--- /dev/null
+\hypertarget{PS__dot_8h}{\section{/home/asherstnev/\-Projects/\-Java.projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\-P\-S\-\_\-dot.h File Reference}
+\label{PS__dot_8h}\index{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\-P\-S\-\_\-dot.\-h@{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\-P\-S\-\_\-dot.\-h}}
+}
+
+
+Various functions for plotting R\-N\-A secondary structures, dot-\/plots and other visualizations.
+
+
+Include dependency graph for P\-S\-\_\-dot.\-h\-:
+\nopagebreak
+\begin{figure}[H]
+\begin{center}
+\leavevmode
+\includegraphics[width=250pt]{PS__dot_8h__incl}
+\end{center}
+\end{figure}
+\subsection*{Functions}
+\begin{DoxyCompactItemize}
+\item
+int \hyperlink{PS__dot_8h_a0873c7cc4cd7a11c9a2cea19dde7e9c9}{P\-S\-\_\-rna\-\_\-plot} (char $\ast$string, char $\ast$structure, char $\ast$file)
+\begin{DoxyCompactList}\small\item\em Produce a secondary structure graph in Post\-Script and write it to 'filename'. \end{DoxyCompactList}\item
+int \hyperlink{PS__dot_8h_a47856b2504b566588785597b6ebb8271}{P\-S\-\_\-rna\-\_\-plot\-\_\-a} (char $\ast$string, char $\ast$structure, char $\ast$file, char $\ast$pre, char $\ast$post)
+\begin{DoxyCompactList}\small\item\em Produce a secondary structure graph in Post\-Script including additional annotation macros and write it to 'filename'. \end{DoxyCompactList}\item
+int \hyperlink{PS__dot_8h_a70834bc8c0aad4fe6824ff76ccb8f329}{gml\-R\-N\-A} (char $\ast$string, char $\ast$structure, char $\ast$ssfile, char option)
+\begin{DoxyCompactList}\small\item\em Produce a secondary structure graph in Graph Meta Language (gml) and write it to a file. \end{DoxyCompactList}\item
+int \hyperlink{PS__dot_8h_add368528755f9a830727b680243541df}{ssv\-\_\-rna\-\_\-plot} (char $\ast$string, char $\ast$structure, char $\ast$ssfile)
+\begin{DoxyCompactList}\small\item\em Produce a secondary structure graph in S\-Struct\-View format. \end{DoxyCompactList}\item
+int \hyperlink{PS__dot_8h_ae7853539b5df98f294b4af434e979304}{svg\-\_\-rna\-\_\-plot} (char $\ast$string, char $\ast$structure, char $\ast$ssfile)
+\begin{DoxyCompactList}\small\item\em Produce a secondary structure plot in S\-V\-G format and write it to a file. \end{DoxyCompactList}\item
+int \hyperlink{PS__dot_8h_a2f6d5953e6a323df898896b8d6614483}{xrna\-\_\-plot} (char $\ast$string, char $\ast$structure, char $\ast$ssfile)
+\begin{DoxyCompactList}\small\item\em Produce a secondary structure plot for further editing in X\-R\-N\-A. \end{DoxyCompactList}\item
+int \hyperlink{PS__dot_8h_a00ea223b5cf02eb2faae5ff29f0d5e12}{P\-S\-\_\-dot\-\_\-plot\-\_\-list} (char $\ast$seq, char $\ast$filename, \hyperlink{structplist}{plist} $\ast$pl, \hyperlink{structplist}{plist} $\ast$mf, char $\ast$comment)
+\begin{DoxyCompactList}\small\item\em Produce a postscript dot-\/plot from two pair lists. \end{DoxyCompactList}\item
+int \hyperlink{PS__dot_8h_aab48d4dac655d688abe921389ac2847c}{ali\-P\-S\-\_\-color\-\_\-aln} (const char $\ast$structure, const char $\ast$filename, const char $\ast$seqs\mbox{[}$\,$\mbox{]}, const char $\ast$names\mbox{[}$\,$\mbox{]})
+\item
+int \hyperlink{PS__dot_8h_a689a97a7e3b8a2df14728b8204d9d57b}{P\-S\-\_\-dot\-\_\-plot} (char $\ast$string, char $\ast$file)
+\begin{DoxyCompactList}\small\item\em Produce postscript dot-\/plot. \end{DoxyCompactList}\end{DoxyCompactItemize}
+
+
+\subsection{Detailed Description}
+Various functions for plotting R\-N\-A secondary structures, dot-\/plots and other visualizations.
