binaries/src/ViennaRNA/doc/latex/plot__layouts_8h.tex

   1 \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}
   2 \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}}
   3 }
   4
   5
   6 Secondary structure plot layout algorithms.
   7
   8
   9 Include dependency graph for plot\-\_\-layouts.\-h\-:
  10 \nopagebreak
  11 \begin{figure}[H]
  12 \begin{center}
  13 \leavevmode
  14 \includegraphics[width=254pt]{plot__layouts_8h__incl}
  15 \end{center}
  16 \end{figure}
  17 This graph shows which files directly or indirectly include this file\-:
  18 \nopagebreak
  19 \begin{figure}[H]
  20 \begin{center}
  21 \leavevmode
  22 \includegraphics[width=250pt]{plot__layouts_8h__dep__incl}
  23 \end{center}
  24 \end{figure}
  25 \subsection*{Macros}
  26 \begin{DoxyCompactItemize}
  27 \item
  28 \#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
  29 \begin{DoxyCompactList}\small\item\em Definition of Plot type {\itshape simple} \end{DoxyCompactList}\item
  30 \#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
  31 \begin{DoxyCompactList}\small\item\em Definition of Plot type {\itshape Naview} \end{DoxyCompactList}\item
  32 \#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
  33 \begin{DoxyCompactList}\small\item\em Definition of Plot type {\itshape Circular} \end{DoxyCompactList}\end{DoxyCompactItemize}
  34 \subsection*{Functions}
  35 \begin{DoxyCompactItemize}
  36 \item
  37 int \hyperlink{plot__layouts_8h_af4b9173e7d3fd361c3c85e6def194123}{simple\-\_\-xy\-\_\-coordinates} (short $\ast$pair\-\_\-table, float $\ast$X, float $\ast$Y)
  38 \begin{DoxyCompactList}\small\item\em Calculate nucleotide coordinates for secondary structure plot the {\itshape Simple way} \end{DoxyCompactList}\item
  39 int \hyperlink{plot__layouts_8h_ac4ea13d35308f09940178d2b05a248c2}{simple\-\_\-circplot\-\_\-coordinates} (short $\ast$pair\-\_\-table, float $\ast$x, float $\ast$y)
  40 \begin{DoxyCompactList}\small\item\em Calculate nucleotide coordinates for {\itshape Circular Plot} \end{DoxyCompactList}\end{DoxyCompactItemize}
  41 \subsection*{Variables}
  42 \begin{DoxyCompactItemize}
  43 \item
  44 int \hyperlink{plot__layouts_8h_a5964c4581431b098b80027d6e14dcdd4}{rna\-\_\-plot\-\_\-type}
  45 \begin{DoxyCompactList}\small\item\em Switch for changing the secondary structure layout algorithm. \end{DoxyCompactList}\end{DoxyCompactItemize}
  46
  47
  48 \subsection{Detailed Description}
  49 Secondary structure plot layout algorithms. c Ronny Lorenz The Vienna\-R\-N\-A Package
  50
  51 \subsection{Macro Definition Documentation}
  52 \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}}
  53 \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}}
  54 \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}
  55
  56
  57 Definition of Plot type {\itshape simple}
  58
  59 This is the plot type definition for several R\-N\-A structure plotting functions telling them to use {\bfseries Simple} plotting algorithm
  60
  61 \begin{DoxySeeAlso}{See Also}
  62 \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()}
  63 \end{DoxySeeAlso}
  64 \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}}
  65 \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}}
  66 \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}
  67
  68
  69 Definition of Plot type {\itshape Naview}
  70
  71 This is the plot type definition for several R\-N\-A structure plotting functions telling them to use {\bfseries Naview} plotting algorithm
  72
  73 \begin{DoxySeeAlso}{See Also}
  74 \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()}
  75 \end{DoxySeeAlso}
  76 \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}}
  77 \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}}
  78 \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}
  79
  80
  81 Definition of Plot type {\itshape Circular}
  82
  83 This is the plot type definition for several R\-N\-A structure plotting functions telling them to produce a {\bfseries Circular plot}
  84
