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-<div class="title">TwoDfold_vars Struct Reference</div> </div>
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<div class="contents">
-
+<h1>TwoDfold_vars Struct Reference</h1><!-- doxytag: class="TwoDfold_vars" -->
<p>Variables compound for 2Dfold MFE folding.
- <a href="structTwoDfold__vars.html#details">More...</a></p>
-<div id="dynsection-0" onclick="return toggleVisibility(this)" class="dynheader closed" style="cursor:pointer;">
- <img id="dynsection-0-trigger" src="closed.png" alt="+"/> Collaboration diagram for TwoDfold_vars:</div>
-<div id="dynsection-0-summary" class="dynsummary" style="display:block;">
-</div>
-<div id="dynsection-0-content" class="dyncontent" style="display:none;">
+<a href="#_details">More...</a></p>
+<div class="dynheader">
+Collaboration diagram for TwoDfold_vars:</div>
+<div class="dynsection">
<div class="center"><img src="structTwoDfold__vars__coll__graph.png" border="0" usemap="#TwoDfold__vars_coll__map" alt="Collaboration graph"/></div>
<map name="TwoDfold__vars_coll__map" id="TwoDfold__vars_coll__map">
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<center><span class="legend">[<a target="top" href="graph_legend.html">legend</a>]</span></center></div>
-<table class="memberdecls">
-<tr class="heading"><td colspan="2"><h2><a name="pub-attribs"></a>
-Data Fields</h2></td></tr>
-<tr class="memitem:ada74adef5f24b4b35c0b25da8223fe26"><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="ada74adef5f24b4b35c0b25da8223fe26"></a>
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-<tr class="memdesc:ada74adef5f24b4b35c0b25da8223fe26"><td class="mdescLeft"> </td><td class="mdescRight">Precomputed energy parameters and model details. <br/></td></tr>
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-int </td><td class="memItemRight" valign="bottom"><a class="el" href="structTwoDfold__vars.html#ade5c7e9337a458ae20bac75abdc52d64">do_backtrack</a></td></tr>
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-char * </td><td class="memItemRight" valign="bottom"><a class="el" href="structTwoDfold__vars.html#aedf60b8b26dae05ad266d3e098d18208">ptype</a></td></tr>
-<tr class="memdesc:aedf60b8b26dae05ad266d3e098d18208"><td class="mdescLeft"> </td><td class="mdescRight">Precomputed array of pair types. <br/></td></tr>
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-char * </td><td class="memItemRight" valign="bottom"><a class="el" href="structTwoDfold__vars.html#a3596f3d4d320318c4b8428e2abc7ab56">sequence</a></td></tr>
-<tr class="memdesc:a3596f3d4d320318c4b8428e2abc7ab56"><td class="mdescLeft"> </td><td class="mdescRight">The input sequence. <br/></td></tr>
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-short * </td><td class="memItemRight" valign="bottom"><a class="el" href="structTwoDfold__vars.html#ab9ee459ffbfb5d2c138a033516056cdc">S1</a></td></tr>
-<tr class="memdesc:ab9ee459ffbfb5d2c138a033516056cdc"><td class="mdescLeft"> </td><td class="mdescRight">The input sequences in numeric form. <br/></td></tr>
-<tr class="memitem:a621ed2ab02116f3f8f5e7120dec429eb"><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="a621ed2ab02116f3f8f5e7120dec429eb"></a>
-unsigned int </td><td class="memItemRight" valign="bottom"><a class="el" href="structTwoDfold__vars.html#a621ed2ab02116f3f8f5e7120dec429eb">maxD1</a></td></tr>
-<tr class="memdesc:a621ed2ab02116f3f8f5e7120dec429eb"><td class="mdescLeft"> </td><td class="mdescRight">Maximum allowed base pair distance to first reference. <br/></td></tr>
-<tr class="memitem:a03f198a4abdb3b784486d2ba5c533aa4"><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="a03f198a4abdb3b784486d2ba5c533aa4"></a>
