--- /dev/null
+\hypertarget{plot__layouts_8h}{\section{/home/asherstnev/\-Projects/\-Java.projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/plot\-\_\-layouts.h File Reference}
+\label{plot__layouts_8h}\index{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/plot\-\_\-layouts.\-h@{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-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=254pt]{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=250pt]{plot__layouts_8h__dep__incl}
+\end{center}
+\end{figure}
+\subsection*{Macros}
+\begin{DoxyCompactItemize}
+\item
+\#define \hyperlink{plot__layouts_8h_ae6d17b9f0a53cf5205a9181e0f8422e9}{V\-R\-N\-A\-\_\-\-P\-L\-O\-T\-\_\-\-T\-Y\-P\-E\-\_\-\-S\-I\-M\-P\-L\-E}~0
+\begin{DoxyCompactList}\small\item\em Definition of Plot type {\itshape simple} \end{DoxyCompactList}\item
+\#define \hyperlink{plot__layouts_8h_a94d4c863ecac2f220f76658afb92f964}{V\-R\-N\-A\-\_\-\-P\-L\-O\-T\-\_\-\-T\-Y\-P\-E\-\_\-\-N\-A\-V\-I\-E\-W}~1
+\begin{DoxyCompactList}\small\item\em Definition of Plot type {\itshape Naview} \end{DoxyCompactList}\item
+\#define \hyperlink{plot__layouts_8h_a8c9eac631348da92136c8363ecdd9fb9}{V\-R\-N\-A\-\_\-\-P\-L\-O\-T\-\_\-\-T\-Y\-P\-E\-\_\-\-C\-I\-R\-C\-U\-L\-A\-R}~2
+\begin{DoxyCompactList}\small\item\em Definition of Plot type {\itshape Circular} \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} \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} \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. \end{DoxyCompactList}\end{DoxyCompactItemize}
+
+
+\subsection{Detailed Description}
+Secondary structure plot layout algorithms. c Ronny Lorenz The Vienna\-R\-N\-A Package
+
+\subsection{Macro Definition Documentation}
+\hypertarget{plot__layouts_8h_ae6d17b9f0a53cf5205a9181e0f8422e9}{\index{plot\-\_\-layouts.\-h@{plot\-\_\-layouts.\-h}!V\-R\-N\-A\-\_\-\-P\-L\-O\-T\-\_\-\-T\-Y\-P\-E\-\_\-\-S\-I\-M\-P\-L\-E@{V\-R\-N\-A\-\_\-\-P\-L\-O\-T\-\_\-\-T\-Y\-P\-E\-\_\-\-S\-I\-M\-P\-L\-E}}
+\index{V\-R\-N\-A\-\_\-\-P\-L\-O\-T\-\_\-\-T\-Y\-P\-E\-\_\-\-S\-I\-M\-P\-L\-E@{V\-R\-N\-A\-\_\-\-P\-L\-O\-T\-\_\-\-T\-Y\-P\-E\-\_\-\-S\-I\-M\-P\-L\-E}!plot_layouts.h@{plot\-\_\-layouts.\-h}}
+\subsubsection[{V\-R\-N\-A\-\_\-\-P\-L\-O\-T\-\_\-\-T\-Y\-P\-E\-\_\-\-S\-I\-M\-P\-L\-E}]{\setlength{\rightskip}{0pt plus 5cm}\#define V\-R\-N\-A\-\_\-\-P\-L\-O\-T\-\_\-\-T\-Y\-P\-E\-\_\-\-S\-I\-M\-P\-L\-E~0}}\label{plot__layouts_8h_ae6d17b9f0a53cf5205a9181e0f8422e9}
+
+
+Definition of Plot type {\itshape simple}
+
+This is the plot type definition for several R\-N\-A 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}{P\-S\-\_\-rna\-\_\-plot\-\_\-a()}, \hyperlink{PS__dot_8h_a0873c7cc4cd7a11c9a2cea19dde7e9c9}{P\-S\-\_\-rna\-\_\-plot()}, \hyperlink{PS__dot_8h_ae7853539b5df98f294b4af434e979304}{svg\-\_\-rna\-\_\-plot()}, \hyperlink{PS__dot_8h_a70834bc8c0aad4fe6824ff76ccb8f329}{gml\-R\-N\-A()}, \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}!V\-R\-N\-A\-\_\-\-P\-L\-O\-T\-\_\-\-T\-Y\-P\-E\-\_\-\-N\-A\-V\-I\-E\-W@{V\-R\-N\-A\-\_\-\-P\-L\-O\-T\-\_\-\-T\-Y\-P\-E\-\_\-\-N\-A\-V\-I\-E\-W}}
+\index{V\-R\-N\-A\-\_\-\-P\-L\-O\-T\-\_\-\-T\-Y\-P\-E\-\_\-\-N\-A\-V\-I\-E\-W@{V\-R\-N\-A\-\_\-\-P\-L\-O\-T\-\_\-\-T\-Y\-P\-E\-\_\-\-N\-A\-V\-I\-E\-W}!plot_layouts.h@{plot\-\_\-layouts.\-h}}
+\subsubsection[{V\-R\-N\-A\-\_\-\-P\-L\-O\-T\-\_\-\-T\-Y\-P\-E\-\_\-\-N\-A\-V\-I\-E\-W}]{\setlength{\rightskip}{0pt plus 5cm}\#define V\-R\-N\-A\-\_\-\-P\-L\-O\-T\-\_\-\-T\-Y\-P\-E\-\_\-\-N\-A\-V\-I\-E\-W~1}}\label{plot__layouts_8h_a94d4c863ecac2f220f76658afb92f964}
+
+
+Definition of Plot type {\itshape Naview}
+
