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+<h1>/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/gquad.h File Reference</h1>
<p>Various functions related to G-quadruplex computations.
-<a href="#details">More...</a></p>
-<div class="textblock"><div id="dynsection-0" onclick="return toggleVisibility(this)" class="dynheader closed" style="cursor:pointer;">
- <img id="dynsection-0-trigger" src="closed.png" alt="+"/> Include dependency graph for gquad.h:</div>
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-</div>
-<div id="dynsection-0-content" class="dyncontent" style="display:none;">
-<div class="center"><img src="gquad_8h__incl.png" border="0" usemap="#_2home_2mescalin_2ronny_2public__html_2programs_2ViennaRNA_2H_2gquad_8h" alt=""/></div>
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+
<p><a href="gquad_8h_source.html">Go to the source code of this file.</a></p>
-<table class="memberdecls">
-<tr class="heading"><td colspan="2"><h2><a name="func-members"></a>
-Functions</h2></td></tr>
-<tr class="memitem:a8b0784c14fa1208d0aebbebdc1318b7a"><td class="memItemLeft" align="right" valign="top">int * </td><td class="memItemRight" valign="bottom"><a class="el" href="gquad_8h.html#a8b0784c14fa1208d0aebbebdc1318b7a">get_gquad_matrix</a> (short *S, <a class="el" href="structparamT.html">paramT</a> *P)</td></tr>
-<tr class="memdesc:a8b0784c14fa1208d0aebbebdc1318b7a"><td class="mdescLeft"> </td><td class="mdescRight">Get a triangular matrix prefilled with minimum free energy contributions of G-quadruplexes. <a href="#a8b0784c14fa1208d0aebbebdc1318b7a"></a><br/></td></tr>
-<tr class="memitem:ae41763215b9c64d2a7b67f0df8a28078"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="gquad_8h.html#ae41763215b9c64d2a7b67f0df8a28078">parse_gquad</a> (const char *struc, int *L, int l[3])</td></tr>
-<tr class="memitem:a54475a8eb898fa1e8af8ab5f5375f3be"><td class="memItemLeft" align="right" valign="top">PRIVATE int </td><td class="memItemRight" valign="bottom"><a class="el" href="gquad_8h.html#a54475a8eb898fa1e8af8ab5f5375f3be">backtrack_GQuad_IntLoop</a> (int c, int i, int j, int type, short *S, int *ggg, int *index, int *p, int *q, <a class="el" href="structparamT.html">paramT</a> *P)</td></tr>
-<tr class="memitem:a118ec7289f1936bd810be7fe50b98212"><td class="memItemLeft" align="right" valign="top">PRIVATE int </td><td class="memItemRight" valign="bottom"><a class="el" href="gquad_8h.html#a118ec7289f1936bd810be7fe50b98212">backtrack_GQuad_IntLoop_L</a> (int c, int i, int j, int type, short *S, int **ggg, int maxdist, int *p, int *q, <a class="el" href="structparamT.html">paramT</a> *P)</td></tr>
+<table border="0" cellpadding="0" cellspacing="0">
+<tr><td colspan="2"><h2>Functions</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int * </td><td class="memItemRight" valign="bottom"><a class="el" href="gquad_8h.html#a8b0784c14fa1208d0aebbebdc1318b7a">get_gquad_matrix</a> (short *S, <a class="el" href="structparamT.html">paramT</a> *P)</td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">Get a triangular matrix prefilled with minimum free energy contributions of G-quadruplexes. <a href="#a8b0784c14fa1208d0aebbebdc1318b7a"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="gquad_8h.html#ae41763215b9c64d2a7b67f0df8a28078">parse_gquad</a> (const char *struc, int *L, int l[3])</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">PRIVATE int </td><td class="memItemRight" valign="bottom"><a class="el" href="gquad_8h.html#a54475a8eb898fa1e8af8ab5f5375f3be">backtrack_GQuad_IntLoop</a> (int c, int i, int j, int type, short *S, int *ggg, int *index, int *p, int *q, <a class="el" href="structparamT.html">paramT</a> *P)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">PRIVATE int </td><td class="memItemRight" valign="bottom"><a class="el" href="gquad_8h.html#a118ec7289f1936bd810be7fe50b98212">backtrack_GQuad_IntLoop_L</a> (int c, int i, int j, int type, short *S, int **ggg, int maxdist, int *p, int *q, <a class="el" href="structparamT.html">paramT</a> *P)</td></tr>
</table>
-<hr/><a name="details" id="details"></a><h2>Detailed Description</h2>
-<div class="textblock"><p>Various functions related to G-quadruplex computations. </p>
-</div><hr/><h2>Function Documentation</h2>
-<a class="anchor" id="a8b0784c14fa1208d0aebbebdc1318b7a"></a>
+<hr/><a name="_details"></a><h2>Detailed Description</h2>
+<p>Various functions related to G-quadruplex computations. </p>
+<hr/><h2>Function Documentation</h2>
