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+<area shape="rect" id="node3" href="data__structures_8h.html" title="All datastructures and typedefs shared among the Vienna RNA Package can be found here." alt="" coords="33,109,167,136"/><area shape="rect" id="node5" href="energy__const_8h.html" title="energy_const.h" alt="" coords="40,184,160,211"/></map>
+</div>
+</div>
+<p><a href="profiledist_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:abe75e90e00a1e5dd8862944ed53dad5d"><td class="memItemLeft" align="right" valign="top">float </td><td class="memItemRight" valign="bottom"><a class="el" href="profiledist_8h.html#abe75e90e00a1e5dd8862944ed53dad5d">profile_edit_distance</a> (const float *T1, const float *T2)</td></tr>
+<tr class="memdesc:abe75e90e00a1e5dd8862944ed53dad5d"><td class="mdescLeft"> </td><td class="mdescRight">Align the 2 probability profiles T1, T2<br/>
+. <a href="#abe75e90e00a1e5dd8862944ed53dad5d"></a><br/></td></tr>
+<tr class="memitem:a8822fd5268be115c6e6cdc92009436cc"><td class="memItemLeft" align="right" valign="top">float * </td><td class="memItemRight" valign="bottom"><a class="el" href="profiledist_8h.html#a8822fd5268be115c6e6cdc92009436cc">Make_bp_profile_bppm</a> (double *bppm, int length)</td></tr>
+<tr class="memdesc:a8822fd5268be115c6e6cdc92009436cc"><td class="mdescLeft"> </td><td class="mdescRight">condense pair probability matrix into a vector containing probabilities for unpaired, upstream paired and downstream paired. <a href="#a8822fd5268be115c6e6cdc92009436cc"></a><br/></td></tr>
+<tr class="memitem:a8e0b4fe3698b3502945116ecc0ba6160"><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="a8e0b4fe3698b3502945116ecc0ba6160"></a>
+void </td><td class="memItemRight" valign="bottom"><a class="el" href="profiledist_8h.html#a8e0b4fe3698b3502945116ecc0ba6160">print_bppm</a> (const float *T)</td></tr>
+<tr class="memdesc:a8e0b4fe3698b3502945116ecc0ba6160"><td class="mdescLeft"> </td><td class="mdescRight">print string representation of probability profile <br/></td></tr>
+<tr class="memitem:a9b0b84a5a45761bf42d7c835dcdb3b85"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="profiledist_8h.html#a9b0b84a5a45761bf42d7c835dcdb3b85">free_profile</a> (float *T)</td></tr>
+<tr class="memdesc:a9b0b84a5a45761bf42d7c835dcdb3b85"><td class="mdescLeft"> </td><td class="mdescRight">free space allocated in Make_bp_profile <a href="#a9b0b84a5a45761bf42d7c835dcdb3b85"></a><br/></td></tr>
+<tr class="memitem:a904c7eaf4a2413567c00ac4891749d18"><td class="memItemLeft" align="right" valign="top">float * </td><td class="memItemRight" valign="bottom"><a class="el" href="profiledist_8h.html#a904c7eaf4a2413567c00ac4891749d18">Make_bp_profile</a> (int length)</td></tr>
+</table>
+<hr/><a name="details" id="details"></a><h2>Detailed Description</h2>
+<div class="textblock"></div><hr/><h2>Function Documentation</h2>
+<a class="anchor" id="abe75e90e00a1e5dd8862944ed53dad5d"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">float profile_edit_distance </td>
+ <td>(</td>
+ <td class="paramtype">const float * </td>
+ <td class="paramname"><em>T1</em>, </td>
+ </tr>
+ <tr>
+ <td class="paramkey"></td>
+ <td></td>
+ <td class="paramtype">const float * </td>
+ <td class="paramname"><em>T2</em> </td>
+ </tr>
+ <tr>
+ <td></td>
+ <td>)</td>
+ <td></td><td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+
+<p>Align the 2 probability profiles T1, T2<br/>
+. </p>
+<p>This is like a Needleman-Wunsch alignment, we should really use affine gap-costs ala Gotoh </p>
+
+</div>
+</div>
+<a class="anchor" id="a8822fd5268be115c6e6cdc92009436cc"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">float* Make_bp_profile_bppm </td>
+ <td>(</td>
+ <td class="paramtype">double * </td>
+ <td class="paramname"><em>bppm</em>, </td>
+ </tr>
+ <tr>
+ <td class="paramkey"></td>
+ <td></td>
+ <td class="paramtype">int </td>
+ <td class="paramname"><em>length</em> </td>
+ </tr>
+ <tr>
+ <td></td>
+ <td>)</td>
+ <td></td><td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+
+<p>condense pair probability matrix into a vector containing probabilities for unpaired, upstream paired and downstream paired. </p>
+<p>This resulting probability profile is used as input for profile_edit_distance</p>
+<dl class="params"><dt>Parameters:</dt><dd>
+ <table class="params">
+ <tr><td class="paramname">bppm</td><td>A pointer to the base pair probability matrix </td></tr>
+ <tr><td class="paramname">length</td><td>The length of the sequence </td></tr>
+ </table>
+ </dd>
+</dl>
+<dl class="section return"><dt>Returns:</dt><dd>The bp profile </dd></dl>
+
+</div>
+</div>
+<a class="anchor" id="a9b0b84a5a45761bf42d7c835dcdb3b85"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">void free_profile </td>
+ <td>(</td>
+ <td class="paramtype">float * </td>
+ <td class="paramname"><em>T</em></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+
+<p>free space allocated in Make_bp_profile </p>
+<p>Backward compatibility only. You can just use plain free() </p>
+
+</div>
+</div>
+<a class="anchor" id="a904c7eaf4a2413567c00ac4891749d18"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">float* Make_bp_profile </td>
+ <td>(</td>
+ <td class="paramtype">int </td>
+ <td class="paramname"><em>length</em></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<dl class="section note"><dt>Note:</dt><dd>This function is NOT threadsafe</dd></dl>
+<dl class="section see"><dt>See also:</dt><dd><a class="el" href="profiledist_8h.html#a8822fd5268be115c6e6cdc92009436cc" title="condense pair probability matrix into a vector containing probabilities for unpaired, upstream paired and downstream paired.">Make_bp_profile_bppm()</a></dd></dl>
+<dl class="deprecated"><dt><b><a class="el" href="deprecated.html#_deprecated000018">Deprecated:</a></b></dt><dd>This function is deprecated and will be removed soon! See <a class="el" href="profiledist_8h.html#a8822fd5268be115c6e6cdc92009436cc">Make_bp_profile_bppm()</a> for a replacement</dd></dl>
+
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