+
+\subsection{Function Documentation}
+\hypertarget{PS__dot_8h_a0873c7cc4cd7a11c9a2cea19dde7e9c9}{\index{P\-S\-\_\-dot.\-h@{P\-S\-\_\-dot.\-h}!P\-S\-\_\-rna\-\_\-plot@{P\-S\-\_\-rna\-\_\-plot}}
+\index{P\-S\-\_\-rna\-\_\-plot@{P\-S\-\_\-rna\-\_\-plot}!PS_dot.h@{P\-S\-\_\-dot.\-h}}
+\subsubsection[{P\-S\-\_\-rna\-\_\-plot}]{\setlength{\rightskip}{0pt plus 5cm}int P\-S\-\_\-rna\-\_\-plot (
+\begin{DoxyParamCaption}
+\item[{char $\ast$}]{string, }
+\item[{char $\ast$}]{structure, }
+\item[{char $\ast$}]{file}
+\end{DoxyParamCaption}
+)}}\label{PS__dot_8h_a0873c7cc4cd7a11c9a2cea19dde7e9c9}
+
+
+Produce a secondary structure graph in Post\-Script 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.
+
+
+\begin{DoxyParams}{Parameters}
+{\em string} & The R\-N\-A sequence \\
+\hline
+{\em structure} & The secondary structure in dot-\/bracket notation \\
+\hline
+{\em file} & The filename of the postscript output \\
+\hline
+\end{DoxyParams}
+\begin{DoxyReturn}{Returns}
+1 on success, 0 otherwise
+\end{DoxyReturn}
+\hypertarget{PS__dot_8h_a47856b2504b566588785597b6ebb8271}{\index{P\-S\-\_\-dot.\-h@{P\-S\-\_\-dot.\-h}!P\-S\-\_\-rna\-\_\-plot\-\_\-a@{P\-S\-\_\-rna\-\_\-plot\-\_\-a}}
+\index{P\-S\-\_\-rna\-\_\-plot\-\_\-a@{P\-S\-\_\-rna\-\_\-plot\-\_\-a}!PS_dot.h@{P\-S\-\_\-dot.\-h}}
+\subsubsection[{P\-S\-\_\-rna\-\_\-plot\-\_\-a}]{\setlength{\rightskip}{0pt plus 5cm}int P\-S\-\_\-rna\-\_\-plot\-\_\-a (
+\begin{DoxyParamCaption}
+\item[{char $\ast$}]{string, }
+\item[{char $\ast$}]{structure, }
+\item[{char $\ast$}]{file, }
+\item[{char $\ast$}]{pre, }
+\item[{char $\ast$}]{post}
+\end{DoxyParamCaption}
+)}}\label{PS__dot_8h_a47856b2504b566588785597b6ebb8271}
+
+
+Produce a secondary structure graph in Post\-Script including additional annotation macros and write it to 'filename'.
+
+Same as \hyperlink{PS__dot_8h_a0873c7cc4cd7a11c9a2cea19dde7e9c9}{P\-S\-\_\-rna\-\_\-plot()} but adds extra Post\-Script macros for various annotations (see generated P\-S code). The 'pre' and 'post' variables contain Post\-Script code that is verbatim copied in the resulting P\-S file just before and after the structure plot. If both arguments ('pre' and 'post') are N\-U\-L\-L, no additional macros will be printed into the Post\-Script.
