\hypertarget{plot__layouts_8h}{
\section{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/plot\_\-layouts.h File Reference}
\label{plot__layouts_8h}\index{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/plot\_\-layouts.h@{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/plot\_\-layouts.h}}
}


Secondary structure plot layout algorithms.  
Include dependency graph for plot\_\-layouts.h:\nopagebreak
\begin{figure}[H]
\begin{center}
\leavevmode
\includegraphics[width=221pt]{plot__layouts_8h__incl}
\end{center}
\end{figure}
This graph shows which files directly or indirectly include this file:\nopagebreak
\begin{figure}[H]
\begin{center}
\leavevmode
\includegraphics[width=221pt]{plot__layouts_8h__dep__incl}
\end{center}
\end{figure}
\subsection*{Defines}
\begin{DoxyCompactItemize}
\item 
\#define \hyperlink{plot__layouts_8h_ae6d17b9f0a53cf5205a9181e0f8422e9}{VRNA\_\-PLOT\_\-TYPE\_\-SIMPLE}~0
\begin{DoxyCompactList}\small\item\em Definition of Plot type {\itshape simple\/}. \item\end{DoxyCompactList}\item 
\#define \hyperlink{plot__layouts_8h_a94d4c863ecac2f220f76658afb92f964}{VRNA\_\-PLOT\_\-TYPE\_\-NAVIEW}~1
\begin{DoxyCompactList}\small\item\em Definition of Plot type {\itshape Naview\/}. \item\end{DoxyCompactList}\item 
\#define \hyperlink{plot__layouts_8h_a8c9eac631348da92136c8363ecdd9fb9}{VRNA\_\-PLOT\_\-TYPE\_\-CIRCULAR}~2
\begin{DoxyCompactList}\small\item\em Definition of Plot type {\itshape Circular\/}. \item\end{DoxyCompactList}\end{DoxyCompactItemize}
\subsection*{Functions}
\begin{DoxyCompactItemize}
\item 
int \hyperlink{plot__layouts_8h_af4b9173e7d3fd361c3c85e6def194123}{simple\_\-xy\_\-coordinates} (short $\ast$pair\_\-table, float $\ast$X, float $\ast$Y)
\begin{DoxyCompactList}\small\item\em Calculate nucleotide coordinates for secondary structure plot the {\itshape Simple way\/}. \item\end{DoxyCompactList}\item 
int \hyperlink{plot__layouts_8h_ac4ea13d35308f09940178d2b05a248c2}{simple\_\-circplot\_\-coordinates} (short $\ast$pair\_\-table, float $\ast$x, float $\ast$y)
\begin{DoxyCompactList}\small\item\em Calculate nucleotide coordinates for {\itshape Circular Plot\/}. \item\end{DoxyCompactList}\end{DoxyCompactItemize}
\subsection*{Variables}
\begin{DoxyCompactItemize}
\item 
int \hyperlink{plot__layouts_8h_a5964c4581431b098b80027d6e14dcdd4}{rna\_\-plot\_\-type}
\begin{DoxyCompactList}\small\item\em Switch for changing the secondary structure layout algorithm. \item\end{DoxyCompactList}\end{DoxyCompactItemize}


\subsection{Detailed Description}
Secondary structure plot layout algorithms. c Ronny Lorenz The ViennaRNA Package 

\subsection{Define Documentation}
\hypertarget{plot__layouts_8h_ae6d17b9f0a53cf5205a9181e0f8422e9}{
\index{plot\_\-layouts.h@{plot\_\-layouts.h}!VRNA\_\-PLOT\_\-TYPE\_\-SIMPLE@{VRNA\_\-PLOT\_\-TYPE\_\-SIMPLE}}
\index{VRNA\_\-PLOT\_\-TYPE\_\-SIMPLE@{VRNA\_\-PLOT\_\-TYPE\_\-SIMPLE}!plot_layouts.h@{plot\_\-layouts.h}}
\subsubsection[{VRNA\_\-PLOT\_\-TYPE\_\-SIMPLE}]{\setlength{\rightskip}{0pt plus 5cm}\#define VRNA\_\-PLOT\_\-TYPE\_\-SIMPLE~0}}
\label{plot__layouts_8h_ae6d17b9f0a53cf5205a9181e0f8422e9}


