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# Line 131 | Line 131 | is declared as
131   is declared as
132   \begin{lstlisting}[float,caption={[A classic Singleton design pattern implementation(I)] Declaration of {\tt IntegratorFactory} class.},label={appendixScheme:singletonDeclaration}]
133  
134 <  class IntegratorFactory {
135 <    public:
136 <      static IntegratorFactory* getInstance();
137 <    protected:
138 <      IntegratorFactory();
139 <    private:
140 <      static IntegratorFactory* instance_;
141 <  };
134 > class IntegratorFactory {
135 > public:
136 >  static IntegratorFactory*
137 >  getInstance();
138 > protected:
139 >  IntegratorFactory();
140 > private:
141 >  static IntegratorFactory* instance_;
142 > };
143 >
144   \end{lstlisting}
145   The corresponding implementation is
146   \begin{lstlisting}[float,caption={[A classic implementation of Singleton design pattern (II)] Implementation of {\tt IntegratorFactory} class.},label={appendixScheme:singletonImplementation}]
# Line 151 | Line 153 | IntegratorFactory* getInstance() {
153    }
154    return instance_;
155   }
156 +
157   \end{lstlisting}
158   Since constructor is declared as {\tt protected}, a client can not
159   instantiate {\tt IntegratorFactory} directly. Moreover, since the
# Line 172 | Line 175 | result.
175   corresponding creator for the type identifier and returns its
176   result.
177   \begin{lstlisting}[float,caption={[The implementation of Factory pattern (I)].},label={appendixScheme:factoryDeclaration}]
175 –  class IntegratorCreator;
176 –  class IntegratorFactory {
177 –    public:
178 –      typedef std::map<string, IntegratorCreator*> CreatorMapType;
178  
179 <      bool registerIntegrator(IntegratorCreator* creator);
179 > class IntegratorFactory {
180 > public:
181 >  typedef std::map<string, IntegratorCreator*> CreatorMapType;
182  
183 <      Integrator* createIntegrator(const string& id, SimInfo* info);
184 <
184 <    private:
185 <      CreatorMapType creatorMap_;
186 <  };
187 < \end{lstlisting}
188 <
189 < \begin{lstlisting}[float,caption={[The implementation of Factory pattern (II)].},label={appendixScheme:factoryDeclarationImplementation}]
190 <  bool IntegratorFactory::unregisterIntegrator(const string& id) {
191 <    return creatorMap_.erase(id) == 1;
183 >  bool registerIntegrator(IntegratorCreator* creator) {
184 >    return creatorMap_.insert(creator->getIdent(), creator).second;
185    }
186  
187 <  Integrator*
188 <  IntegratorFactory::createIntegrator(const string& id, SimInfo* info) {
187 >  Integrator* createIntegrator(const string& id, SimInfo* info) {
188 >    Integrator* result = NULL;
189      CreatorMapType::iterator i = creatorMap_.find(id);
190      if (i != creatorMap_.end()) {
191 <      //invoke functor to create object
199 <      return (i->second)->create(info);
200 <    } else {
201 <      return NULL;
191 >      result = (i->second)->create(info);
192      }
193 +    return result;
194    }
195 +
196 + private:
197 +  CreatorMapType creatorMap_;
198 + };
199   \end{lstlisting}
200 + \begin{lstlisting}[float,caption={[The implementation of Factory pattern (III)]Souce code of creator classes.},label={appendixScheme:integratorCreator}]
201  
202 < \begin{lstlisting}[float,caption={[The implementation of Factory pattern (III)].},label={appendixScheme:integratorCreator}]
203 <
208 <  class IntegratorCreator {
209 <  public:
202 > class IntegratorCreator {
203 > public:
204      IntegratorCreator(const string& ident) : ident_(ident) {}
205  
206      const string& getIdent() const { return ident_; }
207  
208      virtual Integrator* create(SimInfo* info) const = 0;
209  
210 <  private:
210 > private:
211      string ident_;
212 <  };
212 > };
213  
214 <  template<class ConcreteIntegrator>
215 <  class IntegratorBuilder : public IntegratorCreator {
216 <  public:
217 <    IntegratorBuilder(const string& ident) : IntegratorCreator(ident) {}
218 <    virtual  Integrator* create(SimInfo* info) const {
219 <      return new ConcreteIntegrator(info);
220 <    }
221 <  };
214 > template<class ConcreteIntegrator>
215 > class IntegratorBuilder : public IntegratorCreator {
216 > public:
217 >  IntegratorBuilder(const string& ident)
218 >                   : IntegratorCreator(ident) {}
219 >  virtual  Integrator* create(SimInfo* info) const {
220 >    return new ConcreteIntegrator(info);
221 >  }
222 > };
