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Make Progressive as option

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This commit is contained in:
Artur Meski
2018-10-13 21:00:06 +01:00
parent 96b0278136
commit e4ab5999aa
7 changed files with 69 additions and 38 deletions
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11
rs.cc
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@@ -9,6 +9,7 @@ RctSys::RctSys(void)
: current_process_defined(false) : current_process_defined(false)
{ {
ctx_aut = nullptr; ctx_aut = nullptr;
gen_ctxaut_progressive_closure = false;
} }
bool RctSys::hasEntity(std::string name) bool RctSys::hasEntity(std::string name)
@@ -306,6 +307,11 @@ void RctSys::ctxAutEnable(void)
ctx_aut = new CtxAut(opts, this); ctx_aut = new CtxAut(opts, this);
} }
void RctSys::ctxAutEnableProgressiveClosure(void)
{
gen_ctxaut_progressive_closure = true;
}
void RctSys::ctxAutAddState(std::string stateName) void RctSys::ctxAutAddState(std::string stateName)
{ {
assert(ctx_aut != nullptr); assert(ctx_aut != nullptr);
@@ -355,4 +361,9 @@ void RctSys::ctxAutSaveCurrentContextSet(std::string processName)
ctx_aut->saveCurrentContextSet(processID); ctx_aut->saveCurrentContextSet(processID);
} }
void RctSys::ctxAutFinalise(void)
{
ctx_aut->makeProgressive();
}
/** EOF **/ /** EOF **/

4
rs.hh
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@@ -85,12 +85,14 @@ class RctSys
void printSystem(void); void printSystem(void);
void ctxAutEnable(void); void ctxAutEnable(void);
void ctxAutEnableProgressiveClosure(void);
void ctxAutAddState(std::string stateName); void ctxAutAddState(std::string stateName);
void ctxAutSetInitState(std::string stateName); void ctxAutSetInitState(std::string stateName);
void ctxAutAddTransition(std::string srcStateName, std::string dstStateName); void ctxAutAddTransition(std::string srcStateName, std::string dstStateName);
void ctxAutAddTransition(std::string srcStateName, std::string dstStateName, StateConstr *stateConstr); void ctxAutAddTransition(std::string srcStateName, std::string dstStateName, StateConstr *stateConstr);
void ctxAutPushNamedContextEntity(std::string entity_name); void ctxAutPushNamedContextEntity(std::string entity_name);
void ctxAutSaveCurrentContextSet(std::string processName); void ctxAutSaveCurrentContextSet(std::string processName);
void ctxAutFinalise(void);
bool initStatesDefined(void) bool initStatesDefined(void)
{ {
@@ -116,6 +118,8 @@ class RctSys
CtxAut *ctx_aut; CtxAut *ctx_aut;
bool gen_ctxaut_progressive_closure;
EntitiesById entities_ids; EntitiesById entities_ids;
EntitiesByName entities_names; EntitiesByName entities_names;

15
rsin_driver.cc
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@@ -22,6 +22,7 @@ void rsin_driver::initialise(void)
opts = nullptr; opts = nullptr;
use_ctx_aut = false; use_ctx_aut = false;
use_concentrations = false; use_concentrations = false;
use_progressive = false;
} }
rsin_driver::~rsin_driver () rsin_driver::~rsin_driver ()
@@ -106,3 +107,17 @@ void rsin_driver::useContextAutomaton(void)
getReactionSystem()->ctxAutEnable(); getReactionSystem()->ctxAutEnable();
} }
void rsin_driver::makeProgressive(void)
{
use_progressive = true;
if (use_ctx_aut)
{
getReactionSystem()->ctxAutEnableProgressiveClosure();
}
else
{
FERROR("Context automaton not enabled");
}
}
// EOF

4
rsin_driver.hh
View File

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

2
rsin_parser.ll
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@@ -41,6 +41,7 @@ blank [ \t]
"options" return token::OPTIONS; "options" return token::OPTIONS;
"use-context-automaton" return token::USE_CTX_AUT; "use-context-automaton" return token::USE_CTX_AUT;
"use-concentrations" return token::USE_CONCENTRATIONS; "use-concentrations" return token::USE_CONCENTRATIONS;
"make-progressive" return token::MAKE_PROGRESSIVE;
"reactions" return token::REACTIONS; "reactions" return token::REACTIONS;
"initial-contexts" return token::INITIALCONTEXTS; "initial-contexts" return token::INITIALCONTEXTS;
"context-entities" return token::CONTEXTENTITIES; "context-entities" return token::CONTEXTENTITIES;
@@ -128,4 +129,3 @@ rsin_driver::scan_end()
{ {
fclose(yyin); fclose(yyin);
} }

67
rsin_parser.yy
View File

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

4
symrs.cc
View File

@@ -34,12 +34,8 @@ SymRS::SymRS(RctSys *rs, Options *opts)
pv_ca_succ = nullptr; pv_ca_succ = nullptr;
tr_ca = 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->ctx_aut->makeProgressive();
rs->printSystem();
encode(); encode();
} }