+<a class="anchor" id="a8b0784c14fa1208d0aebbebdc1318b7a"></a><!-- doxytag: member="gquad.h::get_gquad_matrix" ref="a8b0784c14fa1208d0aebbebdc1318b7a" args="(short *S, paramT *P)" -->
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<td class="memname">int* get_gquad_matrix </td>
<td>(</td>
- <td class="paramtype">short * </td>
- <td class="paramname"><em>S</em>, </td>
+ <td class="paramtype">short * </td>
+ <td class="paramname"> <em>S</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype"><a class="el" href="structparamT.html">paramT</a> * </td>
- <td class="paramname"><em>P</em> </td>
+ <td class="paramtype"><a class="el" href="structparamT.html">paramT</a> * </td>
+ <td class="paramname"> <em>P</em></td><td> </td>
</tr>
<tr>
<td></td>
<td>)</td>
- <td></td><td></td>
+ <td></td><td></td><td></td>
</tr>
</table>
-</div><div class="memdoc">
+</div>
+<div class="memdoc">
<p>Get a triangular matrix prefilled with minimum free energy contributions of G-quadruplexes. </p>
<p>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[indx[j]+i]. To get the integer array indx see get_jindx().</p>
-<dl class="section see"><dt>See also:</dt><dd>get_jindx(), encode_sequence()</dd></dl>
-<dl class="params"><dt>Parameters:</dt><dd>
- <table class="params">
- <tr><td class="paramname">S</td><td>The encoded sequence </td></tr>
- <tr><td class="paramname">P</td><td>A pointer to the data structure containing the precomputed energy contributions </td></tr>
+<dl class="see"><dt><b>See also:</b></dt><dd>get_jindx(), encode_sequence()</dd></dl>
+<dl><dt><b>Parameters:</b></dt><dd>
+ <table border="0" cellspacing="2" cellpadding="0">
+ <tr><td valign="top"></td><td valign="top"><em>S</em> </td><td>The encoded sequence </td></tr>
+ <tr><td valign="top"></td><td valign="top"><em>P</em> </td><td>A pointer to the data structure containing the precomputed energy contributions </td></tr>
</table>
</dd>
</dl>
-<dl class="section return"><dt>Returns:</dt><dd>A pointer to the G-quadruplex contribution matrix </dd></dl>
+<dl class="return"><dt><b>Returns:</b></dt><dd>A pointer to the G-quadruplex contribution matrix </dd></dl>
</div>
</div>
-<a class="anchor" id="ae41763215b9c64d2a7b67f0df8a28078"></a>
+<a class="anchor" id="ae41763215b9c64d2a7b67f0df8a28078"></a><!-- doxytag: member="gquad.h::parse_gquad" ref="ae41763215b9c64d2a7b67f0df8a28078" args="(const char *struc, int *L, int l[3])" -->
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<div class="memproto">
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<td class="memname">int parse_gquad </td>
<td>(</td>
- <td class="paramtype">const char * </td>
- <td class="paramname"><em>struc</em>, </td>
+ <td class="paramtype">const char * </td>
+ <td class="paramname"> <em>struc</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">int * </td>
- <td class="paramname"><em>L</em>, </td>
+ <td class="paramtype">int * </td>
+ <td class="paramname"> <em>L</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">int </td>
- <td class="paramname"><em>l</em>[3] </td>
+ <td class="paramtype">int </td>
+ <td class="paramname"> <em>l</em>[3]</td><td> </td>
</tr>
<tr>
<td></td>
<td>)</td>
- <td></td><td></td>
+ <td></td><td></td><td></td>
</tr>
</table>
-</div><div class="memdoc">
+</div>
+<div class="memdoc">
<p>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[] 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; ... ; </p>
</div>
</div>
-<a class="anchor" id="a54475a8eb898fa1e8af8ab5f5375f3be"></a>
+<a class="anchor" id="a54475a8eb898fa1e8af8ab5f5375f3be"></a><!-- doxytag: member="gquad.h::backtrack_GQuad_IntLoop" ref="a54475a8eb898fa1e8af8ab5f5375f3be" args="(int c, int i, int j, int type, short *S, int *ggg, int *index, int *p, int *q, paramT *P)" -->
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<td class="memname">PRIVATE int backtrack_GQuad_IntLoop </td>
<td>(</td>
- <td class="paramtype">int </td>
- <td class="paramname"><em>c</em>, </td>
+ <td class="paramtype">int </td>
+ <td class="paramname"> <em>c</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">int </td>
- <td class="paramname"><em>i</em>, </td>
+ <td class="paramtype">int </td>
+ <td class="paramname"> <em>i</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">int </td>
- <td class="paramname"><em>j</em>, </td>
+ <td class="paramtype">int </td>
+ <td class="paramname"> <em>j</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">int </td>
- <td class="paramname"><em>type</em>, </td>
