write more on architecture and include class diagrams

doc/chapter/2architecture.tex

@@ -20,10 +20,11 @@ The structure is as follows:
 For parsing the JSON file the JSON-java library~\cite{leary_json-java:_2018} is used.
 The classes for reading and writing those JSON files are displayed in figure~\ref{fig:io}.
 The internal representation of graphs is further explained in the section~\ref{sec:model}.
+
 \begin{figure}[tp]
     \centering
-    \includegraphics[width=\linewidth]{img/IO.pdf}
-    \caption{Class diagram of the IO package, containing utilities for reading and writing graphs.}
+    \includegraphics[width=\linewidth, trim={0 20cm 0 0}]{img/IO.pdf}
+    \caption{Class diagram of the \enquote{IO} package, containing utilities for reading and writing graphs.}
     \label{fig:io}
 \end{figure}
 
@@ -42,6 +43,8 @@ The internal representation of graphs is further explained in the section~\ref{s
     \label{table:node-attributes}
 \end{longtable}
 
+\newpage
+
 \begin{longtable}{|p{1.8cm}|p{2cm}|p{1.8cm}|p{8.5cm}|}
     \hline
     Attribute & Type & Optional & Explanation \\\hline\hline
@@ -70,7 +73,62 @@ The internal representation of graphs is further explained in the section~\ref{s
 
 \section{Internal graph representation, \enquote{Model}}\label{sec:model}
 One feature that is important to us, is to be able to work with hierarchical graphs (cf. chapter~\ref{ch:progress}).
+Therefore a node not only has edges to other nodes, but also it can contain other nodes and edges.
+So far this is similar to what we described in section~\ref{sec:inputFileFormat}.
+Additionally, there are multiple attributes that are used during the computation or as output variables.
+\begin{itemize}
+    \item The attributes \enquote{shift},  \enquote{sink},  \enquote{root} and  \enquote{align} correspond to the variables used by Brandes and Köpf~\cite{brandes_fast_2001}.
+    They are summarized in table~\ref{table:bk-variables}.
+    \item The \enquote{parent} of a node is the node that contains it in the hierarchy.
+    \item The attributes $x$ and $y$ are the coordinates of the node relative to its parent node.
+\end{itemize}
+Similarly, edges have additional attributes:
+\begin{itemize}
+    \item \enquote{dummy} specifies whether they are dummy edges.
+    \item \enquote{conflicted} corresponds to the variable used by Brandes and Köpf~\cite{brandes_fast_2001} and indicates that this edge won't be drawn vertically.
+    \item \enquote{bindPoints} is a list of bend points for the edge.
+\end{itemize}
+
+A class diagram of the package \enquote{Model} is displayed in figure~\ref{fig:model}.
+
+\begin{figure}[tp]
+    \centering
+    \includegraphics[width=\linewidth, trim={0 6cm 0 0}]{img/Model.pdf}
+    \caption{Class diagram of the \enquote{Model} package.}
+    \label{fig:model}
+\end{figure}
+
+\begin{longtable}{|p{2.8cm}|p{10cm}|}
+    \hline
+    Attribute & Explanation \\\hline\hline
+    root & The root node of the block of this node.
+    Unique for all nodes in the same block. \\\hline
+    sink & The topmost sink in the block graph that can be reached from the block that this node belongs to.
+    Only used for nodes that are the root of a block.
+    Unique for all nodes in the same class. \\\hline
+    shift & The shift of the class that this node belongs to.
+    Only used for nodes that are a sink of a class. \\\hline
+    \caption{Variables also used by Brandes and Köpf~\cite{brandes_fast_2001}}
+    \label{table:bk-variables}
+\end{longtable}
+
+\section{The actual algorithm}\label{sec:theActualAlgorithm}
+This section assumes that the reader is familiar with the node placement algorithm by Brandes and Köpf~\cite{brandes_fast_2001}.
 
+A \enquote{stage} of the algorithm, interface \enquote{AlgorithmStage}, is an interval during which each step of the algorithm is performed in a similar way.
+Each time such a step is performed it returns whether the stage is already finished.
+For example, a forward step in the stage of calculating one extremal layout, class \enquote{ExtremalLayoutCalc}, consists of either a step of calculating the blocks, class \enquote{BlockCalc}, or a step of compacting the layout, class \enquote{Compaction}.
+All the stages are displayed in class diagram~\ref{fig:animated}.
+
+To be able to undo a step each stage needs to implement methods for both forward and backward steps.
+
+\TODO{check figure height}
+\begin{figure}[tp]
+    \centering
+    \includegraphics[width=\linewidth, trim={0 9cm 0 0}]{img/Algorithms_Animated.pdf}
+    \caption{Class diagram of the package \enquote{Algorithms.Animated}.}
+    \label{fig:animated}
+\end{figure}
 
 \section{TODO: More Class Diagrams}\label{sec:classDiagrams}
 \TODO{maybe even into appendix}