1 \hypertarget{PS__dot_8h}{
2 \section{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/PS\_\-dot.h File Reference}
3 \label{PS__dot_8h}\index{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/PS\_\-dot.h@{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/PS\_\-dot.h}}
7 Various functions for plotting RNA secondary structures, dot-\/plots and other visualizations.
8 Include dependency graph for PS\_\-dot.h:\nopagebreak
12 \includegraphics[width=211pt]{PS__dot_8h__incl}
15 \subsection*{Functions}
16 \begin{DoxyCompactItemize}
18 int \hyperlink{PS__dot_8h_a0873c7cc4cd7a11c9a2cea19dde7e9c9}{PS\_\-rna\_\-plot} (char $\ast$string, char $\ast$structure, char $\ast$file)
19 \begin{DoxyCompactList}\small\item\em Produce a secondary structure graph in PostScript and write it to 'filename'. \item\end{DoxyCompactList}\item
20 int \hyperlink{PS__dot_8h_a47856b2504b566588785597b6ebb8271}{PS\_\-rna\_\-plot\_\-a} (char $\ast$string, char $\ast$structure, char $\ast$file, char $\ast$pre, char $\ast$post)
21 \begin{DoxyCompactList}\small\item\em Produce a secondary structure graph in PostScript including additional annotation macros and write it to 'filename'. \item\end{DoxyCompactList}\item
22 int \hyperlink{PS__dot_8h_a70834bc8c0aad4fe6824ff76ccb8f329}{gmlRNA} (char $\ast$string, char $\ast$structure, char $\ast$ssfile, char option)
23 \begin{DoxyCompactList}\small\item\em Produce a secondary structure graph in Graph Meta Language (gml) and write it to a file. \item\end{DoxyCompactList}\item
24 int \hyperlink{PS__dot_8h_add368528755f9a830727b680243541df}{ssv\_\-rna\_\-plot} (char $\ast$string, char $\ast$structure, char $\ast$ssfile)
25 \begin{DoxyCompactList}\small\item\em Produce a secondary structure graph in SStructView format. \item\end{DoxyCompactList}\item
26 int \hyperlink{PS__dot_8h_ae7853539b5df98f294b4af434e979304}{svg\_\-rna\_\-plot} (char $\ast$string, char $\ast$structure, char $\ast$ssfile)
27 \begin{DoxyCompactList}\small\item\em Produce a secondary structure plot in SVG format and write it to a file. \item\end{DoxyCompactList}\item
28 int \hyperlink{PS__dot_8h_a2f6d5953e6a323df898896b8d6614483}{xrna\_\-plot} (char $\ast$string, char $\ast$structure, char $\ast$ssfile)
29 \begin{DoxyCompactList}\small\item\em Produce a secondary structure plot for further editing in XRNA. \item\end{DoxyCompactList}\item
30 int \hyperlink{PS__dot_8h_a00ea223b5cf02eb2faae5ff29f0d5e12}{PS\_\-dot\_\-plot\_\-list} (char $\ast$seq, char $\ast$filename, \hyperlink{structplist}{plist} $\ast$pl, \hyperlink{structplist}{plist} $\ast$mf, char $\ast$comment)
31 \begin{DoxyCompactList}\small\item\em Produce a postscript dot-\/plot from two pair lists. \item\end{DoxyCompactList}\item
32 int \hyperlink{PS__dot_8h_aab48d4dac655d688abe921389ac2847c}{aliPS\_\-color\_\-aln} (const char $\ast$structure, const char $\ast$filename, const char $\ast$seqs\mbox{[}$\,$\mbox{]}, const char $\ast$names\mbox{[}$\,$\mbox{]})
34 int \hyperlink{PS__dot_8h_a689a97a7e3b8a2df14728b8204d9d57b}{PS\_\-dot\_\-plot} (char $\ast$string, char $\ast$file)
35 \begin{DoxyCompactList}\small\item\em Produce postscript dot-\/plot. \item\end{DoxyCompactList}\end{DoxyCompactItemize}