+This is the plot type definition for several R\-N\-A 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}{P\-S\-\_\-rna\-\_\-plot\-\_\-a()}, \hyperlink{PS__dot_8h_a0873c7cc4cd7a11c9a2cea19dde7e9c9}{P\-S\-\_\-rna\-\_\-plot()}, \hyperlink{PS__dot_8h_ae7853539b5df98f294b4af434e979304}{svg\-\_\-rna\-\_\-plot()}, \hyperlink{PS__dot_8h_a70834bc8c0aad4fe6824ff76ccb8f329}{gml\-R\-N\-A()}, \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}!V\-R\-N\-A\-\_\-\-P\-L\-O\-T\-\_\-\-T\-Y\-P\-E\-\_\-\-C\-I\-R\-C\-U\-L\-A\-R@{V\-R\-N\-A\-\_\-\-P\-L\-O\-T\-\_\-\-T\-Y\-P\-E\-\_\-\-C\-I\-R\-C\-U\-L\-A\-R}}
+\index{V\-R\-N\-A\-\_\-\-P\-L\-O\-T\-\_\-\-T\-Y\-P\-E\-\_\-\-C\-I\-R\-C\-U\-L\-A\-R@{V\-R\-N\-A\-\_\-\-P\-L\-O\-T\-\_\-\-T\-Y\-P\-E\-\_\-\-C\-I\-R\-C\-U\-L\-A\-R}!plot_layouts.h@{plot\-\_\-layouts.\-h}}
+\subsubsection[{V\-R\-N\-A\-\_\-\-P\-L\-O\-T\-\_\-\-T\-Y\-P\-E\-\_\-\-C\-I\-R\-C\-U\-L\-A\-R}]{\setlength{\rightskip}{0pt plus 5cm}\#define V\-R\-N\-A\-\_\-\-P\-L\-O\-T\-\_\-\-T\-Y\-P\-E\-\_\-\-C\-I\-R\-C\-U\-L\-A\-R~2}}\label{plot__layouts_8h_a8c9eac631348da92136c8363ecdd9fb9}
+
+
+Definition of Plot type {\itshape Circular}
+
+This is the plot type definition for several R\-N\-A 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}{P\-S\-\_\-rna\-\_\-plot\-\_\-a()}, \hyperlink{PS__dot_8h_a0873c7cc4cd7a11c9a2cea19dde7e9c9}{P\-S\-\_\-rna\-\_\-plot()}, \hyperlink{PS__dot_8h_ae7853539b5df98f294b4af434e979304}{svg\-\_\-rna\-\_\-plot()}, \hyperlink{PS__dot_8h_a70834bc8c0aad4fe6824ff76ccb8f329}{gml\-R\-N\-A()}, \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 (
+\begin{DoxyParamCaption}
+\item[{short $\ast$}]{pair\-\_\-table, }
+\item[{float $\ast$}]{X, }
+\item[{float $\ast$}]{Y}
+\end{DoxyParamCaption}
+)}}\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}{P\-S\-\_\-rna\-\_\-plot\-\_\-a()}, \hyperlink{PS__dot_8h_a0873c7cc4cd7a11c9a2cea19dde7e9c9}{P\-S\-\_\-rna\-\_\-plot}, \hyperlink{PS__dot_8h_ae7853539b5df98f294b4af434e979304}{svg\-\_\-rna\-\_\-plot()}
+\end{DoxySeeAlso}
+
+\begin{DoxyParams}{Parameters}
+{\em pair\-\_\-table} & The pair table of the secondary structure \\
+\hline
+{\em X} & a pointer to an array with enough allocated space to hold the x coordinates \\
+\hline
+{\em Y} & a pointer to an array with enough allocated space to hold the y coordinates \\
+\hline
+\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 (
+\begin{DoxyParamCaption}
+\item[{short $\ast$}]{pair\-\_\-table, }
+\item[{float $\ast$}]{x, }
+\item[{float $\ast$}]{y}
+\end{DoxyParamCaption}
+)}}\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}{P\-S\-\_\-rna\-\_\-plot\-\_\-a()}, \hyperlink{PS__dot_8h_a0873c7cc4cd7a11c9a2cea19dde7e9c9}{P\-S\-\_\-rna\-\_\-plot}, \hyperlink{PS__dot_8h_ae7853539b5df98f294b4af434e979304}{svg\-\_\-rna\-\_\-plot()}
+\end{DoxySeeAlso}
+
+\begin{DoxyParams}{Parameters}
+{\em pair\-\_\-table} & The pair table of the secondary structure \\
+\hline
+{\em x} & a pointer to an array with enough allocated space to hold the x coordinates \\
+\hline
+{\em y} & a pointer to an array with enough allocated space to hold the y coordinates \\
+\hline
+\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 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}{V\-R\-N\-A\-\_\-\-P\-L\-O\-T\-\_\-\-T\-Y\-P\-E\-\_\-\-S\-I\-M\-P\-L\-E}, \hyperlink{plot__layouts_8h_a94d4c863ecac2f220f76658afb92f964}{V\-R\-N\-A\-\_\-\-P\-L\-O\-T\-\_\-\-T\-Y\-P\-E\-\_\-\-N\-A\-V\-I\-E\-W}, \hyperlink{plot__layouts_8h_a8c9eac631348da92136c8363ecdd9fb9}{V\-R\-N\-A\-\_\-\-P\-L\-O\-T\-\_\-\-T\-Y\-P\-E\-\_\-\-C\-I\-R\-C\-U\-L\-A\-R}
+\end{DoxySeeAlso}
git://source.jalview.org / jabaws.git / blobdiff