+ <td class="paramtype">int </td>
+ <td class="paramname"> <em>type</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">short * </td>
- <td class="paramname"><em>S</em>, </td>
+ <td class="paramtype">short * </td>
+ <td class="paramname"> <em>S</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">int * </td>
- <td class="paramname"><em>ggg</em>, </td>
+ <td class="paramtype">int * </td>
+ <td class="paramname"> <em>ggg</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">int * </td>
- <td class="paramname"><em>index</em>, </td>
+ <td class="paramtype">int * </td>
+ <td class="paramname"> <em>index</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">int * </td>
- <td class="paramname"><em>p</em>, </td>
+ <td class="paramtype">int * </td>
+ <td class="paramname"> <em>p</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">int * </td>
- <td class="paramname"><em>q</em>, </td>
+ <td class="paramtype">int * </td>
+ <td class="paramname"> <em>q</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype"><a class="el" href="structparamT.html">paramT</a> * </td>
- <td class="paramname"><em>P</em> </td>
+ <td class="paramtype"><a class="el" href="structparamT.html">paramT</a> * </td>
+ <td class="paramname"> <em>P</em></td><td> </td>
</tr>
<tr>
<td></td>
<td>)</td>
- <td></td><td></td>
+ <td></td><td></td><td></td>
</tr>
</table>
-</div><div class="memdoc">
+</div>
+<div class="memdoc">
<p>backtrack an interior loop like enclosed g-quadruplex with closing pair (i,j)</p>
-<dl class="params"><dt>Parameters:</dt><dd>
- <table class="params">
- <tr><td class="paramname">c</td><td>The total contribution the loop should resemble </td></tr>
- <tr><td class="paramname">i</td><td>position i of enclosing pair </td></tr>
- <tr><td class="paramname">j</td><td>position j of enclosing pair </td></tr>
- <tr><td class="paramname">type</td><td>base pair type of enclosing pair (must be reverse type) </td></tr>
- <tr><td class="paramname">S</td><td>integer encoded sequence </td></tr>
- <tr><td class="paramname">ggg</td><td>triangular matrix containing g-quadruplex contributions </td></tr>
- <tr><td class="paramname">index</td><td>the index for accessing the triangular matrix </td></tr>
- <tr><td class="paramname">p</td><td>here the 5' position of the gquad is stored </td></tr>
- <tr><td class="paramname">q</td><td>here the 3' position of the gquad is stored </td></tr>
- <tr><td class="paramname">P</td><td>the datastructure containing the precalculated contibutions</td></tr>
+<dl><dt><b>Parameters:</b></dt><dd>
+ <table border="0" cellspacing="2" cellpadding="0">
+ <tr><td valign="top"></td><td valign="top"><em>c</em> </td><td>The total contribution the loop should resemble </td></tr>
+ <tr><td valign="top"></td><td valign="top"><em>i</em> </td><td>position i of enclosing pair </td></tr>
+ <tr><td valign="top"></td><td valign="top"><em>j</em> </td><td>position j of enclosing pair </td></tr>
+ <tr><td valign="top"></td><td valign="top"><em>type</em> </td><td>base pair type of enclosing pair (must be reverse type) </td></tr>
+ <tr><td valign="top"></td><td valign="top"><em>S</em> </td><td>integer encoded sequence </td></tr>
+ <tr><td valign="top"></td><td valign="top"><em>ggg</em> </td><td>triangular matrix containing g-quadruplex contributions </td></tr>
+ <tr><td valign="top"></td><td valign="top"><em>index</em> </td><td>the index for accessing the triangular matrix </td></tr>
+ <tr><td valign="top"></td><td valign="top"><em>p</em> </td><td>here the 5' position of the gquad is stored </td></tr>
+ <tr><td valign="top"></td><td valign="top"><em>q</em> </td><td>here the 3' position of the gquad is stored </td></tr>
+ <tr><td valign="top"></td><td valign="top"><em>P</em> </td><td>the datastructure containing the precalculated contibutions</td></tr>
</table>
</dd>
</dl>
-<dl class="section return"><dt>Returns:</dt><dd>1 on success, 0 if no gquad found </dd></dl>
+<dl class="return"><dt><b>Returns:</b></dt><dd>1 on success, 0 if no gquad found </dd></dl>
</div>
</div>
-<a class="anchor" id="a118ec7289f1936bd810be7fe50b98212"></a>
+<a class="anchor" id="a118ec7289f1936bd810be7fe50b98212"></a><!-- doxytag: member="gquad.h::backtrack_GQuad_IntLoop_L" ref="a118ec7289f1936bd810be7fe50b98212" args="(int c, int i, int j, int type, short *S, int **ggg, int maxdist, int *p, int *q, paramT *P)" -->
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<td class="memname">PRIVATE int backtrack_GQuad_IntLoop_L </td>