-unsigned int </td><td class="memItemRight" valign="bottom"><a class="el" href="structTwoDfold__vars.html#a03f198a4abdb3b784486d2ba5c533aa4">maxD2</a></td></tr>
-<tr class="memdesc:a03f198a4abdb3b784486d2ba5c533aa4"><td class="mdescLeft"> </td><td class="mdescRight">Maximum allowed base pair distance to second reference. <br/></td></tr>
-<tr class="memitem:aa11f5bcd8c4fe70a91c155c877c855d5"><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="aa11f5bcd8c4fe70a91c155c877c855d5"></a>
-unsigned int * </td><td class="memItemRight" valign="bottom"><a class="el" href="structTwoDfold__vars.html#aa11f5bcd8c4fe70a91c155c877c855d5">mm1</a></td></tr>
-<tr class="memdesc:aa11f5bcd8c4fe70a91c155c877c855d5"><td class="mdescLeft"> </td><td class="mdescRight">Maximum matching matrix, reference struct 1 disallowed. <br/></td></tr>
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-unsigned int * </td><td class="memItemRight" valign="bottom"><a class="el" href="structTwoDfold__vars.html#a2eaa93316b6beb17531f0c078806036c">mm2</a></td></tr>
-<tr class="memdesc:a2eaa93316b6beb17531f0c078806036c"><td class="mdescLeft"> </td><td class="mdescRight">Maximum matching matrix, reference struct 2 disallowed. <br/></td></tr>
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-int * </td><td class="memItemRight" valign="bottom"><a class="el" href="structTwoDfold__vars.html#a1a20cb06b58b75d1a3dbdbc8bc60d0a7">my_iindx</a></td></tr>
-<tr class="memdesc:a1a20cb06b58b75d1a3dbdbc8bc60d0a7"><td class="mdescLeft"> </td><td class="mdescRight">Index for moving in quadratic distancy dimensions. <br/></td></tr>
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-unsigned int * </td><td class="memItemRight" valign="bottom"><a class="el" href="structTwoDfold__vars.html#a536525b98c1b633d4c5f2da4f8d78c18">referenceBPs1</a></td></tr>
-<tr class="memdesc:a536525b98c1b633d4c5f2da4f8d78c18"><td class="mdescLeft"> </td><td class="mdescRight">Matrix containing number of basepairs of reference structure1 in interval [i,j]. <br/></td></tr>
-<tr class="memitem:aa7abf73c3114cb5f0dc90e702fa9dd0f"><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="aa7abf73c3114cb5f0dc90e702fa9dd0f"></a>
-unsigned int * </td><td class="memItemRight" valign="bottom"><a class="el" href="structTwoDfold__vars.html#aa7abf73c3114cb5f0dc90e702fa9dd0f">referenceBPs2</a></td></tr>
-<tr class="memdesc:aa7abf73c3114cb5f0dc90e702fa9dd0f"><td class="mdescLeft"> </td><td class="mdescRight">Matrix containing number of basepairs of reference structure2 in interval [i,j]. <br/></td></tr>
-<tr class="memitem:af1106e1a592e2dccc92b3452340549e0"><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="af1106e1a592e2dccc92b3452340549e0"></a>
-unsigned int * </td><td class="memItemRight" valign="bottom"><a class="el" href="structTwoDfold__vars.html#af1106e1a592e2dccc92b3452340549e0">bpdist</a></td></tr>
-<tr class="memdesc:af1106e1a592e2dccc92b3452340549e0"><td class="mdescLeft"> </td><td class="mdescRight">Matrix containing base pair distance of reference structure 1 and 2 on interval [i,j]. <br/></td></tr>
+<table border="0" cellpadding="0" cellspacing="0">
+<tr><td colspan="2"><h2>Data Fields</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="ada74adef5f24b4b35c0b25da8223fe26"></a><!-- doxytag: member="TwoDfold_vars::P" ref="ada74adef5f24b4b35c0b25da8223fe26" args="" -->
+<a class="el" href="structparamT.html">paramT</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="structTwoDfold__vars.html#ada74adef5f24b4b35c0b25da8223fe26">P</a></td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">Precomputed energy parameters and model details. <br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="ade5c7e9337a458ae20bac75abdc52d64"></a><!-- doxytag: member="TwoDfold_vars::do_backtrack" ref="ade5c7e9337a458ae20bac75abdc52d64" args="" -->