  85 \begin{DoxySeeAlso}{See Also}
  86 \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()}
  87 \end{DoxySeeAlso}
  88
  89
  90 \subsection{Function Documentation}
  91 \hypertarget{plot__layouts_8h_af4b9173e7d3fd361c3c85e6def194123}{\index{plot\-\_\-layouts.\-h@{plot\-\_\-layouts.\-h}!simple\-\_\-xy\-\_\-coordinates@{simple\-\_\-xy\-\_\-coordinates}}
  92 \index{simple\-\_\-xy\-\_\-coordinates@{simple\-\_\-xy\-\_\-coordinates}!plot_layouts.h@{plot\-\_\-layouts.\-h}}
  93 \subsubsection[{simple\-\_\-xy\-\_\-coordinates}]{\setlength{\rightskip}{0pt plus 5cm}int simple\-\_\-xy\-\_\-coordinates (
  94 \begin{DoxyParamCaption}
  95 \item[{short $\ast$}]{pair\-\_\-table, }
  96 \item[{float $\ast$}]{X, }
  97 \item[{float $\ast$}]{Y}
  98 \end{DoxyParamCaption}
  99 )}}\label{plot__layouts_8h_af4b9173e7d3fd361c3c85e6def194123}
 100
 101
 102 Calculate nucleotide coordinates for secondary structure plot the {\itshape Simple way}
 103
 104 \begin{DoxySeeAlso}{See Also}
 105 \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()}
 106 \end{DoxySeeAlso}
 107
 108 \begin{DoxyParams}{Parameters}
 109 {\em pair\-\_\-table} & The pair table of the secondary structure \\
 110 \hline
 111 {\em X} & a pointer to an array with enough allocated space to hold the x coordinates \\
 112 \hline
 113 {\em Y} & a pointer to an array with enough allocated space to hold the y coordinates \\
 114 \hline
 115 \end{DoxyParams}
 116 \begin{DoxyReturn}{Returns}
 117 length of sequence on success, 0 otherwise
 118 \end{DoxyReturn}
 119 \hypertarget{plot__layouts_8h_ac4ea13d35308f09940178d2b05a248c2}{\index{plot\-\_\-layouts.\-h@{plot\-\_\-layouts.\-h}!simple\-\_\-circplot\-\_\-coordinates@{simple\-\_\-circplot\-\_\-coordinates}}
 120 \index{simple\-\_\-circplot\-\_\-coordinates@{simple\-\_\-circplot\-\_\-coordinates}!plot_layouts.h@{plot\-\_\-layouts.\-h}}
 121 \subsubsection[{simple\-\_\-circplot\-\_\-coordinates}]{\setlength{\rightskip}{0pt plus 5cm}int simple\-\_\-circplot\-\_\-coordinates (
 122 \begin{DoxyParamCaption}
 123 \item[{short $\ast$}]{pair\-\_\-table, }
 124 \item[{float $\ast$}]{x, }
 125 \item[{float $\ast$}]{y}
 126 \end{DoxyParamCaption}
 127 )}}\label{plot__layouts_8h_ac4ea13d35308f09940178d2b05a248c2}
 128
 129
 130 Calculate nucleotide coordinates for {\itshape Circular Plot}
 131
 132 This function calculates the coordinates of nucleotides mapped in equal distancies onto a unit circle.
 133
 134 \begin{DoxyNote}{Note}
 135 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 $P^{t}_y[i] = Y[i] * rs$.
 136 \end{DoxyNote}
 137 \begin{DoxySeeAlso}{See Also}
 138 \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()}
 139 \end{DoxySeeAlso}
 140
 141 \begin{DoxyParams}{Parameters}
 142 {\em pair\-\_\-table} & The pair table of the secondary structure \\
 143 \hline
 144 {\em x} & a pointer to an array with enough allocated space to hold the x coordinates \\
 145 \hline
 146 {\em y} & a pointer to an array with enough allocated space to hold the y coordinates \\
 147 \hline
 148 \end{DoxyParams}
 149 \begin{DoxyReturn}{Returns}
 150 length of sequence on success, 0 otherwise
 151 \end{DoxyReturn}
 152
 153
 154 \subsection{Variable Documentation}
 155 \hypertarget{plot__layouts_8h_a5964c4581431b098b80027d6e14dcdd4}{\index{plot\-\_\-layouts.\-h@{plot\-\_\-layouts.\-h}!rna\-\_\-plot\-\_\-type@{rna\-\_\-plot\-\_\-type}}
 156 \index{rna\-\_\-plot\-\_\-type@{rna\-\_\-plot\-\_\-type}!plot_layouts.h@{plot\-\_\-layouts.\-h}}
 157 \subsubsection[{rna\-\_\-plot\-\_\-type}]{\setlength{\rightskip}{0pt plus 5cm}int rna\-\_\-plot\-\_\-type}}\label{plot__layouts_8h_a5964c4581431b098b80027d6e14dcdd4}
 158
 159
 160 Switch for changing the secondary structure layout algorithm.
 161
 162 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).
 163
 164 \begin{DoxyNote}{Note}
 165 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!
 166 \end{DoxyNote}
 167 \begin{DoxySeeAlso}{See Also}
 168 \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}
 169 \end{DoxySeeAlso}