--- /dev/null
+\hypertarget{fold__vars_8h}{\section{/home/asherstnev/\-Projects/\-Java.projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/fold\-\_\-vars.h File Reference}
+\label{fold__vars_8h}\index{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/fold\-\_\-vars.\-h@{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/fold\-\_\-vars.\-h}}
+}
+
+
+Here all all declarations of the global variables used throughout R\-N\-Alib.
+
+
+Include dependency graph for fold\-\_\-vars.\-h\-:
+\nopagebreak
+\begin{figure}[H]
+\begin{center}
+\leavevmode
+\includegraphics[width=250pt]{fold__vars_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=350pt]{fold__vars_8h__dep__incl}
+\end{center}
+\end{figure}
+\subsection*{Functions}
+\begin{DoxyCompactItemize}
+\item
+void \hyperlink{fold__vars_8h_a4c3257186a796182462f18a5480ac8b3}{set\-\_\-model\-\_\-details} (\hyperlink{structmodel__detailsT}{model\-\_\-details\-T} $\ast$md)
+\begin{DoxyCompactList}\small\item\em Set default model details. \end{DoxyCompactList}\end{DoxyCompactItemize}
+\subsection*{Variables}
+\begin{DoxyCompactItemize}
+\item
+\hypertarget{fold__vars_8h_a0afc287c2464866d94858c39175154af}{int \hyperlink{fold__vars_8h_a0afc287c2464866d94858c39175154af}{fold\-\_\-constrained}}\label{fold__vars_8h_a0afc287c2464866d94858c39175154af}
+
+\begin{DoxyCompactList}\small\item\em Global switch to activate/deactivate folding with structure constraints. \end{DoxyCompactList}\item
+int \hyperlink{fold__vars_8h_a097eccaabd6ae8b4fef83cccff85bb5d}{no\-Lonely\-Pairs}
+\begin{DoxyCompactList}\small\item\em Global switch to avoid/allow helices of length 1. \end{DoxyCompactList}\item
+int \hyperlink{fold__vars_8h_a72b511ed1201f7e23ec437e468790d74}{dangles}
+\begin{DoxyCompactList}\small\item\em Switch the energy model for dangling end contributions (0, 1, 2, 3) \end{DoxyCompactList}\item
+\hypertarget{fold__vars_8h_abf380d09e4f1ab94fc6af57cf0ad5d32}{int \hyperlink{fold__vars_8h_abf380d09e4f1ab94fc6af57cf0ad5d32}{no\-G\-U}}\label{fold__vars_8h_abf380d09e4f1ab94fc6af57cf0ad5d32}
+
+\begin{DoxyCompactList}\small\item\em Global switch to forbid/allow G\-U base pairs at all. \end{DoxyCompactList}\item
+\hypertarget{fold__vars_8h_aa8d1c7b92489179e1eafa562b7bdd259}{int \hyperlink{fold__vars_8h_aa8d1c7b92489179e1eafa562b7bdd259}{no\-\_\-closing\-G\-U}}\label{fold__vars_8h_aa8d1c7b92489179e1eafa562b7bdd259}
+
+\begin{DoxyCompactList}\small\item\em G\-U allowed only inside stacks if set to 1. \end{DoxyCompactList}\item
+int \hyperlink{fold__vars_8h_a4f6265bdf0ead7ff4628a360adbfd77e}{tetra\-\_\-loop}
+\begin{DoxyCompactList}\small\item\em Include special stabilizing energies for some tri-\/, tetra-\/ and hexa-\/loops;. \end{DoxyCompactList}\item
+int \hyperlink{fold__vars_8h_afb1ef1166da85092ae8a325e02dcae71}{energy\-\_\-set}
+\begin{DoxyCompactList}\small\item\em 0 = B\-P; 1=any mit G\-C; 2=any mit A\-U-\/parameter \end{DoxyCompactList}\item
+\hypertarget{fold__vars_8h_af9202a1a09f5828dc731e2d9a10fa111}{int \hyperlink{fold__vars_8h_af9202a1a09f5828dc731e2d9a10fa111}{circ}}\label{fold__vars_8h_af9202a1a09f5828dc731e2d9a10fa111}
+
+\begin{DoxyCompactList}\small\item\em backward compatibility variable.. this does not effect anything \end{DoxyCompactList}\item
