--- trunk/tengDissertation/Appendix.tex	2006/06/09 02:20:39	2837
+++ trunk/tengDissertation/Appendix.tex	2006/06/09 02:41:58	2839
@@ -113,9 +113,9 @@ OOPSE}\cite{Meineke05} and PROTOMOL\cite{Matthey05} \t
 As one of the latest advanced techniques emerged from
 object-oriented community, design patterns were applied in some of
 the modern scientific software applications, such as JMol, {\sc
-OOPSE}\cite{Meineke05} and PROTOMOL\cite{Matthey05} \textit{etc}.
-The following sections enumerates some of the patterns used in {\sc
-OOPSE}.
+OOPSE}\cite{Meineke2005} and PROTOMOL\cite{Matthey2005}
+\textit{etc}. The following sections enumerates some of the patterns
+used in {\sc OOPSE}.
 
 \subsection{\label{appendixSection:singleton}Singleton}
 
@@ -256,21 +256,12 @@ diagram of Visitor patten.} \label{appendixFig:visitor
 diagram of Visitor patten.} \label{appendixFig:visitorUML}
 \end{figure}
 
-%\begin{figure}
-%\centering
-%\includegraphics[width=\linewidth]{hierarchy.eps}
-%\caption[Class hierarchy for ojects in {\sc OOPSE}]{ A diagram of
-%the class hierarchy.
-%\begin{itemize}
-%\item A {\bf StuntDouble} is {\it any} object that can be manipulated by the
-%integrators and minimizers.
-%\item An {\bf Atom} is a fundamental point-particle that can be moved around during a simulation.
-%\item A {\bf DirectionalAtom} is an atom which has {\it orientational} as well as translational degrees of freedom.
-%\item A {\bf RigidBody} is a collection of {\bf Atom}s or {\bf
-%DirectionalAtom}s which behaves as a single unit.
-%\end{itemize}
-%} \label{oopseFig:hierarchy}
-%\end{figure}
+\begin{figure}
+\centering
+\includegraphics[width=\linewidth]{hierarchy.eps}
+\caption[Class hierarchy for ojects in {\sc OOPSE}]{ A diagram of
+the class hierarchy. } \label{oopseFig:hierarchy}
+\end{figure}
 
 \begin{lstlisting}[float,caption={[The implementation of Visitor pattern (II)]Source code of the element classes.},label={appendixScheme:element}]
 
@@ -374,6 +365,14 @@ body in a DMPC molecule is DMPC\_RB\_0.
 on the specifics of the simulation). The names of rigid bodies are
 generated automatically. For example, the name of the first rigid
 body in a DMPC molecule is DMPC\_RB\_0.
+\begin{itemize}
+\item A {\bf StuntDouble} is {\it any} object that can be manipulated by the
+integrators and minimizers.
+\item An {\bf Atom} is a fundamental point-particle that can be moved around during a simulation.
+\item A {\bf DirectionalAtom} is an atom which has {\it orientational} as well as translational degrees of freedom.
+\item A {\bf RigidBody} is a collection of {\bf Atom}s or {\bf
+DirectionalAtom}s which behaves as a single unit.
+\end{itemize}
 
 \section{\label{appendixSection:syntax}Syntax of the Select Command}
 