+
+
+\begin{DoxyParams}{Parameters}
+{\em string} & The R\-N\-A sequence \\
+\hline
+{\em structure} & The secondary structure in dot-\/bracket notation \\
+\hline
+{\em file} & The filename of the postscript output \\
+\hline
+{\em pre} & Post\-Script code to appear before the secondary structure plot \\
+\hline
+{\em post} & Post\-Script code to appear after the secondary structure plot \\
+\hline
+\end{DoxyParams}
+\begin{DoxyReturn}{Returns}
+1 on success, 0 otherwise
+\end{DoxyReturn}
+\hypertarget{PS__dot_8h_a70834bc8c0aad4fe6824ff76ccb8f329}{\index{P\-S\-\_\-dot.\-h@{P\-S\-\_\-dot.\-h}!gml\-R\-N\-A@{gml\-R\-N\-A}}
+\index{gml\-R\-N\-A@{gml\-R\-N\-A}!PS_dot.h@{P\-S\-\_\-dot.\-h}}
+\subsubsection[{gml\-R\-N\-A}]{\setlength{\rightskip}{0pt plus 5cm}int gml\-R\-N\-A (
+\begin{DoxyParamCaption}
+\item[{char $\ast$}]{string, }
+\item[{char $\ast$}]{structure, }
+\item[{char $\ast$}]{ssfile, }
+\item[{char}]{option}
+\end{DoxyParamCaption}
+)}}\label{PS__dot_8h_a70834bc8c0aad4fe6824ff76ccb8f329}
+
+
+Produce a secondary structure graph in Graph Meta Language (gml) and write it to a file.
+
+If 'option' is an uppercase letter the R\-N\-A 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.
+
+
+\begin{DoxyParams}{Parameters}
+{\em string} & The R\-N\-A sequence \\
+\hline
+{\em structure} & The secondary structure in dot-\/bracket notation \\
+\hline
+{\em ssfile} & The filename of the gml output \\
+\hline
+{\em option} & The option flag \\
+\hline
+\end{DoxyParams}
+\begin{DoxyReturn}{Returns}
+1 on success, 0 otherwise
+\end{DoxyReturn}
+\hypertarget{PS__dot_8h_add368528755f9a830727b680243541df}{\index{P\-S\-\_\-dot.\-h@{P\-S\-\_\-dot.\-h}!ssv\-\_\-rna\-\_\-plot@{ssv\-\_\-rna\-\_\-plot}}
+\index{ssv\-\_\-rna\-\_\-plot@{ssv\-\_\-rna\-\_\-plot}!PS_dot.h@{P\-S\-\_\-dot.\-h}}
+\subsubsection[{ssv\-\_\-rna\-\_\-plot}]{\setlength{\rightskip}{0pt plus 5cm}int ssv\-\_\-rna\-\_\-plot (
+\begin{DoxyParamCaption}
+\item[{char $\ast$}]{string, }
+\item[{char $\ast$}]{structure, }
+\item[{char $\ast$}]{ssfile}
+\end{DoxyParamCaption}
+)}}\label{PS__dot_8h_add368528755f9a830727b680243541df}
+
+
+Produce a secondary structure graph in S\-Struct\-View format.
+
+Write coord file for S\-Struct\-View
+
+
+\begin{DoxyParams}{Parameters}
+{\em string} & The R\-N\-A sequence \\
+\hline
+{\em structure} & The secondary structure in dot-\/bracket notation \\
+\hline
+{\em ssfile} & The filename of the ssv output \\
+\hline
+\end{DoxyParams}
+\begin{DoxyReturn}{Returns}
+1 on success, 0 otherwise
+\end{DoxyReturn}
+\hypertarget{PS__dot_8h_ae7853539b5df98f294b4af434e979304}{\index{P\-S\-\_\-dot.\-h@{P\-S\-\_\-dot.\-h}!svg\-\_\-rna\-\_\-plot@{svg\-\_\-rna\-\_\-plot}}
+\index{svg\-\_\-rna\-\_\-plot@{svg\-\_\-rna\-\_\-plot}!PS_dot.h@{P\-S\-\_\-dot.\-h}}
+\subsubsection[{svg\-\_\-rna\-\_\-plot}]{\setlength{\rightskip}{0pt plus 5cm}int svg\-\_\-rna\-\_\-plot (
+\begin{DoxyParamCaption}
+\item[{char $\ast$}]{string, }
+\item[{char $\ast$}]{structure, }
+\item[{char $\ast$}]{ssfile}
+\end{DoxyParamCaption}
+)}}\label{PS__dot_8h_ae7853539b5df98f294b4af434e979304}
+
+
+Produce a secondary structure plot in S\-V\-G format and write it to a file.