+\hypertarget{fold__vars_8h_af2763d55a74663a5e60652b8880baa5b}{int \hyperlink{fold__vars_8h_af2763d55a74663a5e60652b8880baa5b}{csv}}\label{fold__vars_8h_af2763d55a74663a5e60652b8880baa5b}
+
+\begin{DoxyCompactList}\small\item\em generate comma seperated output \end{DoxyCompactList}\item
+int \hyperlink{fold__vars_8h_ac408868ba00671cbc7d1d535105af045}{old\-Ali\-En}
+\item
+int \hyperlink{fold__vars_8h_a0656afca1d2853f9ee6591172f5638de}{ribo}
+\item
+char $\ast$ \hyperlink{fold__vars_8h_a5dbaa0cca2c8c82048a0f0e38e164944}{Ribosum\-File}
+\item
+char $\ast$ \hyperlink{fold__vars_8h_a2695d91cc535d09c2eae5c3884e2ec64}{nonstandards}
+\begin{DoxyCompactList}\small\item\em contains allowed non standard base pairs \end{DoxyCompactList}\item
+double \hyperlink{fold__vars_8h_ab4b11c8d9c758430960896bc3fe82ead}{temperature}
+\begin{DoxyCompactList}\small\item\em Rescale energy parameters to a temperature in deg\-C. \end{DoxyCompactList}\item
+int \hyperlink{fold__vars_8h_af349001ad3b4d008d0051d935b1b6261}{james\-\_\-rule}
+\item
+int \hyperlink{fold__vars_8h_a80c3c5fd35e7479704cc91d2d0367743}{log\-M\-L}
+\item
+int \hyperlink{fold__vars_8h_ab9b2c3a37a5516614c06d0ab54b97cda}{cut\-\_\-point}
+\begin{DoxyCompactList}\small\item\em Marks the position (starting from 1) of the first nucleotide of the second molecule within the concatenated sequence. \end{DoxyCompactList}\item
+\hyperlink{structbondT}{bond\-T} $\ast$ \hyperlink{fold__vars_8h_a0244a629b5ab4f58b77590c3dfd130dc}{base\-\_\-pair}
+\begin{DoxyCompactList}\small\item\em Contains a list of base pairs after a call to \hyperlink{group__mfe__fold_gaadafcb0f140795ae62e5ca027e335a9b}{fold()}. \end{DoxyCompactList}\item
+double $\ast$ \hyperlink{fold__vars_8h_a0f5757427fd5f2f79d6fca0081cd5a52}{pr}
+\begin{DoxyCompactList}\small\item\em A pointer to the base pair probability matrix. \end{DoxyCompactList}\item
+int $\ast$ \hyperlink{fold__vars_8h_a92089ae3a51b5d75a14ce9cc29cc8317}{iindx}
+\begin{DoxyCompactList}\small\item\em index array to move through pr. \end{DoxyCompactList}\item
+double \hyperlink{fold__vars_8h_ad3b22044065acc6dee0af68931b52cfd}{pf\-\_\-scale}
+\begin{DoxyCompactList}\small\item\em A scaling factor used by \hyperlink{group__pf__fold_gadc3db3d98742427e7001a7fd36ef28c2}{pf\-\_\-fold()} to avoid overflows. \end{DoxyCompactList}\item
+int \hyperlink{fold__vars_8h_ad512b5dd4dbec60faccfe137bb474489}{do\-\_\-backtrack}
+\begin{DoxyCompactList}\small\item\em do backtracking, i.\-e. compute secondary structures or base pair probabilities \end{DoxyCompactList}\item
+char \hyperlink{fold__vars_8h_a83bdb43472a259c71e69fa9f70f420c3}{backtrack\-\_\-type}
+\begin{DoxyCompactList}\small\item\em A backtrack array marker for \hyperlink{group__inverse__fold_ga7af026de55d4babad879f2c92559cbbc}{inverse\-\_\-fold()} \end{DoxyCompactList}\item
+\hypertarget{fold__vars_8h_a25f2bdcdf56e813d288845484a13d704}{int \hyperlink{fold__vars_8h_a25f2bdcdf56e813d288845484a13d704}{gquad}}\label{fold__vars_8h_a25f2bdcdf56e813d288845484a13d704}
+
+\begin{DoxyCompactList}\small\item\em Allow G-\/quadruplex formation. \end{DoxyCompactList}\end{DoxyCompactItemize}
+
+
+\subsection{Detailed Description}
+Here all all declarations of the global variables used throughout R\-N\-Alib.