+int </td><td class="memItemRight" valign="bottom"><a class="el" href="structTwoDfold__vars.html#ade5c7e9337a458ae20bac75abdc52d64">do_backtrack</a></td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">Flag whether to do backtracing of the structure(s) or not. <br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="aedf60b8b26dae05ad266d3e098d18208"></a><!-- doxytag: member="TwoDfold_vars::ptype" ref="aedf60b8b26dae05ad266d3e098d18208" args="" -->
+char * </td><td class="memItemRight" valign="bottom"><a class="el" href="structTwoDfold__vars.html#aedf60b8b26dae05ad266d3e098d18208">ptype</a></td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">Precomputed array of pair types. <br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="a3596f3d4d320318c4b8428e2abc7ab56"></a><!-- doxytag: member="TwoDfold_vars::sequence" ref="a3596f3d4d320318c4b8428e2abc7ab56" args="" -->
+char * </td><td class="memItemRight" valign="bottom"><a class="el" href="structTwoDfold__vars.html#a3596f3d4d320318c4b8428e2abc7ab56">sequence</a></td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">The input sequence. <br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="ab9ee459ffbfb5d2c138a033516056cdc"></a><!-- doxytag: member="TwoDfold_vars::S1" ref="ab9ee459ffbfb5d2c138a033516056cdc" args="" -->
+short * </td><td class="memItemRight" valign="bottom"><a class="el" href="structTwoDfold__vars.html#ab9ee459ffbfb5d2c138a033516056cdc">S1</a></td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">The input sequences in numeric form. <br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="a621ed2ab02116f3f8f5e7120dec429eb"></a><!-- doxytag: member="TwoDfold_vars::maxD1" ref="a621ed2ab02116f3f8f5e7120dec429eb" args="" -->
+unsigned int </td><td class="memItemRight" valign="bottom"><a class="el" href="structTwoDfold__vars.html#a621ed2ab02116f3f8f5e7120dec429eb">maxD1</a></td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">Maximum allowed base pair distance to first reference. <br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="a03f198a4abdb3b784486d2ba5c533aa4"></a><!-- doxytag: member="TwoDfold_vars::maxD2" ref="a03f198a4abdb3b784486d2ba5c533aa4" args="" -->
+unsigned int </td><td class="memItemRight" valign="bottom"><a class="el" href="structTwoDfold__vars.html#a03f198a4abdb3b784486d2ba5c533aa4">maxD2</a></td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">Maximum allowed base pair distance to second reference. <br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="aa11f5bcd8c4fe70a91c155c877c855d5"></a><!-- doxytag: member="TwoDfold_vars::mm1" ref="aa11f5bcd8c4fe70a91c155c877c855d5" args="" -->
+unsigned int * </td><td class="memItemRight" valign="bottom"><a class="el" href="structTwoDfold__vars.html#aa11f5bcd8c4fe70a91c155c877c855d5">mm1</a></td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">Maximum matching matrix, reference struct 1 disallowed. <br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="a2eaa93316b6beb17531f0c078806036c"></a><!-- doxytag: member="TwoDfold_vars::mm2" ref="a2eaa93316b6beb17531f0c078806036c" args="" -->
+unsigned int * </td><td class="memItemRight" valign="bottom"><a class="el" href="structTwoDfold__vars.html#a2eaa93316b6beb17531f0c078806036c">mm2</a></td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">Maximum matching matrix, reference struct 2 disallowed. <br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="a1a20cb06b58b75d1a3dbdbc8bc60d0a7"></a><!-- doxytag: member="TwoDfold_vars::my_iindx" ref="a1a20cb06b58b75d1a3dbdbc8bc60d0a7" args="" -->