38 \subsection{Detailed Description}
39 Various functions for plotting RNA secondary structures, dot-\/plots and other visualizations.
41 \subsection{Function Documentation}
42 \hypertarget{PS__dot_8h_a0873c7cc4cd7a11c9a2cea19dde7e9c9}{
43 \index{PS\_\-dot.h@{PS\_\-dot.h}!PS\_\-rna\_\-plot@{PS\_\-rna\_\-plot}}
44 \index{PS\_\-rna\_\-plot@{PS\_\-rna\_\-plot}!PS_dot.h@{PS\_\-dot.h}}
45 \subsubsection[{PS\_\-rna\_\-plot}]{\setlength{\rightskip}{0pt plus 5cm}int PS\_\-rna\_\-plot (char $\ast$ {\em string}, \/ char $\ast$ {\em structure}, \/ char $\ast$ {\em file})}}
46 \label{PS__dot_8h_a0873c7cc4cd7a11c9a2cea19dde7e9c9}
49 Produce a secondary structure graph in PostScript and write it to 'filename'. Note that this function has changed from previous versions and now expects the structure to be plotted in dot-\/bracket notation as an argument. It does not make use of the global \hyperlink{fold__vars_8h_a0244a629b5ab4f58b77590c3dfd130dc}{base\_\-pair} array anymore.
52 \begin{DoxyParams}{Parameters}
53 \item[{\em string}]The RNA sequence \item[{\em structure}]The secondary structure in dot-\/bracket notation \item[{\em file}]The filename of the postscript output \end{DoxyParams}
54 \begin{DoxyReturn}{Returns}
55 1 on success, 0 otherwise
57 \hypertarget{PS__dot_8h_a47856b2504b566588785597b6ebb8271}{
58 \index{PS\_\-dot.h@{PS\_\-dot.h}!PS\_\-rna\_\-plot\_\-a@{PS\_\-rna\_\-plot\_\-a}}
59 \index{PS\_\-rna\_\-plot\_\-a@{PS\_\-rna\_\-plot\_\-a}!PS_dot.h@{PS\_\-dot.h}}
60 \subsubsection[{PS\_\-rna\_\-plot\_\-a}]{\setlength{\rightskip}{0pt plus 5cm}int PS\_\-rna\_\-plot\_\-a (char $\ast$ {\em string}, \/ char $\ast$ {\em structure}, \/ char $\ast$ {\em file}, \/ char $\ast$ {\em pre}, \/ char $\ast$ {\em post})}}
61 \label{PS__dot_8h_a47856b2504b566588785597b6ebb8271}
64 Produce a secondary structure graph in PostScript including additional annotation macros and write it to 'filename'. Same as \hyperlink{PS__dot_8h_a0873c7cc4cd7a11c9a2cea19dde7e9c9}{PS\_\-rna\_\-plot()} but adds extra PostScript macros for various annotations (see generated PS code). The 'pre' and 'post' variables contain PostScript code that is verbatim copied in the resulting PS file just before and after the structure plot. If both arguments ('pre' and 'post') are NULL, no additional macros will be printed into the PostScript.
67 \begin{DoxyParams}{Parameters}
68 \item[{\em string}]The RNA sequence \item[{\em structure}]The secondary structure in dot-\/bracket notation \item[{\em file}]The filename of the postscript output \item[{\em pre}]PostScript code to appear before the secondary structure plot \item[{\em post}]PostScript code to appear after the secondary structure plot \end{DoxyParams}
69 \begin{DoxyReturn}{Returns}
70 1 on success, 0 otherwise
72 \hypertarget{PS__dot_8h_a70834bc8c0aad4fe6824ff76ccb8f329}{
73 \index{PS\_\-dot.h@{PS\_\-dot.h}!gmlRNA@{gmlRNA}}
74 \index{gmlRNA@{gmlRNA}!PS_dot.h@{PS\_\-dot.h}}
75 \subsubsection[{gmlRNA}]{\setlength{\rightskip}{0pt plus 5cm}int gmlRNA (char $\ast$ {\em string}, \/ char $\ast$ {\em structure}, \/ char $\ast$ {\em ssfile}, \/ char {\em option})}}
76 \label{PS__dot_8h_a70834bc8c0aad4fe6824ff76ccb8f329}
79 Produce a secondary structure graph in Graph Meta Language (gml) and write it to a file. If 'option' is an uppercase letter the RNA sequence is used to label nodes, if 'option' equals {\itshape 'X'\/} or {\itshape 'x'\/} the resulting file will coordinates for an initial layout of the graph.
