Make Progressive as option

rs.cc

@@ -9,6 +9,7 @@ RctSys::RctSys(void)
   : current_process_defined(false)
 {
   ctx_aut = nullptr;
+  gen_ctxaut_progressive_closure = false;
 }
 
 bool RctSys::hasEntity(std::string name)
@@ -306,6 +307,11 @@ void RctSys::ctxAutEnable(void)
   ctx_aut = new CtxAut(opts, this);
 }
 
+void RctSys::ctxAutEnableProgressiveClosure(void)
+{
+  gen_ctxaut_progressive_closure = true;
+}
+
 void RctSys::ctxAutAddState(std::string stateName)
 {
   assert(ctx_aut != nullptr);
@@ -355,4 +361,9 @@ void RctSys::ctxAutSaveCurrentContextSet(std::string processName)
   ctx_aut->saveCurrentContextSet(processID);
 }
 
+void RctSys::ctxAutFinalise(void)
+{
+  ctx_aut->makeProgressive();
+}
+
 /** EOF **/

rs.hh

@@ -85,12 +85,14 @@ class RctSys
     void printSystem(void);
 
     void ctxAutEnable(void);
+    void ctxAutEnableProgressiveClosure(void);
     void ctxAutAddState(std::string stateName);
     void ctxAutSetInitState(std::string stateName);
     void ctxAutAddTransition(std::string srcStateName, std::string dstStateName);
     void ctxAutAddTransition(std::string srcStateName, std::string dstStateName, StateConstr *stateConstr);
     void ctxAutPushNamedContextEntity(std::string entity_name);
     void ctxAutSaveCurrentContextSet(std::string processName);
+    void ctxAutFinalise(void);
 
     bool initStatesDefined(void)
     {
@@ -116,6 +118,8 @@ class RctSys
 
     CtxAut *ctx_aut;
 
+    bool gen_ctxaut_progressive_closure;
+
     EntitiesById entities_ids;
     EntitiesByName entities_names;
 

rsin_driver.cc

@@ -22,6 +22,7 @@ void rsin_driver::initialise(void)
   opts = nullptr;
   use_ctx_aut = false;
   use_concentrations = false;
+  use_progressive = false;
 }
 
 rsin_driver::~rsin_driver ()
@@ -106,3 +107,17 @@ void rsin_driver::useContextAutomaton(void)
   getReactionSystem()->ctxAutEnable();
 }
 
+void rsin_driver::makeProgressive(void)
+{
+  use_progressive = true;
+  if (use_ctx_aut)
+  {
+    getReactionSystem()->ctxAutEnableProgressiveClosure();
+  }
+  else
+  {
+    FERROR("Context automaton not enabled");
+  }
+}
+
+// EOF

rsin_driver.hh

@@ -35,6 +35,7 @@ class rsin_driver
     // options in configuration file:
     bool use_ctx_aut;
     bool use_concentrations;
+    bool use_progressive;
 
     // Handling the scanner
     void scan_begin();
@@ -60,7 +61,7 @@ class rsin_driver
       ensureOptionsAllowed();
       use_concentrations = true;
     };
-
+    void makeProgressive(void);
     void ensureReactionSystemReady(void);
     void setupReactionSystem(void);
 
@@ -78,4 +79,3 @@ class rsin_driver
 };
 
 #endif
-

rsin_parser.ll

@@ -41,6 +41,7 @@ blank [ \t]
 "options"				        return token::OPTIONS;
 "use-context-automaton"	return token::USE_CTX_AUT;
 "use-concentrations"	  return token::USE_CONCENTRATIONS;
+"make-progressive"      return token::MAKE_PROGRESSIVE;
 "reactions"             return token::REACTIONS;
 "initial-contexts"      return token::INITIALCONTEXTS;
 "context-entities"      return token::CONTEXTENTITIES;
@@ -128,4 +129,3 @@ rsin_driver::scan_end()
 {
   fclose(yyin);
 }
-

rsin_parser.yy

@@ -46,7 +46,7 @@ class rsin_driver;
 #include "rsin_driver.hh"
 }
 
-%token OPTIONS USE_CTX_AUT USE_CONCENTRATIONS
+%token OPTIONS USE_CTX_AUT USE_CONCENTRATIONS MAKE_PROGRESSIVE
 %token REACTIONS INITIALCONTEXTS CONTEXTENTITIES RSCTLKFORM
 %token CONTEXTAUTOMATON STATES INITSTATE TRANSITIONS
 %token EQ LCB RCB LRB RRB LSB RSB LAB RAB COL SEMICOL DOT COMMA RARR
@@ -77,34 +77,40 @@ class rsin_driver;
 
 %start system;
 
