165,15 +165,6 @@ goto_level(Level) :-
   ).
 
 
-indent(Doc, Level) :-
-  \+ (
-    between(0, Level, _),
-    \+ (
-      write(Doc, '  ')
-    )
-  ).
-
-
 increment_counter :-
   nb_getval(current_counters, OldCounters),
   append(HigherCounters, [LastCounter], OldCounters),

install-macos.sh

 #!/bin/sh
-brew install swi-prolog gsl libsbml gnuplot
+brew install swi-prolog gsl libsbml gnuplot graphviz

models.pl

@@ -491,10 +491,23 @@ optional(Item, List) :-
 
 list_items(Options) :-
   all_ids(Options, Ids),
-  list_ids(Ids).
+  list_ids(Options, Ids).
 
 
 list_ids(Ids) :-
+  list_ids([], Ids).
+
+
+list_ids(Options, Ids) :-
+  optional(indent: Indent, Options),
+  default(Indent, 0),
+  (
+    member(recursive, Options)
+  ->
+    Recursive = yes
+  ;
+    Recursive = no
+  ),
   retractall(listed_item(_, _)),
   set_counter(list_item_counter, 0),
   \+ (
@@ -503,7 +516,16 @@ list_ids(Ids) :-
       count(list_item_counter, Counter),
       assertz(listed_item(Counter, Id)),
       item(Id, _, _, Item),
-      format('[~d] ~w\n', [Counter, Item])
+      indent(Indent),
+      format('[~d] ~w\n', [Counter, Item]),
+      (
+        Recursive = yes
+      ->
+        SubIndent is Indent + 1,
+        list_items([indent: SubIndent, recursive, parent: Id])
+      ;
+        true
+      )
     )
   ).
 

util.pl

@@ -9,7 +9,9 @@
     list_to_equals/2,
     list/1,
     nth0_eqq/3,
-    executable_filename/1
+    executable_filename/1,
+    indent/1,
+    indent/2
   ]).
 
 name_variables(L) :-
@@ -108,6 +110,19 @@ executable_filename(Filename) :-
   current_prolog_flag(os_argv, [_Swipl, _X, Filename | _]).
 
 
+indent(Level) :-
+  indent(user_output, Level).
+
+
+indent(Stream, Level) :-
+  \+ (
+    between(0, Level, _),
+    \+ (
+      write(Stream, '  ')
+    )
+  ).
+
+
 user:message_hook(_Msg, warning, _Lines) :-
   catch(
     count(warnings, _),