--- /dev/null
+\hypertarget{RNAstruct_8h}{\section{/home/asherstnev/\-Projects/\-Java.projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\-R\-N\-Astruct.h File Reference}
+\label{RNAstruct_8h}\index{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\-R\-N\-Astruct.\-h@{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\-R\-N\-Astruct.\-h}}
+}
+
+
+Parsing and Coarse Graining of Structures.
+
+
+\subsection*{Functions}
+\begin{DoxyCompactItemize}
+\item
+char $\ast$ \hyperlink{RNAstruct_8h_a07b7e90e712559a1992fba3ac6d21bbd}{b2\-H\-I\-T} (const char $\ast$structure)
+\begin{DoxyCompactList}\small\item\em Converts the full structure from bracket notation to the H\-I\-T notation including root. \end{DoxyCompactList}\item
+char $\ast$ \hyperlink{RNAstruct_8h_a9c80d92391f2833549a8b6dac92233f0}{b2\-C} (const char $\ast$structure)
+\begin{DoxyCompactList}\small\item\em Converts the full structure from bracket notation to the a coarse grained notation using the 'H' 'B' 'I' 'M' and 'R' identifiers. \end{DoxyCompactList}\item
+char $\ast$ \hyperlink{RNAstruct_8h_a5cd2feb367feeacad0c03cb7ddba5f10}{b2\-Shapiro} (const char $\ast$structure)
+\begin{DoxyCompactList}\small\item\em Converts the full structure from bracket notation to the {\itshape weighted} coarse grained notation using the 'H' 'B' 'I' 'M' 'S' 'E' and 'R' identifiers. \end{DoxyCompactList}\item
+char $\ast$ \hyperlink{RNAstruct_8h_a880d33066dd95441e5fbb73c57ed1c3e}{add\-\_\-root} (const char $\ast$structure)
+\begin{DoxyCompactList}\small\item\em Adds a root to an un-\/rooted tree in any except bracket notation. \end{DoxyCompactList}\item
+char $\ast$ \hyperlink{RNAstruct_8h_abe3d815b420dc4553bfb23511198b4c6}{expand\-\_\-\-Shapiro} (const char $\ast$coarse)
+\begin{DoxyCompactList}\small\item\em Inserts missing 'S' identifiers in unweighted coarse grained structures as obtained from \hyperlink{RNAstruct_8h_a9c80d92391f2833549a8b6dac92233f0}{b2\-C()}. \end{DoxyCompactList}\item
+char $\ast$ \hyperlink{RNAstruct_8h_a78d73cd54a068ef2812812771cdddc6f}{expand\-\_\-\-Full} (const char $\ast$structure)
+\begin{DoxyCompactList}\small\item\em Convert the full structure from bracket notation to the expanded notation including root. \end{DoxyCompactList}\item
+char $\ast$ \hyperlink{RNAstruct_8h_a260c4b622093b76a883bf96628280de1}{unexpand\-\_\-\-Full} (const char $\ast$ffull)
+\begin{DoxyCompactList}\small\item\em Restores the bracket notation from an expanded full or H\-I\-T tree, that is any tree using only identifiers 'U' 'P' and 'R'. \end{DoxyCompactList}\item
+char $\ast$ \hyperlink{RNAstruct_8h_a09a80253ac7b6bae606871ba7c6e5136}{unweight} (const char $\ast$wcoarse)
+\begin{DoxyCompactList}\small\item\em Strip weights from any weighted tree. \end{DoxyCompactList}\item
+void \hyperlink{RNAstruct_8h_a1054c4477d53b31d79d4cb132100e87a}{unexpand\-\_\-aligned\-\_\-\-F} (char $\ast$align\mbox{[}2\mbox{]})
+\begin{DoxyCompactList}\small\item\em Converts two aligned structures in expanded notation. \end{DoxyCompactList}\item
+void \hyperlink{RNAstruct_8h_a3c79042e6bf6f01706bf30ec9e69e8ac}{parse\-\_\-structure} (const char $\ast$structure)
+\begin{DoxyCompactList}\small\item\em Collects a statistic of structure elements of the full structure in bracket notation. \end{DoxyCompactList}\end{DoxyCompactItemize}