-system: 
+system:
 	| OPTIONS LCB options RCB system
-    | REACTIONS LCB reactionsets RCB system
-    | INITIALCONTEXTS LCB initstates RCB system
-    | CONTEXTENTITIES LCB actionentities RCB system
+  | REACTIONS LCB reactionsets RCB system
+  | INITIALCONTEXTS LCB initstates RCB system
+  | CONTEXTENTITIES LCB actionentities RCB system
 	| CONTEXTAUTOMATON LCB ctxaut RCB system
-    | RSCTLKFORM LCB IDENTIFIER COL rsctlk_form RCB system {
-        driver.addFormRSCTLK(*$3, $5);
-        free($3);
-    }
-    ;
+  {
+    driver.getReactionSystem()->ctxAutFinalise();
+  }
+  | RSCTLKFORM LCB IDENTIFIER COL rsctlk_form RCB system {
+    driver.addFormRSCTLK(*$3, $5);
+    free($3);
+  }
+  ;
 
 options:
 	| options option SEMICOL
 	;
 
 option:
-	| USE_CTX_AUT { 
-		driver.useContextAutomaton(); 
+	| USE_CTX_AUT {
+		driver.useContextAutomaton();
 	}
 	| USE_CONCENTRATIONS {
 		driver.useConcentrations();
 	}
+  | MAKE_PROGRESSIVE {
+    driver.makeProgressive();
+  }
 	;
 
-/* 
+/*
  * -------------------------
- *         REACTIONS 
+ *         REACTIONS
  * -------------------------
  */
 
@@ -113,11 +119,11 @@ reactionsets:
 	;
 
 process_reactions: processname LCB reactions RCB SEMICOL
-	
+
 processname: IDENTIFIER {
 		driver.getReactionSystem()->setCurrentProcess(*$1);
 		free($1);
-	}	
+	}
 
 reactions:
     | reactions reaction SEMICOL
@@ -146,7 +152,7 @@ reactant: IDENTIFIER {
 
 inhibitors:
     inhibitor
-    | inhibitors COMMA inhibitor 
+    | inhibitors COMMA inhibitor
     ;
 
 inhibitor:
@@ -180,7 +186,7 @@ initstates:
 
 initstate:
     | entity
-    | initstate COMMA entity 
+    | initstate COMMA entity
     ;
 
 entity: IDENTIFIER {
@@ -191,7 +197,7 @@ entity: IDENTIFIER {
 
 /*******************************************/
 
-actionentities: 
+actionentities:
     | actentity
     | actionentities COMMA actentity
     ;
@@ -201,7 +207,7 @@ actentity: IDENTIFIER {
         free($1);
     }
     ;
-	
+
 /*******************************************/
 
 ctxaut:
@@ -226,11 +232,11 @@ autinitstate: IDENTIFIER {
 		free($1);
 	}
 	;
-	
+
 auttransitions:
 	| auttrans
 	| auttrans SEMICOL auttransitions
-	;	
+	;
 
 auttrans: LCB proc_ctxsets RCB COL IDENTIFIER RARR IDENTIFIER {
 		driver.getReactionSystem()->ctxAutAddTransition(*$5, *$7);
@@ -243,22 +249,22 @@ auttrans: LCB proc_ctxsets RCB COL IDENTIFIER RARR IDENTIFIER {
         free($7);
     }
 	;
-  
+
 proc_ctxsets:
   | proc_ctxsets single_proc_ctxset
   ;
-  
+
 single_proc_ctxset: IDENTIFIER EQ LCB contextset RCB {
   driver.getReactionSystem()->ctxAutSaveCurrentContextSet(*$1);
 		free($1);
 	}
 	;
-	
+
 contextset:
 	| ctxentity
 	| contextset COMMA ctxentity
 	;
-		
+
 ctxentity: IDENTIFIER {
 		driver.getReactionSystem()->ctxAutPushNamedContextEntity(*$1);
 		free($1);
@@ -266,7 +272,7 @@ ctxentity: IDENTIFIER {
 	;
 
 /* formulae */
-	
+
 state_constr: IDENTIFIER DOT IDENTIFIER {
         $$ = new StateConstr(*$1, *$3);
         free($1);
@@ -324,7 +330,7 @@ state_constr: IDENTIFIER DOT IDENTIFIER {
 //     }
 //     ;
 
-rsctlk_form: 
+rsctlk_form:
     IDENTIFIER DOT IDENTIFIER {
         $$ = new FormRSCTLK(*$1, *$3);
         free($1);
@@ -371,7 +377,7 @@ rsctlk_form:
     }
     | AG rsctlk_form {
         $$ = new FormRSCTLK(RSCTLK_AG, $2);
-    } 
+    }
     | UK LSB IDENTIFIER RSB LRB rsctlk_form RRB {
         Agents_f agents;
         agents.insert(*$3);
@@ -411,7 +417,7 @@ rsctlk_form:
     // }
 
 	  /* contexts as boolean formulae  */
-    | E LAB state_constr RAB X rsctlk_form { 
+    | E LAB state_constr RAB X rsctlk_form {
         $$ = new FormRSCTLK(RSCTLK_EX_ACT, $3, $6);
     }
     | E LAB state_constr RAB U LRB rsctlk_form COMMA rsctlk_form RRB {
@@ -443,4 +449,3 @@ yy::rsin_parser::error(const yy::rsin_parser::location_type &l, const std::strin
 {
     driver.error(l, m);
 }
-

symrs.cc

@@ -34,12 +34,8 @@ SymRS::SymRS(RctSys *rs, Options *opts)
   pv_ca_succ = nullptr;
   tr_ca = nullptr;
 
-  // TODO: this should be triggered by the parser and it should depend
-  //       on an option in the input file
   rs->ctx_aut->makeProgressive();
 
-  rs->printSystem();
-
   encode();
 }