-\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}}
+\hypertarget{gquad_8h}{
+\section{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/gquad.h File Reference}
+\label{gquad_8h}\index{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/gquad.h@{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/gquad.h}}
}
Various functions related to G-\/quadruplex computations.
-
-
-Include dependency graph for gquad.\-h\-:
-\nopagebreak
+Include dependency graph for gquad.h:\nopagebreak
\begin{figure}[H]
\begin{center}
\leavevmode
-\includegraphics[width=250pt]{gquad_8h__incl}
+\includegraphics[width=209pt]{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{]})
+int $\ast$ \hyperlink{gquad_8h_a8b0784c14fa1208d0aebbebdc1318b7a}{get\_\-gquad\_\-matrix} (short $\ast$S, \hyperlink{structparamT}{paramT} $\ast$P)
+\begin{DoxyCompactList}\small\item\em Get a triangular matrix prefilled with minimum free energy contributions of G-\/quadruplexes. \item\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)
+PRIVATE int \hyperlink{gquad_8h_a54475a8eb898fa1e8af8ab5f5375f3be}{backtrack\_\-GQuad\_\-IntLoop} (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}{paramT} $\ast$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$$\ast$ggg, int maxdist, int $\ast$p, int $\ast$q, \hyperlink{structparamT}{param\-T} $\ast$P)
+PRIVATE int \hyperlink{gquad_8h_a118ec7289f1936bd810be7fe50b98212}{backtrack\_\-GQuad\_\-IntLoop\_\-L} (int c, int i, int j, int type, short $\ast$S, int $\ast$$\ast$ggg, int maxdist, int $\ast$p, int $\ast$q, \hyperlink{structparamT}{paramT} $\ast$P)
\end{DoxyCompactItemize}
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}
-
+\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 (short $\ast$ {\em S}, \/ {\bf paramT} $\ast$ {\em P})}}
+\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().
+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 INF. 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()
+\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}
+\item[{\em S}]The encoded sequence \item[{\em P}]A pointer to the data structure containing the precomputed energy contributions \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}
+\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 (const char $\ast$ {\em struc}, \/ int $\ast$ {\em L}, \/ int {\em l}\mbox{[}3\mbox{]})}}
+\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\_\-GQuad\_\-IntLoop@{backtrack\_\-GQuad\_\-IntLoop}}
+\index{backtrack\_\-GQuad\_\-IntLoop@{backtrack\_\-GQuad\_\-IntLoop}!gquad.h@{gquad.h}}
+\subsubsection[{backtrack\_\-GQuad\_\-IntLoop}]{\setlength{\rightskip}{0pt plus 5cm}PRIVATE int backtrack\_\-GQuad\_\-IntLoop (int {\em c}, \/ int {\em i}, \/ int {\em j}, \/ int {\em type}, \/ short $\ast$ {\em S}, \/ int $\ast$ {\em ggg}, \/ int $\ast$ {\em index}, \/ int $\ast$ {\em p}, \/ int $\ast$ {\em q}, \/ {\bf paramT} $\ast$ {\em P})}}
+\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}
+\item[{\em c}]The total contribution the loop should resemble \item[{\em i}]position i of enclosing pair \item[{\em j}]position j of enclosing pair \item[{\em type}]base pair type of enclosing pair (must be reverse type) \item[{\em S}]integer encoded sequence \item[{\em ggg}]triangular matrix containing g-\/quadruplex contributions \item[{\em index}]the index for accessing the triangular matrix \item[{\em p}]here the 5' position of the gquad is stored \item[{\em q}]here the 3' position of the gquad is stored \item[{\em P}]the datastructure containing the precalculated contibutions\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$$\ast$}]{ggg, }
-\item[{int}]{maxdist, }
-\item[{int $\ast$}]{p, }
-\item[{int $\ast$}]{q, }
-\item[{{\bf param\-T} $\ast$}]{P}
-\end{DoxyParamCaption}
-)}}\label{gquad_8h_a118ec7289f1936bd810be7fe50b98212}
+\hypertarget{gquad_8h_a118ec7289f1936bd810be7fe50b98212}{
+\index{gquad.h@{gquad.h}!backtrack\_\-GQuad\_\-IntLoop\_\-L@{backtrack\_\-GQuad\_\-IntLoop\_\-L}}
+\index{backtrack\_\-GQuad\_\-IntLoop\_\-L@{backtrack\_\-GQuad\_\-IntLoop\_\-L}!gquad.h@{gquad.h}}
+\subsubsection[{backtrack\_\-GQuad\_\-IntLoop\_\-L}]{\setlength{\rightskip}{0pt plus 5cm}PRIVATE int backtrack\_\-GQuad\_\-IntLoop\_\-L (int {\em c}, \/ int {\em i}, \/ int {\em j}, \/ int {\em type}, \/ short $\ast$ {\em S}, \/ int $\ast$$\ast$ {\em ggg}, \/ int {\em maxdist}, \/ int $\ast$ {\em p}, \/ int $\ast$ {\em q}, \/ {\bf paramT} $\ast$ {\em P})}}
+\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}
+\item[{\em c}]The total contribution the loop should resemble \item[{\em i}]position i of enclosing pair \item[{\em j}]position j of enclosing pair \item[{\em type}]base pair type of enclosing pair (must be reverse type) \item[{\em S}]integer encoded sequence \item[{\em ggg}]triangular matrix containing g-\/quadruplex contributions \item[{\em p}]here the 5' position of the gquad is stored \item[{\em q}]here the 3' position of the gquad is stored \item[{\em P}]the datastructure containing the precalculated contibutions\end{DoxyParams}
\begin{DoxyReturn}{Returns}
1 on success, 0 if no gquad found
\end{DoxyReturn}
git://source.jalview.org / jabaws.git / blobdiff