+int * </td><td class="memItemRight" valign="bottom"><a class="el" href="structTwoDfold__vars.html#a1a20cb06b58b75d1a3dbdbc8bc60d0a7">my_iindx</a></td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">Index for moving in quadratic distancy dimensions. <br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="a536525b98c1b633d4c5f2da4f8d78c18"></a><!-- doxytag: member="TwoDfold_vars::referenceBPs1" ref="a536525b98c1b633d4c5f2da4f8d78c18" args="" -->
+unsigned int * </td><td class="memItemRight" valign="bottom"><a class="el" href="structTwoDfold__vars.html#a536525b98c1b633d4c5f2da4f8d78c18">referenceBPs1</a></td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">Matrix containing number of basepairs of reference structure1 in interval [i,j]. <br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="aa7abf73c3114cb5f0dc90e702fa9dd0f"></a><!-- doxytag: member="TwoDfold_vars::referenceBPs2" ref="aa7abf73c3114cb5f0dc90e702fa9dd0f" args="" -->
+unsigned int * </td><td class="memItemRight" valign="bottom"><a class="el" href="structTwoDfold__vars.html#aa7abf73c3114cb5f0dc90e702fa9dd0f">referenceBPs2</a></td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">Matrix containing number of basepairs of reference structure2 in interval [i,j]. <br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="af1106e1a592e2dccc92b3452340549e0"></a><!-- doxytag: member="TwoDfold_vars::bpdist" ref="af1106e1a592e2dccc92b3452340549e0" args="" -->
+unsigned int * </td><td class="memItemRight" valign="bottom"><a class="el" href="structTwoDfold__vars.html#af1106e1a592e2dccc92b3452340549e0">bpdist</a></td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">Matrix containing base pair distance of reference structure 1 and 2 on interval [i,j]. <br/></td></tr>
</table>
-<hr/><a name="details" id="details"></a><h2>Detailed Description</h2>
-<div class="textblock"><p>Variables compound for 2Dfold MFE folding. </p>
-<dl class="section see"><dt>See also:</dt><dd><a class="el" href="group__kl__neighborhood__mfe.html#gac9284f132cf0eaa0a2f43590eda05488" title="Get a structure of type TwoDfold_vars prefilled with current global settings.">get_TwoDfold_variables()</a>, <a class="el" href="group__kl__neighborhood__mfe.html#ga05bf4f31d216b1b160fd2d3d68e9b487" title="Destroy a TwoDfold_vars datastructure without memory loss.">destroy_TwoDfold_variables()</a>, <a class="el" href="group__kl__neighborhood__mfe.html#ga47da790166020558d27323aef489703e" title="Compute MFE's and representative for distance partitioning.">TwoDfoldList()</a> </dd></dl>
-</div><hr/>The documentation for this struct was generated from the following file:<ul>
-<li>/home/mescalin/ronny/public_html/programs/ViennaRNA/H/<a class="el" href="data__structures_8h_source.html">data_structures.h</a></li>
+<hr/><a name="_details"></a><h2>Detailed Description</h2>
+<p>Variables compound for 2Dfold MFE folding. </p>
+<dl class="see"><dt><b>See also:</b></dt><dd><a class="el" href="group__kl__neighborhood__mfe.html#gac9284f132cf0eaa0a2f43590eda05488" title="Get a structure of type TwoDfold_vars prefilled with current global settings.">get_TwoDfold_variables()</a>, <a class="el" href="group__kl__neighborhood__mfe.html#ga05bf4f31d216b1b160fd2d3d68e9b487" title="Destroy a TwoDfold_vars datastructure without memory loss.">destroy_TwoDfold_variables()</a>, <a class="el" href="group__kl__neighborhood__mfe.html#ga47da790166020558d27323aef489703e" title="Compute MFE's and representative for distance partitioning.">TwoDfoldList()</a> </dd></dl>
+<hr/>The documentation for this struct was generated from the following file:<ul>
+<li>/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/<a class="el" href="data__structures_8h_source.html">data_structures.h</a></li>
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