82 \begin{DoxyParams}{Parameters}
83 \item[{\em string}]The RNA sequence \item[{\em structure}]The secondary structure in dot-\/bracket notation \item[{\em ssfile}]The filename of the gml output \item[{\em option}]The option flag \end{DoxyParams}
84 \begin{DoxyReturn}{Returns}
85 1 on success, 0 otherwise
87 \hypertarget{PS__dot_8h_add368528755f9a830727b680243541df}{
88 \index{PS\_\-dot.h@{PS\_\-dot.h}!ssv\_\-rna\_\-plot@{ssv\_\-rna\_\-plot}}
89 \index{ssv\_\-rna\_\-plot@{ssv\_\-rna\_\-plot}!PS_dot.h@{PS\_\-dot.h}}
90 \subsubsection[{ssv\_\-rna\_\-plot}]{\setlength{\rightskip}{0pt plus 5cm}int ssv\_\-rna\_\-plot (char $\ast$ {\em string}, \/ char $\ast$ {\em structure}, \/ char $\ast$ {\em ssfile})}}
91 \label{PS__dot_8h_add368528755f9a830727b680243541df}
94 Produce a secondary structure graph in SStructView format. Write coord file for SStructView
97 \begin{DoxyParams}{Parameters}
98 \item[{\em string}]The RNA sequence \item[{\em structure}]The secondary structure in dot-\/bracket notation \item[{\em ssfile}]The filename of the ssv output \end{DoxyParams}
99 \begin{DoxyReturn}{Returns}
100 1 on success, 0 otherwise
102 \hypertarget{PS__dot_8h_ae7853539b5df98f294b4af434e979304}{
103 \index{PS\_\-dot.h@{PS\_\-dot.h}!svg\_\-rna\_\-plot@{svg\_\-rna\_\-plot}}
104 \index{svg\_\-rna\_\-plot@{svg\_\-rna\_\-plot}!PS_dot.h@{PS\_\-dot.h}}
105 \subsubsection[{svg\_\-rna\_\-plot}]{\setlength{\rightskip}{0pt plus 5cm}int svg\_\-rna\_\-plot (char $\ast$ {\em string}, \/ char $\ast$ {\em structure}, \/ char $\ast$ {\em ssfile})}}
106 \label{PS__dot_8h_ae7853539b5df98f294b4af434e979304}
109 Produce a secondary structure plot in SVG format and write it to a file.
110 \begin{DoxyParams}{Parameters}
111 \item[{\em string}]The RNA sequence \item[{\em structure}]The secondary structure in dot-\/bracket notation \item[{\em ssfile}]The filename of the svg output \end{DoxyParams}
112 \begin{DoxyReturn}{Returns}
113 1 on success, 0 otherwise
115 \hypertarget{PS__dot_8h_a2f6d5953e6a323df898896b8d6614483}{
116 \index{PS\_\-dot.h@{PS\_\-dot.h}!xrna\_\-plot@{xrna\_\-plot}}
117 \index{xrna\_\-plot@{xrna\_\-plot}!PS_dot.h@{PS\_\-dot.h}}
118 \subsubsection[{xrna\_\-plot}]{\setlength{\rightskip}{0pt plus 5cm}int xrna\_\-plot (char $\ast$ {\em string}, \/ char $\ast$ {\em structure}, \/ char $\ast$ {\em ssfile})}}
119 \label{PS__dot_8h_a2f6d5953e6a323df898896b8d6614483}
122 Produce a secondary structure plot for further editing in XRNA.
123 \begin{DoxyParams}{Parameters}
124 \item[{\em string}]The RNA sequence \item[{\em structure}]The secondary structure in dot-\/bracket notation \item[{\em ssfile}]The filename of the xrna output \end{DoxyParams}
125 \begin{DoxyReturn}{Returns}
126 1 on success, 0 otherwise
128 \hypertarget{PS__dot_8h_a00ea223b5cf02eb2faae5ff29f0d5e12}{
129 \index{PS\_\-dot.h@{PS\_\-dot.h}!PS\_\-dot\_\-plot\_\-list@{PS\_\-dot\_\-plot\_\-list}}
130 \index{PS\_\-dot\_\-plot\_\-list@{PS\_\-dot\_\-plot\_\-list}!PS_dot.h@{PS\_\-dot.h}}
131 \subsubsection[{PS\_\-dot\_\-plot\_\-list}]{\setlength{\rightskip}{0pt plus 5cm}int PS\_\-dot\_\-plot\_\-list (char $\ast$ {\em seq}, \/ char $\ast$ {\em filename}, \/ {\bf plist} $\ast$ {\em pl}, \/ {\bf plist} $\ast$ {\em mf}, \/ char $\ast$ {\em comment})}}
132 \label{PS__dot_8h_a00ea223b5cf02eb2faae5ff29f0d5e12}
135 Produce a postscript dot-\/plot from two pair lists. This function reads two \hyperlink{structplist}{plist} structures (e.g. base pair probabilities and a secondary structure) as produced by \hyperlink{group__pf__fold_ga03e15e831a31b1154855ab47edbdb019}{assign\_\-plist\_\-from\_\-pr()} and \hyperlink{fold_8h_adaa59b81664e2e36cb9932e891558fae}{assign\_\-plist\_\-from\_\-db()} and produces a postscript \char`\"{}dot plot\char`\"{} that is written to 'filename'.\par
136 Using base pair probabilities in the first and mfe structure in the second \hyperlink{structplist}{plist}, the resulting \char`\"{}dot plot\char`\"{} represents each base pairing probability by a square of corresponding area in a upper triangle matrix. The lower part of the matrix contains the minimum free energy structure.