+
+
+\begin{DoxyParams}{Parameters}
+{\em string} & The R\-N\-A sequence \\
+\hline
+{\em structure} & The secondary structure in dot-\/bracket notation \\
+\hline
+{\em ssfile} & The filename of the svg output \\
+\hline
+\end{DoxyParams}
+\begin{DoxyReturn}{Returns}
+1 on success, 0 otherwise
+\end{DoxyReturn}
+\hypertarget{PS__dot_8h_a2f6d5953e6a323df898896b8d6614483}{\index{P\-S\-\_\-dot.\-h@{P\-S\-\_\-dot.\-h}!xrna\-\_\-plot@{xrna\-\_\-plot}}
+\index{xrna\-\_\-plot@{xrna\-\_\-plot}!PS_dot.h@{P\-S\-\_\-dot.\-h}}
+\subsubsection[{xrna\-\_\-plot}]{\setlength{\rightskip}{0pt plus 5cm}int xrna\-\_\-plot (
+\begin{DoxyParamCaption}
+\item[{char $\ast$}]{string, }
+\item[{char $\ast$}]{structure, }
+\item[{char $\ast$}]{ssfile}
+\end{DoxyParamCaption}
+)}}\label{PS__dot_8h_a2f6d5953e6a323df898896b8d6614483}
+
+
+Produce a secondary structure plot for further editing in X\-R\-N\-A.
+
+
+\begin{DoxyParams}{Parameters}
+{\em string} & The R\-N\-A sequence \\
+\hline
+{\em structure} & The secondary structure in dot-\/bracket notation \\
+\hline
+{\em ssfile} & The filename of the xrna output \\
+\hline
+\end{DoxyParams}
+\begin{DoxyReturn}{Returns}
+1 on success, 0 otherwise
+\end{DoxyReturn}
+\hypertarget{PS__dot_8h_a00ea223b5cf02eb2faae5ff29f0d5e12}{\index{P\-S\-\_\-dot.\-h@{P\-S\-\_\-dot.\-h}!P\-S\-\_\-dot\-\_\-plot\-\_\-list@{P\-S\-\_\-dot\-\_\-plot\-\_\-list}}
+\index{P\-S\-\_\-dot\-\_\-plot\-\_\-list@{P\-S\-\_\-dot\-\_\-plot\-\_\-list}!PS_dot.h@{P\-S\-\_\-dot.\-h}}
+\subsubsection[{P\-S\-\_\-dot\-\_\-plot\-\_\-list}]{\setlength{\rightskip}{0pt plus 5cm}int P\-S\-\_\-dot\-\_\-plot\-\_\-list (
+\begin{DoxyParamCaption}
+\item[{char $\ast$}]{seq, }
+\item[{char $\ast$}]{filename, }
+\item[{{\bf plist} $\ast$}]{pl, }
+\item[{{\bf plist} $\ast$}]{mf, }
+\item[{char $\ast$}]{comment}
+\end{DoxyParamCaption}
+)}}\label{PS__dot_8h_a00ea223b5cf02eb2faae5ff29f0d5e12}
+
+
+Produce a postscript dot-\/plot from two pair lists.
+
+This function reads two 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
+ Using base pair probabilities in the first and mfe structure in the second 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.