+\subsection*{Variables}
+\begin{DoxyCompactItemize}
+\item
+\hypertarget{RNAstruct_8h_a3f31e0e48125601bfa57b52f8b038e8e}{int \hyperlink{RNAstruct_8h_a3f31e0e48125601bfa57b52f8b038e8e}{loop\-\_\-size} \mbox{[}S\-T\-R\-U\-C\mbox{]}}\label{RNAstruct_8h_a3f31e0e48125601bfa57b52f8b038e8e}
+
+\begin{DoxyCompactList}\small\item\em contains a list of all loop sizes. loop\-\_\-size\mbox{[}0\mbox{]} contains the number of external bases. \end{DoxyCompactList}\item
+\hypertarget{RNAstruct_8h_a8218c0d581a3fba2a1a56a196abe19a5}{int \hyperlink{RNAstruct_8h_a8218c0d581a3fba2a1a56a196abe19a5}{helix\-\_\-size} \mbox{[}S\-T\-R\-U\-C\mbox{]}}\label{RNAstruct_8h_a8218c0d581a3fba2a1a56a196abe19a5}
+
+\begin{DoxyCompactList}\small\item\em contains a list of all stack sizes. \end{DoxyCompactList}\item
+\hypertarget{RNAstruct_8h_aef14e2f8ab3f61e8e659ba6b9003b08a}{int \hyperlink{RNAstruct_8h_aef14e2f8ab3f61e8e659ba6b9003b08a}{loop\-\_\-degree} \mbox{[}S\-T\-R\-U\-C\mbox{]}}\label{RNAstruct_8h_aef14e2f8ab3f61e8e659ba6b9003b08a}
+
+\begin{DoxyCompactList}\small\item\em contains the corresponding list of loop degrees. \end{DoxyCompactList}\item
+\hypertarget{RNAstruct_8h_a439fcb9f8d4f9f4d2227fde5fbfecb30}{int \hyperlink{RNAstruct_8h_a439fcb9f8d4f9f4d2227fde5fbfecb30}{loops}}\label{RNAstruct_8h_a439fcb9f8d4f9f4d2227fde5fbfecb30}
+
+\begin{DoxyCompactList}\small\item\em contains the number of loops ( and therefore of stacks ). \end{DoxyCompactList}\item
+\hypertarget{RNAstruct_8h_add2f952597e02d66e1116a9d11d252d6}{int \hyperlink{RNAstruct_8h_add2f952597e02d66e1116a9d11d252d6}{unpaired}}\label{RNAstruct_8h_add2f952597e02d66e1116a9d11d252d6}
+
+\begin{DoxyCompactList}\small\item\em contains the number of unpaired bases. \end{DoxyCompactList}\item
+\hypertarget{RNAstruct_8h_a6341cbb704924824e0236c1dce791032}{int \hyperlink{RNAstruct_8h_a6341cbb704924824e0236c1dce791032}{pairs}}\label{RNAstruct_8h_a6341cbb704924824e0236c1dce791032}
+
+\begin{DoxyCompactList}\small\item\em contains the number of base pairs in the last parsed structure. \end{DoxyCompactList}\end{DoxyCompactItemize}
+
+
+\subsection{Detailed Description}
+Parsing and Coarse Graining of Structures. \begin{DoxyVerb}Example:
+\end{DoxyVerb}
+ \begin{DoxyVerb}* .((..(((...)))..((..)))). is the bracket or full tree
+* becomes expanded: - expand_Full() -
+* ((U)(((U)(U)((((U)(U)(U)P)P)P)(U)(U)(((U)(U)P)P)P)P)(U)R)
+* HIT: - b2HIT() -
+* ((U1)((U2)((U3)P3)(U2)((U2)P2)P2)(U1)R)
+* Coarse: - b2C() -
+* ((H)((H)M)R)
+* becomes expanded: - expand_Shapiro() -
+* (((((H)S)((H)S)M)S)R)
+* weighted Shapiro: - b2Shapiro() -
+* ((((((H3)S3)((H2)S2)M4)S2)E2)R)
+* \end{DoxyVerb}
+
+
+\subsection{Function Documentation}
+\hypertarget{RNAstruct_8h_a07b7e90e712559a1992fba3ac6d21bbd}{\index{R\-N\-Astruct.\-h@{R\-N\-Astruct.\-h}!b2\-H\-I\-T@{b2\-H\-I\-T}}
+\index{b2\-H\-I\-T@{b2\-H\-I\-T}!RNAstruct.h@{R\-N\-Astruct.\-h}}
+\subsubsection[{b2\-H\-I\-T}]{\setlength{\rightskip}{0pt plus 5cm}char$\ast$ b2\-H\-I\-T (
+\begin{DoxyParamCaption}
+\item[{const char $\ast$}]{structure}
+\end{DoxyParamCaption}
+)}}\label{RNAstruct_8h_a07b7e90e712559a1992fba3ac6d21bbd}
+
+
+Converts the full structure from bracket notation to the H\-I\-T notation including root.