Definition of Plot type {\itshape simple\/}. This is the plot type definition for several RNA structure plotting functions telling them to use {\bfseries Simple} plotting algorithm

\begin{DoxySeeAlso}{See also}
\hyperlink{plot__layouts_8h_a5964c4581431b098b80027d6e14dcdd4}{rna\_\-plot\_\-type}, \hyperlink{PS__dot_8h_a47856b2504b566588785597b6ebb8271}{PS\_\-rna\_\-plot\_\-a()}, \hyperlink{PS__dot_8h_a0873c7cc4cd7a11c9a2cea19dde7e9c9}{PS\_\-rna\_\-plot()}, \hyperlink{PS__dot_8h_ae7853539b5df98f294b4af434e979304}{svg\_\-rna\_\-plot()}, \hyperlink{PS__dot_8h_a70834bc8c0aad4fe6824ff76ccb8f329}{gmlRNA()}, \hyperlink{PS__dot_8h_add368528755f9a830727b680243541df}{ssv\_\-rna\_\-plot()}, \hyperlink{PS__dot_8h_a2f6d5953e6a323df898896b8d6614483}{xrna\_\-plot()} 
\end{DoxySeeAlso}
\hypertarget{plot__layouts_8h_a94d4c863ecac2f220f76658afb92f964}{
\index{plot\_\-layouts.h@{plot\_\-layouts.h}!VRNA\_\-PLOT\_\-TYPE\_\-NAVIEW@{VRNA\_\-PLOT\_\-TYPE\_\-NAVIEW}}
\index{VRNA\_\-PLOT\_\-TYPE\_\-NAVIEW@{VRNA\_\-PLOT\_\-TYPE\_\-NAVIEW}!plot_layouts.h@{plot\_\-layouts.h}}
\subsubsection[{VRNA\_\-PLOT\_\-TYPE\_\-NAVIEW}]{\setlength{\rightskip}{0pt plus 5cm}\#define VRNA\_\-PLOT\_\-TYPE\_\-NAVIEW~1}}
\label{plot__layouts_8h_a94d4c863ecac2f220f76658afb92f964}


Definition of Plot type {\itshape Naview\/}. This is the plot type definition for several RNA structure plotting functions telling them to use {\bfseries Naview} plotting algorithm

\begin{DoxySeeAlso}{See also}
\hyperlink{plot__layouts_8h_a5964c4581431b098b80027d6e14dcdd4}{rna\_\-plot\_\-type}, \hyperlink{PS__dot_8h_a47856b2504b566588785597b6ebb8271}{PS\_\-rna\_\-plot\_\-a()}, \hyperlink{PS__dot_8h_a0873c7cc4cd7a11c9a2cea19dde7e9c9}{PS\_\-rna\_\-plot()}, \hyperlink{PS__dot_8h_ae7853539b5df98f294b4af434e979304}{svg\_\-rna\_\-plot()}, \hyperlink{PS__dot_8h_a70834bc8c0aad4fe6824ff76ccb8f329}{gmlRNA()}, \hyperlink{PS__dot_8h_add368528755f9a830727b680243541df}{ssv\_\-rna\_\-plot()}, \hyperlink{PS__dot_8h_a2f6d5953e6a323df898896b8d6614483}{xrna\_\-plot()} 
\end{DoxySeeAlso}
\hypertarget{plot__layouts_8h_a8c9eac631348da92136c8363ecdd9fb9}{
\index{plot\_\-layouts.h@{plot\_\-layouts.h}!VRNA\_\-PLOT\_\-TYPE\_\-CIRCULAR@{VRNA\_\-PLOT\_\-TYPE\_\-CIRCULAR}}
\index{VRNA\_\-PLOT\_\-TYPE\_\-CIRCULAR@{VRNA\_\-PLOT\_\-TYPE\_\-CIRCULAR}!plot_layouts.h@{plot\_\-layouts.h}}
\subsubsection[{VRNA\_\-PLOT\_\-TYPE\_\-CIRCULAR}]{\setlength{\rightskip}{0pt plus 5cm}\#define VRNA\_\-PLOT\_\-TYPE\_\-CIRCULAR~2}}
\label{plot__layouts_8h_a8c9eac631348da92136c8363ecdd9fb9}