223   \end{lstlisting}
224  
225   \subsection{\label{appendixSection:visitorPattern}Visitor}
# Line 241 | Line 236 | extensively.
236  
237   \begin{figure}
238   \centering
239 < \includegraphics[width=\linewidth]{architecture.eps}
239 > \includegraphics[width=\linewidth]{visitor.eps}
240   \caption[The architecture of {\sc OOPSE}] {Overview of the structure
241   of {\sc OOPSE}} \label{appendixFig:visitorUML}
242   \end{figure}
243  
244   \begin{lstlisting}[float,caption={[The implementation of Visitor pattern (I)]Source code of the visitor classes.},label={appendixScheme:visitor}]
245 <  class BaseVisitor{
246 <    public:
247 <      virtual void visit(Atom* atom);
248 <      virtual void visit(DirectionalAtom* datom);
249 <      virtual void visit(RigidBody* rb);
250 <  };
245 >
246 > class BaseVisitor{
247 > public:
248 >  virtual void visit(Atom* atom);
249 >  virtual void visit(DirectionalAtom* datom);
250 >  virtual void visit(RigidBody* rb);
251 > };
252 >
253   \end{lstlisting}
254  
255   \begin{lstlisting}[float,caption={[The implementation of Visitor pattern (II)]Source code of the element classes.},label={appendixScheme:element}]
259 –  class StuntDouble {
260 –    public:
261 –      virtual void accept(BaseVisitor* v) = 0;
262 –  };
256  
257 <  class Atom: public StuntDouble {
258 <    public:
259 <      virtual void accept{BaseVisitor* v*} {v->visit(this);}
260 <  };
257 > class StuntDouble {
258 > public:
259 >  virtual void accept(BaseVisitor* v) = 0;
260 > };
261  
262 <  class DirectionalAtom: public Atom {
263 <    public:
264 <      virtual void accept{BaseVisitor* v*} {v->visit(this);}
265 <  };
262 > class Atom: public StuntDouble {
263 > public:
264 >  virtual void accept{BaseVisitor* v*} {
265 >    v->visit(this);
266 >  }
267 > };
268  
269 <  class RigidBody: public StuntDouble {
270 <    public:
271 <      virtual void accept{BaseVisitor* v*} {v->visit(this);}
272 <  };
269 > class DirectionalAtom: public Atom {
270 > public:
271 >  virtual void accept{BaseVisitor* v*} {
272 >    v->visit(this);
273 >  }
274 > };
275  
276 + class RigidBody: public StuntDouble {
277 + public:
278 +  virtual void accept{BaseVisitor* v*} {
279 +    v->visit(this);
280 +  }
281 + };
282 +
283   \end{lstlisting}
284 +
285   \section{\label{appendixSection:concepts}Concepts}
286  
287   OOPSE manipulates both traditional atoms as well as some objects
288   that {\it behave like atoms}.  These objects can be rigid
289   collections of atoms or atoms which have orientational degrees of
290 < freedom.  Here is a diagram of the class heirarchy:
291 <
292 < %\begin{figure}
293 < %\centering
294 < %\includegraphics[width=3in]{heirarchy.eps}
295 < %\caption[Class heirarchy for StuntDoubles in {\sc oopse}-3.0]{ \\
296 < %The class heirarchy of StuntDoubles in {\sc oopse}-3.0. The
297 < %selection syntax allows the user to select any of the objects that
298 < %are descended from a StuntDouble.} \label{oopseFig:heirarchy}
299 < %\end{figure}
300 <
290 > freedom.  A diagram of the class heirarchy is illustrated in
291 > Fig.~\ref{oopseFig:heirarchy}. Every Molecule, Atom and
292 > DirectionalAtom in {\sc OOPSE} have their own names which are
293 > specified in the {\tt .md} file. In contrast, RigidBodies are
294 > denoted by their membership and index inside a particular molecule:
295 > [MoleculeName]\_RB\_[index] (the contents inside the brackets depend
296 > on the specifics of the simulation). The names of rigid bodies are
297 > generated automatically. For example, the name of the first rigid
298 > body in a DMPC molecule is DMPC\_RB\_0.
299 > \begin{figure}
300 > \centering
301 > \includegraphics[width=\linewidth]{heirarchy.eps}
302 > \caption[Class heirarchy for ojects in {\sc OOPSE}]{ A diagram of
303 > the class heirarchy.
304   \begin{itemize}
305   \item A {\bf StuntDouble} is {\it any} object that can be manipulated by the
306   integrators and minimizers.
# Line 301 | Line 309 | DirectionalAtom}s which behaves as a single unit.
309   \item A {\bf RigidBody} is a collection of {\bf Atom}s or {\bf
310   DirectionalAtom}s which behaves as a single unit.
311   \end{itemize}
312 <
313 < Every Molecule, Atom and DirectionalAtom in {\sc OOPSE} have their
306 < own names which are specified in the {\tt .md} file. In contrast,
307 < RigidBodies are denoted by their membership and index inside a
308 < particular molecule: [MoleculeName]\_RB\_[index] (the contents
309 < inside the brackets depend on the specifics of the simulation). The
310 < names of rigid bodies are generated automatically. For example, the
311 < name of the first rigid body in a DMPC molecule is DMPC\_RB\_0.
312 > } \label{oopseFig:heirarchy}
313 > \end{figure}
314  
315   \section{\label{appendixSection:syntax}Syntax of the Select Command}
316  

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