APM: RSMC version 1.0 (not 1.0a) from ipisvn

rs.hh

@@ -0,0 +1,99 @@
+/*
+    Copyright (c) 2012-2014
+    Artur Meski <meski@ipipan.waw.pl>
+
+    Reuse of the code or its part for any purpose
+    without the author's permission is strictly prohibited.
+*/
+
+#ifndef RS_RS_HH
+#define RS_RS_HH
+
+#include <iostream>
+#include <set>
+#include <map>
+#include <vector>
+#include <string>
+#include <cstdlib>
+#include "macro.hh"
+#include "options.hh"
+#include "memtime.hh"
+
+using std::cout;
+using std::endl;
+
+class RctSys
+{
+    friend class SymRS;
+    friend class SymRSstate;
+public:
+    typedef unsigned int Atom;
+    typedef std::set<Atom> Atoms;
+    struct Reaction {
+        Atoms rctt;
+        Atoms inhib;
+        Atoms prod;
+    };
+    typedef std::vector<Reaction> Reactions;
+    typedef std::vector<std::string> AtomsByIds;
+    typedef std::map<std::string, Atom> AtomsByName;
+    typedef std::set<Atoms> AtomsSets;
+private:
+    Reactions reactions;
+    AtomsSets initStates;
+
+    Atoms actionAtoms;
+
+    AtomsByIds atoms_ids;
+    AtomsByName atoms_names;
+
+    Atoms tmpReactants;
+    Atoms tmpInhibitors;
+    Atoms tmpProducts;
+
+    Atoms tmpState;
+
+    Atom getAtomID(std::string atomName);
+
+    Options *opts;
+
+public:
+    void setOptions(Options *opts)
+    {
+        this->opts = opts;
+    }
+    bool hasAtom(std::string atomName);
+    void addAtom(std::string atomName);
+    std::string getAtomName(Atom atomID);
+    void pushReactant(std::string atomName);
+    void pushInhibitor(std::string atomName);
+    void pushProduct(std::string atomName);
+    void commitReaction(void);
+    std::string atomToStr(const Atom atom) {
+        return atoms_ids[atom];
+    }
+    std::string atomsToStr(const Atoms &atoms);
+    void showReactions(void);
+    void pushStateAtom(std::string atomName);
+    void commitInitState(void);
+    void addActionAtom(std::string atomName);
+    bool isActionAtom(Atom atom);
+    void resetInitStates(void) {
+        initStates.clear();
+    }
+    unsigned int getAtomsSize(void) {
+        return atoms_ids.size();
+    }
+    unsigned int getReactionsSize(void) {
+        return reactions.size();
+    }
+    unsigned int getActionsSize(void) {
+        return actionAtoms.size();
+    }
+    void showInitialStates(void);
+    void showActionAtoms(void);
+    void printSystem(void);
+};
+
+#endif
+