+
+
+\begin{DoxyParams}{Parameters}
+{\em structure} & \\
+\hline
+\end{DoxyParams}
+\begin{DoxyReturn}{Returns}
+
+\end{DoxyReturn}
+\hypertarget{RNAstruct_8h_a9c80d92391f2833549a8b6dac92233f0}{\index{R\-N\-Astruct.\-h@{R\-N\-Astruct.\-h}!b2\-C@{b2\-C}}
+\index{b2\-C@{b2\-C}!RNAstruct.h@{R\-N\-Astruct.\-h}}
+\subsubsection[{b2\-C}]{\setlength{\rightskip}{0pt plus 5cm}char$\ast$ b2\-C (
+\begin{DoxyParamCaption}
+\item[{const char $\ast$}]{structure}
+\end{DoxyParamCaption}
+)}}\label{RNAstruct_8h_a9c80d92391f2833549a8b6dac92233f0}
+
+
+Converts the full structure from bracket notation to the a coarse grained notation using the 'H' 'B' 'I' 'M' and 'R' identifiers.
+
+
+\begin{DoxyParams}{Parameters}
+{\em structure} & \\
+\hline
+\end{DoxyParams}
+\begin{DoxyReturn}{Returns}
+
+\end{DoxyReturn}
+\hypertarget{RNAstruct_8h_a5cd2feb367feeacad0c03cb7ddba5f10}{\index{R\-N\-Astruct.\-h@{R\-N\-Astruct.\-h}!b2\-Shapiro@{b2\-Shapiro}}
+\index{b2\-Shapiro@{b2\-Shapiro}!RNAstruct.h@{R\-N\-Astruct.\-h}}
+\subsubsection[{b2\-Shapiro}]{\setlength{\rightskip}{0pt plus 5cm}char$\ast$ b2\-Shapiro (
+\begin{DoxyParamCaption}
+\item[{const char $\ast$}]{structure}
+\end{DoxyParamCaption}
+)}}\label{RNAstruct_8h_a5cd2feb367feeacad0c03cb7ddba5f10}
+
+
+Converts the full structure from bracket notation to the {\itshape weighted} coarse grained notation using the 'H' 'B' 'I' 'M' 'S' 'E' and 'R' identifiers.
+
+
+\begin{DoxyParams}{Parameters}
+{\em structure} & \\
+\hline
+\end{DoxyParams}
+\begin{DoxyReturn}{Returns}
+
+\end{DoxyReturn}
+\hypertarget{RNAstruct_8h_a880d33066dd95441e5fbb73c57ed1c3e}{\index{R\-N\-Astruct.\-h@{R\-N\-Astruct.\-h}!add\-\_\-root@{add\-\_\-root}}
+\index{add\-\_\-root@{add\-\_\-root}!RNAstruct.h@{R\-N\-Astruct.\-h}}
+\subsubsection[{add\-\_\-root}]{\setlength{\rightskip}{0pt plus 5cm}char$\ast$ add\-\_\-root (
+\begin{DoxyParamCaption}
+\item[{const char $\ast$}]{structure}
+\end{DoxyParamCaption}
+)}}\label{RNAstruct_8h_a880d33066dd95441e5fbb73c57ed1c3e}
+
+
+Adds a root to an un-\/rooted tree in any except bracket notation.