<td>(</td>
- <td class="paramtype">int </td>
- <td class="paramname"><em>c</em>, </td>
+ <td class="paramtype">int </td>
+ <td class="paramname"> <em>c</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">int </td>
- <td class="paramname"><em>i</em>, </td>
+ <td class="paramtype">int </td>
+ <td class="paramname"> <em>i</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">int </td>
- <td class="paramname"><em>j</em>, </td>
+ <td class="paramtype">int </td>
+ <td class="paramname"> <em>j</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">int </td>
- <td class="paramname"><em>type</em>, </td>
+ <td class="paramtype">int </td>
+ <td class="paramname"> <em>type</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">short * </td>
- <td class="paramname"><em>S</em>, </td>
+ <td class="paramtype">short * </td>
+ <td class="paramname"> <em>S</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">int ** </td>
- <td class="paramname"><em>ggg</em>, </td>
+ <td class="paramtype">int ** </td>
+ <td class="paramname"> <em>ggg</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">int </td>
- <td class="paramname"><em>maxdist</em>, </td>
+ <td class="paramtype">int </td>
+ <td class="paramname"> <em>maxdist</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">int * </td>
- <td class="paramname"><em>p</em>, </td>
+ <td class="paramtype">int * </td>
+ <td class="paramname"> <em>p</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">int * </td>
- <td class="paramname"><em>q</em>, </td>
+ <td class="paramtype">int * </td>
+ <td class="paramname"> <em>q</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype"><a class="el" href="structparamT.html">paramT</a> * </td>
- <td class="paramname"><em>P</em> </td>
+ <td class="paramtype"><a class="el" href="structparamT.html">paramT</a> * </td>
+ <td class="paramname"> <em>P</em></td><td> </td>
</tr>
<tr>
<td></td>
<td>)</td>
- <td></td><td></td>
+ <td></td><td></td><td></td>
</tr>
</table>
-</div><div class="memdoc">
+</div>
+<div class="memdoc">
<p>backtrack an interior loop like enclosed g-quadruplex with closing pair (i,j) with underlying Lfold matrix</p>
-<dl class="params"><dt>Parameters:</dt><dd>
- <table class="params">
- <tr><td class="paramname">c</td><td>The total contribution the loop should resemble </td></tr>
- <tr><td class="paramname">i</td><td>position i of enclosing pair </td></tr>
- <tr><td class="paramname">j</td><td>position j of enclosing pair </td></tr>
- <tr><td class="paramname">type</td><td>base pair type of enclosing pair (must be reverse type) </td></tr>
- <tr><td class="paramname">S</td><td>integer encoded sequence </td></tr>
- <tr><td class="paramname">ggg</td><td>triangular matrix containing g-quadruplex contributions </td></tr>
- <tr><td class="paramname">p</td><td>here the 5' position of the gquad is stored </td></tr>
- <tr><td class="paramname">q</td><td>here the 3' position of the gquad is stored </td></tr>
- <tr><td class="paramname">P</td><td>the datastructure containing the precalculated contibutions</td></tr>
+<dl><dt><b>Parameters:</b></dt><dd>
+ <table border="0" cellspacing="2" cellpadding="0">
+ <tr><td valign="top"></td><td valign="top"><em>c</em> </td><td>The total contribution the loop should resemble </td></tr>
+ <tr><td valign="top"></td><td valign="top"><em>i</em> </td><td>position i of enclosing pair </td></tr>
+ <tr><td valign="top"></td><td valign="top"><em>j</em> </td><td>position j of enclosing pair </td></tr>
+ <tr><td valign="top"></td><td valign="top"><em>type</em> </td><td>base pair type of enclosing pair (must be reverse type) </td></tr>
+ <tr><td valign="top"></td><td valign="top"><em>S</em> </td><td>integer encoded sequence </td></tr>
+ <tr><td valign="top"></td><td valign="top"><em>ggg</em> </td><td>triangular matrix containing g-quadruplex contributions </td></tr>
+ <tr><td valign="top"></td><td valign="top"><em>p</em> </td><td>here the 5' position of the gquad is stored </td></tr>
+ <tr><td valign="top"></td><td valign="top"><em>q</em> </td><td>here the 3' position of the gquad is stored </td></tr>
+ <tr><td valign="top"></td><td valign="top"><em>P</em> </td><td>the datastructure containing the precalculated contibutions</td></tr>
</table>
</dd>
</dl>
-<dl class="section return"><dt>Returns:</dt><dd>1 on success, 0 if no gquad found </dd></dl>
+<dl class="return"><dt><b>Returns:</b></dt><dd>1 on success, 0 if no gquad found </dd></dl>
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