+
+\subsection{Function Documentation}
+\hypertarget{fold__vars_8h_a4c3257186a796182462f18a5480ac8b3}{\index{fold\-\_\-vars.\-h@{fold\-\_\-vars.\-h}!set\-\_\-model\-\_\-details@{set\-\_\-model\-\_\-details}}
+\index{set\-\_\-model\-\_\-details@{set\-\_\-model\-\_\-details}!fold_vars.h@{fold\-\_\-vars.\-h}}
+\subsubsection[{set\-\_\-model\-\_\-details}]{\setlength{\rightskip}{0pt plus 5cm}void set\-\_\-model\-\_\-details (
+\begin{DoxyParamCaption}
+\item[{{\bf model\-\_\-details\-T} $\ast$}]{md}
+\end{DoxyParamCaption}
+)}}\label{fold__vars_8h_a4c3257186a796182462f18a5480ac8b3}
+
+
+Set default model details.
+
+Use this function if you wish to initialize a \hyperlink{structmodel__detailsT}{model\-\_\-details\-T} data structure with its default values, i.\-e. the global model settings
+
+\begin{DoxySeeAlso}{See Also}
+
+\end{DoxySeeAlso}
+
+\begin{DoxyParams}{Parameters}
+{\em md} & A pointer to the data structure that shall be initialized \\
+\hline
+\end{DoxyParams}
+
+
+\subsection{Variable Documentation}
+\hypertarget{fold__vars_8h_a097eccaabd6ae8b4fef83cccff85bb5d}{\index{fold\-\_\-vars.\-h@{fold\-\_\-vars.\-h}!no\-Lonely\-Pairs@{no\-Lonely\-Pairs}}
+\index{no\-Lonely\-Pairs@{no\-Lonely\-Pairs}!fold_vars.h@{fold\-\_\-vars.\-h}}
+\subsubsection[{no\-Lonely\-Pairs}]{\setlength{\rightskip}{0pt plus 5cm}int no\-Lonely\-Pairs}}\label{fold__vars_8h_a097eccaabd6ae8b4fef83cccff85bb5d}
+
+
+Global switch to avoid/allow helices of length 1.