+
+
+\begin{DoxyParams}{Parameters}
+{\em structure} & \\
+\hline
+\end{DoxyParams}
+\begin{DoxyReturn}{Returns}
+
+\end{DoxyReturn}
+\hypertarget{RNAstruct_8h_abe3d815b420dc4553bfb23511198b4c6}{\index{R\-N\-Astruct.\-h@{R\-N\-Astruct.\-h}!expand\-\_\-\-Shapiro@{expand\-\_\-\-Shapiro}}
+\index{expand\-\_\-\-Shapiro@{expand\-\_\-\-Shapiro}!RNAstruct.h@{R\-N\-Astruct.\-h}}
+\subsubsection[{expand\-\_\-\-Shapiro}]{\setlength{\rightskip}{0pt plus 5cm}char$\ast$ expand\-\_\-\-Shapiro (
+\begin{DoxyParamCaption}
+\item[{const char $\ast$}]{coarse}
+\end{DoxyParamCaption}
+)}}\label{RNAstruct_8h_abe3d815b420dc4553bfb23511198b4c6}
+
+
+Inserts missing 'S' identifiers in unweighted coarse grained structures as obtained from \hyperlink{RNAstruct_8h_a9c80d92391f2833549a8b6dac92233f0}{b2\-C()}.
+
+
+\begin{DoxyParams}{Parameters}
+{\em coarse} & \\
+\hline
+\end{DoxyParams}
+\begin{DoxyReturn}{Returns}
+
+\end{DoxyReturn}
+\hypertarget{RNAstruct_8h_a78d73cd54a068ef2812812771cdddc6f}{\index{R\-N\-Astruct.\-h@{R\-N\-Astruct.\-h}!expand\-\_\-\-Full@{expand\-\_\-\-Full}}
+\index{expand\-\_\-\-Full@{expand\-\_\-\-Full}!RNAstruct.h@{R\-N\-Astruct.\-h}}
+\subsubsection[{expand\-\_\-\-Full}]{\setlength{\rightskip}{0pt plus 5cm}char$\ast$ expand\-\_\-\-Full (
+\begin{DoxyParamCaption}
+\item[{const char $\ast$}]{structure}
+\end{DoxyParamCaption}
+)}}\label{RNAstruct_8h_a78d73cd54a068ef2812812771cdddc6f}
+
+
+Convert the full structure from bracket notation to the expanded notation including root.
+
+
+\begin{DoxyParams}{Parameters}
+{\em structure} & \\
+\hline
+\end{DoxyParams}
+\begin{DoxyReturn}{Returns}
+
+\end{DoxyReturn}
+\hypertarget{RNAstruct_8h_a260c4b622093b76a883bf96628280de1}{\index{R\-N\-Astruct.\-h@{R\-N\-Astruct.\-h}!unexpand\-\_\-\-Full@{unexpand\-\_\-\-Full}}
+\index{unexpand\-\_\-\-Full@{unexpand\-\_\-\-Full}!RNAstruct.h@{R\-N\-Astruct.\-h}}
+\subsubsection[{unexpand\-\_\-\-Full}]{\setlength{\rightskip}{0pt plus 5cm}char$\ast$ unexpand\-\_\-\-Full (
+\begin{DoxyParamCaption}
+\item[{const char $\ast$}]{ffull}
+\end{DoxyParamCaption}
+)}}\label{RNAstruct_8h_a260c4b622093b76a883bf96628280de1}
+
+
+Restores the bracket notation from an expanded full or H\-I\-T tree, that is any tree using only identifiers 'U' 'P' and 'R'.
