--- /dev/null
+\hypertarget{gquad_8h}{\section{/home/asherstnev/\-Projects/\-Java.projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/gquad.h File Reference}
+\label{gquad_8h}\index{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/gquad.\-h@{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/gquad.\-h}}
+}
+
+
+Various functions related to G-\/quadruplex computations.
+
+
+Include dependency graph for gquad.\-h\-:
+\nopagebreak
+\begin{figure}[H]
+\begin{center}
+\leavevmode
+\includegraphics[width=250pt]{gquad_8h__incl}
+\end{center}
+\end{figure}
+\subsection*{Functions}
+\begin{DoxyCompactItemize}
+\item
+int $\ast$ \hyperlink{gquad_8h_a8b0784c14fa1208d0aebbebdc1318b7a}{get\-\_\-gquad\-\_\-matrix} (short $\ast$S, \hyperlink{structparamT}{param\-T} $\ast$P)
+\begin{DoxyCompactList}\small\item\em Get a triangular matrix prefilled with minimum free energy contributions of G-\/quadruplexes. \end{DoxyCompactList}\item
+int \hyperlink{gquad_8h_ae41763215b9c64d2a7b67f0df8a28078}{parse\-\_\-gquad} (const char $\ast$struc, int $\ast$L, int l\mbox{[}3\mbox{]})
+\item
+P\-R\-I\-V\-A\-T\-E int \hyperlink{gquad_8h_a54475a8eb898fa1e8af8ab5f5375f3be}{backtrack\-\_\-\-G\-Quad\-\_\-\-Int\-Loop} (int c, int i, int j, int type, short $\ast$S, int $\ast$ggg, int $\ast$index, int $\ast$p, int $\ast$q, \hyperlink{structparamT}{param\-T} $\ast$P)
+\item
+P\-R\-I\-V\-A\-T\-E int \hyperlink{gquad_8h_a118ec7289f1936bd810be7fe50b98212}{backtrack\-\_\-\-G\-Quad\-\_\-\-Int\-Loop\-\_\-\-L} (int c, int i, int j, int type, short $\ast$S, int $\ast$$\ast$ggg, int maxdist, int $\ast$p, int $\ast$q, \hyperlink{structparamT}{param\-T} $\ast$P)
+\end{DoxyCompactItemize}
+
+
+\subsection{Detailed Description}
+Various functions related to G-\/quadruplex computations.
+
+\subsection{Function Documentation}
+\hypertarget{gquad_8h_a8b0784c14fa1208d0aebbebdc1318b7a}{\index{gquad.\-h@{gquad.\-h}!get\-\_\-gquad\-\_\-matrix@{get\-\_\-gquad\-\_\-matrix}}
+\index{get\-\_\-gquad\-\_\-matrix@{get\-\_\-gquad\-\_\-matrix}!gquad.h@{gquad.\-h}}
+\subsubsection[{get\-\_\-gquad\-\_\-matrix}]{\setlength{\rightskip}{0pt plus 5cm}int$\ast$ get\-\_\-gquad\-\_\-matrix (
+\begin{DoxyParamCaption}
+\item[{short $\ast$}]{S, }
+\item[{{\bf param\-T} $\ast$}]{P}
+\end{DoxyParamCaption}
+)}}\label{gquad_8h_a8b0784c14fa1208d0aebbebdc1318b7a}
+
+
+Get a triangular matrix prefilled with minimum free energy contributions of G-\/quadruplexes.
+
+At each position ij in the matrix, the minimum free energy of any G-\/quadruplex delimited by i and j is stored. If no G-\/quadruplex formation is possible, the matrix element is set to I\-N\-F. Access the elements in the matrix via matrix\mbox{[}indx\mbox{[}j\mbox{]}+i\mbox{]}. To get the integer array indx see get\-\_\-jindx().
+
+\begin{DoxySeeAlso}{See Also}
+get\-\_\-jindx(), encode\-\_\-sequence()
+\end{DoxySeeAlso}
+
+\begin{DoxyParams}{Parameters}
+{\em S} & The encoded sequence \\
+\hline
+{\em P} & A pointer to the data structure containing the precomputed energy contributions \\
+\hline
+\end{DoxyParams}
+\begin{DoxyReturn}{Returns}
+A pointer to the G-\/quadruplex contribution matrix
+\end{DoxyReturn}
+\hypertarget{gquad_8h_ae41763215b9c64d2a7b67f0df8a28078}{\index{gquad.\-h@{gquad.\-h}!parse\-\_\-gquad@{parse\-\_\-gquad}}
+\index{parse\-\_\-gquad@{parse\-\_\-gquad}!gquad.h@{gquad.\-h}}
+\subsubsection[{parse\-\_\-gquad}]{\setlength{\rightskip}{0pt plus 5cm}int parse\-\_\-gquad (
+\begin{DoxyParamCaption}
+\item[{const char $\ast$}]{struc, }
+\item[{int $\ast$}]{L, }
+\item[{int}]{l\mbox{[}3\mbox{]}}
+\end{DoxyParamCaption}
+)}}\label{gquad_8h_ae41763215b9c64d2a7b67f0df8a28078}