+
+Disallow all pairs which can only occur as lonely pairs (i.\-e. as helix of length 1). This avoids lonely base pairs in the predicted structures in most cases. \hypertarget{fold__vars_8h_a72b511ed1201f7e23ec437e468790d74}{\index{fold\-\_\-vars.\-h@{fold\-\_\-vars.\-h}!dangles@{dangles}}
+\index{dangles@{dangles}!fold_vars.h@{fold\-\_\-vars.\-h}}
+\subsubsection[{dangles}]{\setlength{\rightskip}{0pt plus 5cm}int dangles}}\label{fold__vars_8h_a72b511ed1201f7e23ec437e468790d74}
+
+
+Switch the energy model for dangling end contributions (0, 1, 2, 3)
+
+If set to 0 no stabilizing energies are assigned to bases adjacent to helices in free ends and multiloops (so called dangling ends). Normally (dangles = 1) dangling end energies are assigned only to unpaired bases and a base cannot participate simultaneously in two dangling ends. In the partition function algorithm \hyperlink{group__pf__fold_gadc3db3d98742427e7001a7fd36ef28c2}{pf\-\_\-fold()} these checks are neglected. If \hyperlink{fold__vars_8h_a72b511ed1201f7e23ec437e468790d74}{dangles} is set to 2, all folding routines will follow this convention. This treatment of dangling ends gives more favorable energies to helices directly adjacent to one another, which can be beneficial since such helices often do engage in stabilizing interactions through co-\/axial stacking.\par
+ If dangles = 3 co-\/axial stacking is explicitly included for adjacent helices in mutli-\/loops. The option affects only mfe folding and energy evaluation (\hyperlink{group__mfe__fold_gaadafcb0f140795ae62e5ca027e335a9b}{fold()} and \hyperlink{group__eval_gaf93986cb3cb29770ec9cca69c9fab8cf}{energy\-\_\-of\-\_\-structure()}), as well as suboptimal folding (\hyperlink{group__subopt__wuchty_ga700f662506a233e42dd7fda74fafd40e}{subopt()}) via re-\/evaluation of energies. Co-\/axial stacking with one intervening mismatch is not considered so far.
+
+Default is 2 in most algorithms, partition function algorithms can only handle 0 and 2 \hypertarget{fold__vars_8h_a4f6265bdf0ead7ff4628a360adbfd77e}{\index{fold\-\_\-vars.\-h@{fold\-\_\-vars.\-h}!tetra\-\_\-loop@{tetra\-\_\-loop}}
+\index{tetra\-\_\-loop@{tetra\-\_\-loop}!fold_vars.h@{fold\-\_\-vars.\-h}}
+\subsubsection[{tetra\-\_\-loop}]{\setlength{\rightskip}{0pt plus 5cm}int tetra\-\_\-loop}}\label{fold__vars_8h_a4f6265bdf0ead7ff4628a360adbfd77e}
+
+
+Include special stabilizing energies for some tri-\/, tetra-\/ and hexa-\/loops;.
+
+default is 1. \hypertarget{fold__vars_8h_afb1ef1166da85092ae8a325e02dcae71}{\index{fold\-\_\-vars.\-h@{fold\-\_\-vars.\-h}!energy\-\_\-set@{energy\-\_\-set}}
+\index{energy\-\_\-set@{energy\-\_\-set}!fold_vars.h@{fold\-\_\-vars.\-h}}
+\subsubsection[{energy\-\_\-set}]{\setlength{\rightskip}{0pt plus 5cm}int energy\-\_\-set}}\label{fold__vars_8h_afb1ef1166da85092ae8a325e02dcae71}
+
+
+0 = B\-P; 1=any mit G\-C; 2=any mit A\-U-\/parameter
+
+If set to 1 or 2\-: fold sequences from an artificial alphabet A\-B\-C\-D..., where A pairs B, C pairs D, etc. using either G\-C (1) or A\-U parameters (2); default is 0, you probably don't want to change it. \hypertarget{fold__vars_8h_ac408868ba00671cbc7d1d535105af045}{\index{fold\-\_\-vars.\-h@{fold\-\_\-vars.\-h}!old\-Ali\-En@{old\-Ali\-En}}
+\index{old\-Ali\-En@{old\-Ali\-En}!fold_vars.h@{fold\-\_\-vars.\-h}}