138 \begin{DoxySeeAlso}{See also}
139 \hyperlink{group__pf__fold_ga03e15e831a31b1154855ab47edbdb019}{assign\_\-plist\_\-from\_\-pr()}, \hyperlink{fold_8h_adaa59b81664e2e36cb9932e891558fae}{assign\_\-plist\_\-from\_\-db()}
142 \begin{DoxyParams}{Parameters}
143 \item[{\em seq}]The RNA sequence \item[{\em filename}]A filename for the postscript output \item[{\em pl}]The base pair probability pairlist \item[{\em mf}]The mfe secondary structure pairlist \item[{\em comment}]A comment \end{DoxyParams}
144 \begin{DoxyReturn}{Returns}
145 1 if postscript was successfully written, 0 otherwise
147 \hypertarget{PS__dot_8h_aab48d4dac655d688abe921389ac2847c}{
148 \index{PS\_\-dot.h@{PS\_\-dot.h}!aliPS\_\-color\_\-aln@{aliPS\_\-color\_\-aln}}
149 \index{aliPS\_\-color\_\-aln@{aliPS\_\-color\_\-aln}!PS_dot.h@{PS\_\-dot.h}}
150 \subsubsection[{aliPS\_\-color\_\-aln}]{\setlength{\rightskip}{0pt plus 5cm}int aliPS\_\-color\_\-aln (const char $\ast$ {\em structure}, \/ const char $\ast$ {\em filename}, \/ const char $\ast$ {\em seqs}\mbox{[}$\,$\mbox{]}, \/ const char $\ast$ {\em names}\mbox{[}$\,$\mbox{]})}}
151 \label{PS__dot_8h_aab48d4dac655d688abe921389ac2847c}
152 PS\_\-color\_\-aln for duplexes \hypertarget{PS__dot_8h_a689a97a7e3b8a2df14728b8204d9d57b}{
153 \index{PS\_\-dot.h@{PS\_\-dot.h}!PS\_\-dot\_\-plot@{PS\_\-dot\_\-plot}}
154 \index{PS\_\-dot\_\-plot@{PS\_\-dot\_\-plot}!PS_dot.h@{PS\_\-dot.h}}
155 \subsubsection[{PS\_\-dot\_\-plot}]{\setlength{\rightskip}{0pt plus 5cm}int PS\_\-dot\_\-plot (char $\ast$ {\em string}, \/ char $\ast$ {\em file})}}
156 \label{PS__dot_8h_a689a97a7e3b8a2df14728b8204d9d57b}
159 Produce postscript dot-\/plot. Wrapper to PS\_\-dot\_\-plot\_\-list
161 Reads base pair probabilities produced by \hyperlink{group__pf__fold_gadc3db3d98742427e7001a7fd36ef28c2}{pf\_\-fold()} from the global array \hyperlink{fold__vars_8h_a0f5757427fd5f2f79d6fca0081cd5a52}{pr} and the pair list \hyperlink{fold__vars_8h_a0244a629b5ab4f58b77590c3dfd130dc}{base\_\-pair} produced by \hyperlink{group__mfe__fold_gaadafcb0f140795ae62e5ca027e335a9b}{fold()} and produces a postscript \char`\"{}dot plot\char`\"{} that is written to 'filename'. The \char`\"{}dot plot\char`\"{} represents each base pairing probability by a square of corresponding area in a upper triangle matrix. The lower part of the matrix contains the minimum free energy \begin{DoxyNote}{Note}
162 DO NOT USE THIS FUNCTION ANYMORE SINCE IT IS NOT THREADSAFE
165 \item[\hyperlink{deprecated__deprecated000019}{Deprecated}]This function is deprecated and will be removed soon! Use \hyperlink{PS__dot_8h_a00ea223b5cf02eb2faae5ff29f0d5e12}{PS\_\-dot\_\-plot\_\-list()} instead! \end{Desc}