+
+\begin{DoxySeeAlso}{See Also}
+\hyperlink{group__pf__fold_ga03e15e831a31b1154855ab47edbdb019}{assign\-\_\-plist\-\_\-from\-\_\-pr()}, \hyperlink{fold_8h_adaa59b81664e2e36cb9932e891558fae}{assign\-\_\-plist\-\_\-from\-\_\-db()}
+\end{DoxySeeAlso}
+
+\begin{DoxyParams}{Parameters}
+{\em seq} & The R\-N\-A sequence \\
+\hline
+{\em filename} & A filename for the postscript output \\
+\hline
+{\em pl} & The base pair probability pairlist \\
+\hline
+{\em mf} & The mfe secondary structure pairlist \\
+\hline
+{\em comment} & A comment \\
+\hline
+\end{DoxyParams}
+\begin{DoxyReturn}{Returns}
+1 if postscript was successfully written, 0 otherwise
+\end{DoxyReturn}
+\hypertarget{PS__dot_8h_aab48d4dac655d688abe921389ac2847c}{\index{P\-S\-\_\-dot.\-h@{P\-S\-\_\-dot.\-h}!ali\-P\-S\-\_\-color\-\_\-aln@{ali\-P\-S\-\_\-color\-\_\-aln}}
+\index{ali\-P\-S\-\_\-color\-\_\-aln@{ali\-P\-S\-\_\-color\-\_\-aln}!PS_dot.h@{P\-S\-\_\-dot.\-h}}
+\subsubsection[{ali\-P\-S\-\_\-color\-\_\-aln}]{\setlength{\rightskip}{0pt plus 5cm}int ali\-P\-S\-\_\-color\-\_\-aln (
+\begin{DoxyParamCaption}
+\item[{const char $\ast$}]{structure, }
+\item[{const char $\ast$}]{filename, }
+\item[{const char $\ast$}]{seqs\mbox{[}$\,$\mbox{]}, }
+\item[{const char $\ast$}]{names\mbox{[}$\,$\mbox{]}}
+\end{DoxyParamCaption}
+)}}\label{PS__dot_8h_aab48d4dac655d688abe921389ac2847c}
+P\-S\-\_\-color\-\_\-aln for duplexes \hypertarget{PS__dot_8h_a689a97a7e3b8a2df14728b8204d9d57b}{\index{P\-S\-\_\-dot.\-h@{P\-S\-\_\-dot.\-h}!P\-S\-\_\-dot\-\_\-plot@{P\-S\-\_\-dot\-\_\-plot}}
+\index{P\-S\-\_\-dot\-\_\-plot@{P\-S\-\_\-dot\-\_\-plot}!PS_dot.h@{P\-S\-\_\-dot.\-h}}
+\subsubsection[{P\-S\-\_\-dot\-\_\-plot}]{\setlength{\rightskip}{0pt plus 5cm}int P\-S\-\_\-dot\-\_\-plot (
+\begin{DoxyParamCaption}
+\item[{char $\ast$}]{string, }
+\item[{char $\ast$}]{file}
+\end{DoxyParamCaption}
+)}}\label{PS__dot_8h_a689a97a7e3b8a2df14728b8204d9d57b}
+
+
+Produce postscript dot-\/plot.
+
+Wrapper to P\-S\-\_\-dot\-\_\-plot\-\_\-list
+
+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}
+D\-O N\-O\-T U\-S\-E T\-H\-I\-S F\-U\-N\-C\-T\-I\-O\-N A\-N\-Y\-M\-O\-R\-E S\-I\-N\-C\-E I\-T I\-S N\-O\-T T\-H\-R\-E\-A\-D\-S\-A\-F\-E
+\end{DoxyNote}
+\begin{DoxyRefDesc}{Deprecated}
+\item[\hyperlink{deprecated__deprecated000019}{Deprecated}]This function is deprecated and will be removed soon! Use \hyperlink{PS__dot_8h_a00ea223b5cf02eb2faae5ff29f0d5e12}{P\-S\-\_\-dot\-\_\-plot\-\_\-list()} instead! \end{DoxyRefDesc}
git://source.jalview.org / jabaws.git / blobdiff