+\subsubsection[{old\-Ali\-En}]{\setlength{\rightskip}{0pt plus 5cm}int old\-Ali\-En}}\label{fold__vars_8h_ac408868ba00671cbc7d1d535105af045}
+use old alifold energies (with gaps) \hypertarget{fold__vars_8h_a0656afca1d2853f9ee6591172f5638de}{\index{fold\-\_\-vars.\-h@{fold\-\_\-vars.\-h}!ribo@{ribo}}
+\index{ribo@{ribo}!fold_vars.h@{fold\-\_\-vars.\-h}}
+\subsubsection[{ribo}]{\setlength{\rightskip}{0pt plus 5cm}int ribo}}\label{fold__vars_8h_a0656afca1d2853f9ee6591172f5638de}
+use ribosum matrices \hypertarget{fold__vars_8h_a5dbaa0cca2c8c82048a0f0e38e164944}{\index{fold\-\_\-vars.\-h@{fold\-\_\-vars.\-h}!Ribosum\-File@{Ribosum\-File}}
+\index{Ribosum\-File@{Ribosum\-File}!fold_vars.h@{fold\-\_\-vars.\-h}}
+\subsubsection[{Ribosum\-File}]{\setlength{\rightskip}{0pt plus 5cm}char$\ast$ Ribosum\-File}}\label{fold__vars_8h_a5dbaa0cca2c8c82048a0f0e38e164944}
+warning this variable will vanish in the future ribosums will be compiled in instead \hypertarget{fold__vars_8h_a2695d91cc535d09c2eae5c3884e2ec64}{\index{fold\-\_\-vars.\-h@{fold\-\_\-vars.\-h}!nonstandards@{nonstandards}}
+\index{nonstandards@{nonstandards}!fold_vars.h@{fold\-\_\-vars.\-h}}
+\subsubsection[{nonstandards}]{\setlength{\rightskip}{0pt plus 5cm}char$\ast$ nonstandards}}\label{fold__vars_8h_a2695d91cc535d09c2eae5c3884e2ec64}
+
+
+contains allowed non standard base pairs
+
+Lists additional base pairs that will be allowed to form in addition to G\-C, C\-G, A\-U, U\-A, G\-U and U\-G. Nonstandard base pairs are given a stacking energy of 0. \hypertarget{fold__vars_8h_ab4b11c8d9c758430960896bc3fe82ead}{\index{fold\-\_\-vars.\-h@{fold\-\_\-vars.\-h}!temperature@{temperature}}
+\index{temperature@{temperature}!fold_vars.h@{fold\-\_\-vars.\-h}}
+\subsubsection[{temperature}]{\setlength{\rightskip}{0pt plus 5cm}double temperature}}\label{fold__vars_8h_ab4b11c8d9c758430960896bc3fe82ead}
+
+
+Rescale energy parameters to a temperature in deg\-C.
+
+Default is 37\-C. You have to call the update\-\_\-...\-\_\-params() functions after changing this parameter. \hypertarget{fold__vars_8h_af349001ad3b4d008d0051d935b1b6261}{\index{fold\-\_\-vars.\-h@{fold\-\_\-vars.\-h}!james\-\_\-rule@{james\-\_\-rule}}
+\index{james\-\_\-rule@{james\-\_\-rule}!fold_vars.h@{fold\-\_\-vars.\-h}}
+\subsubsection[{james\-\_\-rule}]{\setlength{\rightskip}{0pt plus 5cm}int james\-\_\-rule}}\label{fold__vars_8h_af349001ad3b4d008d0051d935b1b6261}
+interior loops of size 2 get energy 0.\-8\-Kcal and no mismatches, default 1 \hypertarget{fold__vars_8h_a80c3c5fd35e7479704cc91d2d0367743}{\index{fold\-\_\-vars.\-h@{fold\-\_\-vars.\-h}!log\-M\-L@{log\-M\-L}}
+\index{log\-M\-L@{log\-M\-L}!fold_vars.h@{fold\-\_\-vars.\-h}}
+\subsubsection[{log\-M\-L}]{\setlength{\rightskip}{0pt plus 5cm}int log\-M\-L}}\label{fold__vars_8h_a80c3c5fd35e7479704cc91d2d0367743}
+use logarithmic multiloop energy function \hypertarget{fold__vars_8h_ab9b2c3a37a5516614c06d0ab54b97cda}{\index{fold\-\_\-vars.\-h@{fold\-\_\-vars.\-h}!cut\-\_\-point@{cut\-\_\-point}}
+\index{cut\-\_\-point@{cut\-\_\-point}!fold_vars.h@{fold\-\_\-vars.\-h}}
+\subsubsection[{cut\-\_\-point}]{\setlength{\rightskip}{0pt plus 5cm}int cut\-\_\-point}}\label{fold__vars_8h_ab9b2c3a37a5516614c06d0ab54b97cda}
+
+
+Marks the position (starting from 1) of the first nucleotide of the second molecule within the concatenated sequence.