+given a dot-\/bracket structure (possibly) containing gquads encoded by '+' signs, find first gquad, return end position or 0 if none found Upon return L and l\mbox{[}\mbox{]} contain the number of stacked layers, as well as the lengths of the linker regions. To parse a string with many gquads, call parse\-\_\-gquad repeatedly e.\-g. end1 = parse\-\_\-gquad(struc, \&\-L, l); ... ; end2 = parse\-\_\-gquad(struc+end1, \&L, l); end2+=end1; ... ; end3 = parse\-\_\-gquad(struc+end2, \&L, l); end3+=end2; ... ; \hypertarget{gquad_8h_a54475a8eb898fa1e8af8ab5f5375f3be}{\index{gquad.\-h@{gquad.\-h}!backtrack\-\_\-\-G\-Quad\-\_\-\-Int\-Loop@{backtrack\-\_\-\-G\-Quad\-\_\-\-Int\-Loop}}
+\index{backtrack\-\_\-\-G\-Quad\-\_\-\-Int\-Loop@{backtrack\-\_\-\-G\-Quad\-\_\-\-Int\-Loop}!gquad.h@{gquad.\-h}}
+\subsubsection[{backtrack\-\_\-\-G\-Quad\-\_\-\-Int\-Loop}]{\setlength{\rightskip}{0pt plus 5cm}P\-R\-I\-V\-A\-T\-E int backtrack\-\_\-\-G\-Quad\-\_\-\-Int\-Loop (
+\begin{DoxyParamCaption}
+\item[{int}]{c, }
+\item[{int}]{i, }
+\item[{int}]{j, }
+\item[{int}]{type, }
+\item[{short $\ast$}]{S, }
+\item[{int $\ast$}]{ggg, }
+\item[{int $\ast$}]{index, }
+\item[{int $\ast$}]{p, }
+\item[{int $\ast$}]{q, }
+\item[{{\bf param\-T} $\ast$}]{P}
+\end{DoxyParamCaption}
+)}}\label{gquad_8h_a54475a8eb898fa1e8af8ab5f5375f3be}
+backtrack an interior loop like enclosed g-\/quadruplex with closing pair (i,j)
+
+
+\begin{DoxyParams}{Parameters}
+{\em c} & The total contribution the loop should resemble \\
+\hline
+{\em i} & position i of enclosing pair \\
+\hline
+{\em j} & position j of enclosing pair \\
+\hline
+{\em type} & base pair type of enclosing pair (must be reverse type) \\
+\hline
+{\em S} & integer encoded sequence \\
+\hline
+{\em ggg} & triangular matrix containing g-\/quadruplex contributions \\
+\hline
+{\em index} & the index for accessing the triangular matrix \\
+\hline
+{\em p} & here the 5' position of the gquad is stored \\
+\hline
+{\em q} & here the 3' position of the gquad is stored \\
+\hline
+{\em P} & the datastructure containing the precalculated contibutions\\
+\hline
+\end{DoxyParams}
+\begin{DoxyReturn}{Returns}
+1 on success, 0 if no gquad found
+\end{DoxyReturn}
+\hypertarget{gquad_8h_a118ec7289f1936bd810be7fe50b98212}{\index{gquad.\-h@{gquad.\-h}!backtrack\-\_\-\-G\-Quad\-\_\-\-Int\-Loop\-\_\-\-L@{backtrack\-\_\-\-G\-Quad\-\_\-\-Int\-Loop\-\_\-\-L}}
+\index{backtrack\-\_\-\-G\-Quad\-\_\-\-Int\-Loop\-\_\-\-L@{backtrack\-\_\-\-G\-Quad\-\_\-\-Int\-Loop\-\_\-\-L}!gquad.h@{gquad.\-h}}
+\subsubsection[{backtrack\-\_\-\-G\-Quad\-\_\-\-Int\-Loop\-\_\-\-L}]{\setlength{\rightskip}{0pt plus 5cm}P\-R\-I\-V\-A\-T\-E int backtrack\-\_\-\-G\-Quad\-\_\-\-Int\-Loop\-\_\-\-L (
+\begin{DoxyParamCaption}
+\item[{int}]{c, }
+\item[{int}]{i, }
+\item[{int}]{j, }
+\item[{int}]{type, }
+\item[{short $\ast$}]{S, }
+\item[{int $\ast$$\ast$}]{ggg, }
+\item[{int}]{maxdist, }
+\item[{int $\ast$}]{p, }
+\item[{int $\ast$}]{q, }
+\item[{{\bf param\-T} $\ast$}]{P}
+\end{DoxyParamCaption}
+)}}\label{gquad_8h_a118ec7289f1936bd810be7fe50b98212}
+backtrack an interior loop like enclosed g-\/quadruplex with closing pair (i,j) with underlying Lfold matrix
+
+
+\begin{DoxyParams}{Parameters}
+{\em c} & The total contribution the loop should resemble \\
+\hline
+{\em i} & position i of enclosing pair \\
+\hline
+{\em j} & position j of enclosing pair \\
+\hline
+{\em type} & base pair type of enclosing pair (must be reverse type) \\
+\hline
+{\em S} & integer encoded sequence \\
+\hline
+{\em ggg} & triangular matrix containing g-\/quadruplex contributions \\
+\hline
+{\em p} & here the 5' position of the gquad is stored \\
+\hline
+{\em q} & here the 3' position of the gquad is stored \\
+\hline
+{\em P} & the datastructure containing the precalculated contibutions\\
+\hline
+\end{DoxyParams}
+\begin{DoxyReturn}{Returns}
+1 on success, 0 if no gquad found
+\end{DoxyReturn}
git://source.jalview.org / jabaws.git / blobdiff