Definition of Plot type {\itshape Circular\/}. This is the plot type definition for several RNA structure plotting functions telling them to produce a {\bfseries Circular plot}

\begin{DoxySeeAlso}{See also}
\hyperlink{plot__layouts_8h_a5964c4581431b098b80027d6e14dcdd4}{rna\_\-plot\_\-type}, \hyperlink{PS__dot_8h_a47856b2504b566588785597b6ebb8271}{PS\_\-rna\_\-plot\_\-a()}, \hyperlink{PS__dot_8h_a0873c7cc4cd7a11c9a2cea19dde7e9c9}{PS\_\-rna\_\-plot()}, \hyperlink{PS__dot_8h_ae7853539b5df98f294b4af434e979304}{svg\_\-rna\_\-plot()}, \hyperlink{PS__dot_8h_a70834bc8c0aad4fe6824ff76ccb8f329}{gmlRNA()}, \hyperlink{PS__dot_8h_add368528755f9a830727b680243541df}{ssv\_\-rna\_\-plot()}, \hyperlink{PS__dot_8h_a2f6d5953e6a323df898896b8d6614483}{xrna\_\-plot()} 
\end{DoxySeeAlso}


\subsection{Function Documentation}
\hypertarget{plot__layouts_8h_af4b9173e7d3fd361c3c85e6def194123}{
\index{plot\_\-layouts.h@{plot\_\-layouts.h}!simple\_\-xy\_\-coordinates@{simple\_\-xy\_\-coordinates}}
\index{simple\_\-xy\_\-coordinates@{simple\_\-xy\_\-coordinates}!plot_layouts.h@{plot\_\-layouts.h}}
\subsubsection[{simple\_\-xy\_\-coordinates}]{\setlength{\rightskip}{0pt plus 5cm}int simple\_\-xy\_\-coordinates (short $\ast$ {\em pair\_\-table}, \/  float $\ast$ {\em X}, \/  float $\ast$ {\em Y})}}
\label{plot__layouts_8h_af4b9173e7d3fd361c3c85e6def194123}


Calculate nucleotide coordinates for secondary structure plot the {\itshape Simple way\/}. \begin{DoxySeeAlso}{See also}
\hyperlink{utils_8h_a89c32307ee50a0026f4a3131fac0845a}{make\_\-pair\_\-table()}, \hyperlink{plot__layouts_8h_a5964c4581431b098b80027d6e14dcdd4}{rna\_\-plot\_\-type}, \hyperlink{plot__layouts_8h_ac4ea13d35308f09940178d2b05a248c2}{simple\_\-circplot\_\-coordinates()}, naview\_\-xy\_\-coordinates(), \hyperlink{PS__dot_8h_a47856b2504b566588785597b6ebb8271}{PS\_\-rna\_\-plot\_\-a()}, \hyperlink{PS__dot_8h_a0873c7cc4cd7a11c9a2cea19dde7e9c9}{PS\_\-rna\_\-plot}, \hyperlink{PS__dot_8h_ae7853539b5df98f294b4af434e979304}{svg\_\-rna\_\-plot()}
\end{DoxySeeAlso}

\begin{DoxyParams}{Parameters}
\item[{\em pair\_\-table}]The pair table of the secondary structure \item[{\em X}]a pointer to an array with enough allocated space to hold the x coordinates \item[{\em Y}]a pointer to an array with enough allocated space to hold the y coordinates \end{DoxyParams}
\begin{DoxyReturn}{Returns}
length of sequence on success, 0 otherwise 
\end{DoxyReturn}
\hypertarget{plot__layouts_8h_ac4ea13d35308f09940178d2b05a248c2}{
\index{plot\_\-layouts.h@{plot\_\-layouts.h}!simple\_\-circplot\_\-coordinates@{simple\_\-circplot\_\-coordinates}}
\index{simple\_\-circplot\_\-coordinates@{simple\_\-circplot\_\-coordinates}!plot_layouts.h@{plot\_\-layouts.h}}
\subsubsection[{simple\_\-circplot\_\-coordinates}]{\setlength{\rightskip}{0pt plus 5cm}int simple\_\-circplot\_\-coordinates (short $\ast$ {\em pair\_\-table}, \/  float $\ast$ {\em x}, \/  float $\ast$ {\em y})}}
\label{plot__layouts_8h_ac4ea13d35308f09940178d2b05a248c2}