+
+To evaluate the energy of a duplex structure (a structure formed by two strands), concatenate the to sequences and set it to the first base of the second strand in the concatenated sequence. The default value of -\/1 stands for single molecule folding. The cut\-\_\-point variable is also used by \hyperlink{PS__dot_8h_a0873c7cc4cd7a11c9a2cea19dde7e9c9}{P\-S\-\_\-rna\-\_\-plot()} and \hyperlink{PS__dot_8h_a689a97a7e3b8a2df14728b8204d9d57b}{P\-S\-\_\-dot\-\_\-plot()} to mark the chain break in postscript plots. \hypertarget{fold__vars_8h_a0244a629b5ab4f58b77590c3dfd130dc}{\index{fold\-\_\-vars.\-h@{fold\-\_\-vars.\-h}!base\-\_\-pair@{base\-\_\-pair}}
+\index{base\-\_\-pair@{base\-\_\-pair}!fold_vars.h@{fold\-\_\-vars.\-h}}
+\subsubsection[{base\-\_\-pair}]{\setlength{\rightskip}{0pt plus 5cm}{\bf bond\-T}$\ast$ base\-\_\-pair}}\label{fold__vars_8h_a0244a629b5ab4f58b77590c3dfd130dc}
+
+
+Contains a list of base pairs after a call to \hyperlink{group__mfe__fold_gaadafcb0f140795ae62e5ca027e335a9b}{fold()}.
+
+base\-\_\-pair\mbox{[}0\mbox{]}.i contains the total number of pairs. \begin{DoxyRefDesc}{Deprecated}
+\item[\hyperlink{deprecated__deprecated000008}{Deprecated}]Do not use this variable anymore! \end{DoxyRefDesc}
+\hypertarget{fold__vars_8h_a0f5757427fd5f2f79d6fca0081cd5a52}{\index{fold\-\_\-vars.\-h@{fold\-\_\-vars.\-h}!pr@{pr}}
+\index{pr@{pr}!fold_vars.h@{fold\-\_\-vars.\-h}}
+\subsubsection[{pr}]{\setlength{\rightskip}{0pt plus 5cm}double$\ast$ pr}}\label{fold__vars_8h_a0f5757427fd5f2f79d6fca0081cd5a52}
+
+
+A pointer to the base pair probability matrix.
+
+\begin{DoxyRefDesc}{Deprecated}
+\item[\hyperlink{deprecated__deprecated000009}{Deprecated}]Do not use this variable anymore! \end{DoxyRefDesc}
+\hypertarget{fold__vars_8h_a92089ae3a51b5d75a14ce9cc29cc8317}{\index{fold\-\_\-vars.\-h@{fold\-\_\-vars.\-h}!iindx@{iindx}}
+\index{iindx@{iindx}!fold_vars.h@{fold\-\_\-vars.\-h}}
+\subsubsection[{iindx}]{\setlength{\rightskip}{0pt plus 5cm}int$\ast$ iindx}}\label{fold__vars_8h_a92089ae3a51b5d75a14ce9cc29cc8317}
+
+
+index array to move through pr.
