1 \hypertarget{gquad_8h}{
2 \section{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/gquad.h File Reference}
3 \label{gquad_8h}\index{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/gquad.h@{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/gquad.h}}
7 Various functions related to G-\/quadruplex computations.
8 Include dependency graph for gquad.h:\nopagebreak
12 \includegraphics[width=209pt]{gquad_8h__incl}
15 \subsection*{Functions}
16 \begin{DoxyCompactItemize}
18 int $\ast$ \hyperlink{gquad_8h_a8b0784c14fa1208d0aebbebdc1318b7a}{get\_\-gquad\_\-matrix} (short $\ast$S, \hyperlink{structparamT}{paramT} $\ast$P)
19 \begin{DoxyCompactList}\small\item\em Get a triangular matrix prefilled with minimum free energy contributions of G-\/quadruplexes. \item\end{DoxyCompactList}\item
20 int \hyperlink{gquad_8h_ae41763215b9c64d2a7b67f0df8a28078}{parse\_\-gquad} (const char $\ast$struc, int $\ast$L, int l\mbox{[}3\mbox{]})
22 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)
24 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)
25 \end{DoxyCompactItemize}
28 \subsection{Detailed Description}
29 Various functions related to G-\/quadruplex computations.
31 \subsection{Function Documentation}
32 \hypertarget{gquad_8h_a8b0784c14fa1208d0aebbebdc1318b7a}{
33 \index{gquad.h@{gquad.h}!get\_\-gquad\_\-matrix@{get\_\-gquad\_\-matrix}}
34 \index{get\_\-gquad\_\-matrix@{get\_\-gquad\_\-matrix}!gquad.h@{gquad.h}}
35 \subsubsection[{get\_\-gquad\_\-matrix}]{\setlength{\rightskip}{0pt plus 5cm}int$\ast$ get\_\-gquad\_\-matrix (short $\ast$ {\em S}, \/ {\bf paramT} $\ast$ {\em P})}}
36 \label{gquad_8h_a8b0784c14fa1208d0aebbebdc1318b7a}
39 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().
41 \begin{DoxySeeAlso}{See also}
42 get\_\-jindx(), encode\_\-sequence()
45 \begin{DoxyParams}{Parameters}
46 \item[{\em S}]The encoded sequence \item[{\em P}]A pointer to the data structure containing the precomputed energy contributions \end{DoxyParams}
47 \begin{DoxyReturn}{Returns}
48 A pointer to the G-\/quadruplex contribution matrix
50 \hypertarget{gquad_8h_ae41763215b9c64d2a7b67f0df8a28078}{
51 \index{gquad.h@{gquad.h}!parse\_\-gquad@{parse\_\-gquad}}
52 \index{parse\_\-gquad@{parse\_\-gquad}!gquad.h@{gquad.h}}
53 \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{]})}}
54 \label{gquad_8h_ae41763215b9c64d2a7b67f0df8a28078}
55 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}{
56 \index{gquad.h@{gquad.h}!backtrack\_\-GQuad\_\-IntLoop@{backtrack\_\-GQuad\_\-IntLoop}}
57 \index{backtrack\_\-GQuad\_\-IntLoop@{backtrack\_\-GQuad\_\-IntLoop}!gquad.h@{gquad.h}}
58 \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})}}
59 \label{gquad_8h_a54475a8eb898fa1e8af8ab5f5375f3be}
60 backtrack an interior loop like enclosed g-\/quadruplex with closing pair (i,j)
63 \begin{DoxyParams}{Parameters}
64 \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}
65 \begin{DoxyReturn}{Returns}
66 1 on success, 0 if no gquad found
68 \hypertarget{gquad_8h_a118ec7289f1936bd810be7fe50b98212}{
69 \index{gquad.h@{gquad.h}!backtrack\_\-GQuad\_\-IntLoop\_\-L@{backtrack\_\-GQuad\_\-IntLoop\_\-L}}
70 \index{backtrack\_\-GQuad\_\-IntLoop\_\-L@{backtrack\_\-GQuad\_\-IntLoop\_\-L}!gquad.h@{gquad.h}}
71 \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})}}
72 \label{gquad_8h_a118ec7289f1936bd810be7fe50b98212}
73 backtrack an interior loop like enclosed g-\/quadruplex with closing pair (i,j) with underlying Lfold matrix
76 \begin{DoxyParams}{Parameters}
77 \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}
78 \begin{DoxyReturn}{Returns}
79 1 on success, 0 if no gquad found