+
+
+\begin{DoxyParams}{Parameters}
+{\em ffull} & \\
+\hline
+\end{DoxyParams}
+\begin{DoxyReturn}{Returns}
+
+\end{DoxyReturn}
+\hypertarget{RNAstruct_8h_a09a80253ac7b6bae606871ba7c6e5136}{\index{R\-N\-Astruct.\-h@{R\-N\-Astruct.\-h}!unweight@{unweight}}
+\index{unweight@{unweight}!RNAstruct.h@{R\-N\-Astruct.\-h}}
+\subsubsection[{unweight}]{\setlength{\rightskip}{0pt plus 5cm}char$\ast$ unweight (
+\begin{DoxyParamCaption}
+\item[{const char $\ast$}]{wcoarse}
+\end{DoxyParamCaption}
+)}}\label{RNAstruct_8h_a09a80253ac7b6bae606871ba7c6e5136}
+
+
+Strip weights from any weighted tree.
+
+
+\begin{DoxyParams}{Parameters}
+{\em wcoarse} & \\
+\hline
+\end{DoxyParams}
+\begin{DoxyReturn}{Returns}
+
+\end{DoxyReturn}
+\hypertarget{RNAstruct_8h_a1054c4477d53b31d79d4cb132100e87a}{\index{R\-N\-Astruct.\-h@{R\-N\-Astruct.\-h}!unexpand\-\_\-aligned\-\_\-\-F@{unexpand\-\_\-aligned\-\_\-\-F}}
+\index{unexpand\-\_\-aligned\-\_\-\-F@{unexpand\-\_\-aligned\-\_\-\-F}!RNAstruct.h@{R\-N\-Astruct.\-h}}
+\subsubsection[{unexpand\-\_\-aligned\-\_\-\-F}]{\setlength{\rightskip}{0pt plus 5cm}void unexpand\-\_\-aligned\-\_\-\-F (
+\begin{DoxyParamCaption}
+\item[{char $\ast$}]{align\mbox{[}2\mbox{]}}
+\end{DoxyParamCaption}
+)}}\label{RNAstruct_8h_a1054c4477d53b31d79d4cb132100e87a}
+
+
+Converts two aligned structures in expanded notation.
+
+Takes two aligned structures as produced by \hyperlink{treedist_8h_a3b21f1925f7071f46d93431a835217bb}{tree\-\_\-edit\-\_\-distance()} function back to bracket notation with '\-\_\-' as the gap character. The result overwrites the input.
+
+
+\begin{DoxyParams}{Parameters}
+{\em align} & \\
+\hline
+\end{DoxyParams}
+\hypertarget{RNAstruct_8h_a3c79042e6bf6f01706bf30ec9e69e8ac}{\index{R\-N\-Astruct.\-h@{R\-N\-Astruct.\-h}!parse\-\_\-structure@{parse\-\_\-structure}}
+\index{parse\-\_\-structure@{parse\-\_\-structure}!RNAstruct.h@{R\-N\-Astruct.\-h}}
+\subsubsection[{parse\-\_\-structure}]{\setlength{\rightskip}{0pt plus 5cm}void parse\-\_\-structure (
+\begin{DoxyParamCaption}
+\item[{const char $\ast$}]{structure}
+\end{DoxyParamCaption}
+)}}\label{RNAstruct_8h_a3c79042e6bf6f01706bf30ec9e69e8ac}
+
+
+Collects a statistic of structure elements of the full structure in bracket notation.
+
+The function writes to the following global variables\-: \hyperlink{RNAstruct_8h_a3f31e0e48125601bfa57b52f8b038e8e}{loop\-\_\-size}, \hyperlink{RNAstruct_8h_aef14e2f8ab3f61e8e659ba6b9003b08a}{loop\-\_\-degree}, \hyperlink{RNAstruct_8h_a8218c0d581a3fba2a1a56a196abe19a5}{helix\-\_\-size}, \hyperlink{RNAstruct_8h_a439fcb9f8d4f9f4d2227fde5fbfecb30}{loops}, \hyperlink{RNAstruct_8h_a6341cbb704924824e0236c1dce791032}{pairs}, \hyperlink{RNAstruct_8h_add2f952597e02d66e1116a9d11d252d6}{unpaired}
+
+
+\begin{DoxyParams}{Parameters}
+{\em structure} & \\
+\hline
+\end{DoxyParams}
+\begin{DoxyReturn}{Returns}
+
+\end{DoxyReturn}
git://source.jalview.org / jabaws.git / blobdiff