+
+The probability for base i and j to form a pair is in pr\mbox{[}iindx\mbox{[}i\mbox{]}-\/j\mbox{]}. \begin{DoxyRefDesc}{Deprecated}
+\item[\hyperlink{deprecated__deprecated000010}{Deprecated}]Do not use this variable anymore! \end{DoxyRefDesc}
+\hypertarget{fold__vars_8h_ad3b22044065acc6dee0af68931b52cfd}{\index{fold\-\_\-vars.\-h@{fold\-\_\-vars.\-h}!pf\-\_\-scale@{pf\-\_\-scale}}
+\index{pf\-\_\-scale@{pf\-\_\-scale}!fold_vars.h@{fold\-\_\-vars.\-h}}
+\subsubsection[{pf\-\_\-scale}]{\setlength{\rightskip}{0pt plus 5cm}double pf\-\_\-scale}}\label{fold__vars_8h_ad3b22044065acc6dee0af68931b52cfd}
+
+
+A scaling factor used by \hyperlink{group__pf__fold_gadc3db3d98742427e7001a7fd36ef28c2}{pf\-\_\-fold()} to avoid overflows.
+
+Should be set to approximately $exp{((-F/kT)/length)}$, where $F$ is an estimate for the ensemble free energy, for example the minimum free energy. You must call \hyperlink{group__pf__fold_ga384e927890f9c034ff09fa66da102d28}{update\-\_\-pf\-\_\-params()} after changing this parameter.\par
+ If pf\-\_\-scale is -\/1 (the default) , an estimate will be provided automatically when computing partition functions, e.\-g. \hyperlink{group__pf__fold_gadc3db3d98742427e7001a7fd36ef28c2}{pf\-\_\-fold()} The automatic estimate is usually insufficient for sequences more than a few hundred bases long. \hypertarget{fold__vars_8h_ad512b5dd4dbec60faccfe137bb474489}{\index{fold\-\_\-vars.\-h@{fold\-\_\-vars.\-h}!do\-\_\-backtrack@{do\-\_\-backtrack}}
+\index{do\-\_\-backtrack@{do\-\_\-backtrack}!fold_vars.h@{fold\-\_\-vars.\-h}}
+\subsubsection[{do\-\_\-backtrack}]{\setlength{\rightskip}{0pt plus 5cm}int do\-\_\-backtrack}}\label{fold__vars_8h_ad512b5dd4dbec60faccfe137bb474489}
+
+
+do backtracking, i.\-e. compute secondary structures or base pair probabilities
+
+If 0, do not calculate pair probabilities in \hyperlink{group__pf__fold_gadc3db3d98742427e7001a7fd36ef28c2}{pf\-\_\-fold()}; this is about twice as fast. Default is 1. \hypertarget{fold__vars_8h_a83bdb43472a259c71e69fa9f70f420c3}{\index{fold\-\_\-vars.\-h@{fold\-\_\-vars.\-h}!backtrack\-\_\-type@{backtrack\-\_\-type}}
+\index{backtrack\-\_\-type@{backtrack\-\_\-type}!fold_vars.h@{fold\-\_\-vars.\-h}}
+\subsubsection[{backtrack\-\_\-type}]{\setlength{\rightskip}{0pt plus 5cm}char backtrack\-\_\-type}}\label{fold__vars_8h_a83bdb43472a259c71e69fa9f70f420c3}
+
+
+A backtrack array marker for \hyperlink{group__inverse__fold_ga7af026de55d4babad879f2c92559cbbc}{inverse\-\_\-fold()}
+
+If set to 'C'\-: force (1,N) to be paired, 'M' fold as if the sequence were inside a multi-\/loop. Otherwise ('F') the usual mfe structure is computed.
\ No newline at end of file
git://source.jalview.org / jabaws.git / blobdiff