Calculate nucleotide coordinates for {\itshape Circular Plot\/}. This function calculates the coordinates of nucleotides mapped in equal distancies onto a unit circle.

\begin{DoxyNote}{Note}
In order to draw nice arcs using quadratic bezier curves that connect base pairs one may calculate a second tangential point $P^t$ in addition to the actual R$^{\mbox{2}}$  coordinates. the simplest way to do so may be to compute a radius scaling factor $rs$ in the interval $[0,1]$ that weights the proportion of base pair span to the actual length of the sequence. This scaling factor can then be used to calculate the coordinates for $P^t$, i.e. $ P^{t}_x[i] = X[i] * rs$ and $P^{t}_y[i] = Y[i] * rs$.
\end{DoxyNote}
\begin{DoxySeeAlso}{See also}
\hyperlink{utils_8h_a89c32307ee50a0026f4a3131fac0845a}{make\_\-pair\_\-table()}, \hyperlink{plot__layouts_8h_a5964c4581431b098b80027d6e14dcdd4}{rna\_\-plot\_\-type}, \hyperlink{plot__layouts_8h_af4b9173e7d3fd361c3c85e6def194123}{simple\_\-xy\_\-coordinates()}, naview\_\-xy\_\-coordinates(), \hyperlink{PS__dot_8h_a47856b2504b566588785597b6ebb8271}{PS\_\-rna\_\-plot\_\-a()}, \hyperlink{PS__dot_8h_a0873c7cc4cd7a11c9a2cea19dde7e9c9}{PS\_\-rna\_\-plot}, \hyperlink{PS__dot_8h_ae7853539b5df98f294b4af434e979304}{svg\_\-rna\_\-plot()}
\end{DoxySeeAlso}

\begin{DoxyParams}{Parameters}
\item[{\em pair\_\-table}]The pair table of the secondary structure \item[{\em x}]a pointer to an array with enough allocated space to hold the x coordinates \item[{\em y}]a pointer to an array with enough allocated space to hold the y coordinates \end{DoxyParams}
\begin{DoxyReturn}{Returns}
length of sequence on success, 0 otherwise 
\end{DoxyReturn}


\subsection{Variable Documentation}
\hypertarget{plot__layouts_8h_a5964c4581431b098b80027d6e14dcdd4}{
\index{plot\_\-layouts.h@{plot\_\-layouts.h}!rna\_\-plot\_\-type@{rna\_\-plot\_\-type}}
\index{rna\_\-plot\_\-type@{rna\_\-plot\_\-type}!plot_layouts.h@{plot\_\-layouts.h}}
\subsubsection[{rna\_\-plot\_\-type}]{\setlength{\rightskip}{0pt plus 5cm}int {\bf rna\_\-plot\_\-type}}}
\label{plot__layouts_8h_a5964c4581431b098b80027d6e14dcdd4}


Switch for changing the secondary structure layout algorithm. Current possibility are 0 for a simple radial drawing or 1 for the modified radial drawing taken from the {\itshape naview\/} program of Bruccoleri \& Heinrich (1988).

\begin{DoxyNote}{Note}
To provide thread safety please do not rely on this global variable in future implementations but pass a plot type flag directly to the function that decides which layout algorithm it may use!
\end{DoxyNote}
\begin{DoxySeeAlso}{See also}
\hyperlink{plot__layouts_8h_ae6d17b9f0a53cf5205a9181e0f8422e9}{VRNA\_\-PLOT\_\-TYPE\_\-SIMPLE}, \hyperlink{plot__layouts_8h_a94d4c863ecac2f220f76658afb92f964}{VRNA\_\-PLOT\_\-TYPE\_\-NAVIEW}, \hyperlink{plot__layouts_8h_a8c9eac631348da92136c8363ecdd9fb9}{VRNA\_\-PLOT\_\-TYPE\_\-CIRCULAR} 
\end{DoxySeeAlso}
