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+<a href="#func-members">Functions</a> |
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+<div class="title">alifold.h File Reference<div class="ingroups"><a class="el" href="group__consensus__fold.html">Predicting Consensus Structures from Alignment(s)</a></div></div> </div>
+</div><!--header-->
+<div class="contents">
+
+<p>compute various properties (consensus MFE structures, partition function, Boltzmann distributed stochastic samples, ...) for RNA sequence alignments
+<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 alifold.h:</div>
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+<p><a href="alifold_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:ac484c6bd429bafbd353b91044508d8e9"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="alifold_8h.html#ac484c6bd429bafbd353b91044508d8e9">update_alifold_params</a> (void)</td></tr>
+<tr class="memdesc:ac484c6bd429bafbd353b91044508d8e9"><td class="mdescLeft"> </td><td class="mdescRight">Update the energy parameters for alifold function. <a href="#ac484c6bd429bafbd353b91044508d8e9"></a><br/></td></tr>
+<tr class="memitem:ga4cf00f0659e5f0480335d69e797f05b1"><td class="memItemLeft" align="right" valign="top">float </td><td class="memItemRight" valign="bottom"><a class="el" href="group__consensus__mfe__fold.html#ga4cf00f0659e5f0480335d69e797f05b1">alifold</a> (const char **strings, char *structure)</td></tr>
+<tr class="memdesc:ga4cf00f0659e5f0480335d69e797f05b1"><td class="mdescLeft"> </td><td class="mdescRight">Compute MFE and according consensus structure of an alignment of sequences. <a href="group__consensus__mfe__fold.html#ga4cf00f0659e5f0480335d69e797f05b1"></a><br/></td></tr>
+<tr class="memitem:gadbd3b0b1c144cbfb4efe704b2b260f96"><td class="memItemLeft" align="right" valign="top">float </td><td class="memItemRight" valign="bottom"><a class="el" href="group__consensus__mfe__fold.html#gadbd3b0b1c144cbfb4efe704b2b260f96">circalifold</a> (const char **strings, char *structure)</td></tr>
+<tr class="memdesc:gadbd3b0b1c144cbfb4efe704b2b260f96"><td class="mdescLeft"> </td><td class="mdescRight">Compute MFE and according structure of an alignment of sequences assuming the sequences are circular instead of linear. <a href="group__consensus__mfe__fold.html#gadbd3b0b1c144cbfb4efe704b2b260f96"></a><br/></td></tr>
+<tr class="memitem:ga72095e4554b5d577250ea14c42acc49e"><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="ga72095e4554b5d577250ea14c42acc49e"></a>
+void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__consensus__mfe__fold.html#ga72095e4554b5d577250ea14c42acc49e">free_alifold_arrays</a> (void)</td></tr>
+<tr class="memdesc:ga72095e4554b5d577250ea14c42acc49e"><td class="mdescLeft"> </td><td class="mdescRight">Free the memory occupied by MFE alifold functions. <br/></td></tr>
+<tr class="memitem:gaa2d600be90844094ec145ea14a314d2f"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="group__consensus__fold.html#gaa2d600be90844094ec145ea14a314d2f">get_mpi</a> (char *Alseq[], int n_seq, int length, int *mini)</td></tr>
+<tr class="memdesc:gaa2d600be90844094ec145ea14a314d2f"><td class="mdescLeft"> </td><td class="mdescRight">Get the mean pairwise identity in steps from ?to?(ident) <a href="group__consensus__fold.html#gaa2d600be90844094ec145ea14a314d2f"></a><br/></td></tr>
+<tr class="memitem:ga5e125c9586fcd4e2e1559fe76f7289cc"><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="ga5e125c9586fcd4e2e1559fe76f7289cc"></a>
+float ** </td><td class="memItemRight" valign="bottom"><a class="el" href="group__consensus__fold.html#ga5e125c9586fcd4e2e1559fe76f7289cc">readribosum</a> (char *name)</td></tr>
+<tr class="memdesc:ga5e125c9586fcd4e2e1559fe76f7289cc"><td class="mdescLeft"> </td><td class="mdescRight">Read a ribosum or other user-defined scoring matrix. <br/></td></tr>
+<tr class="memitem:ga1c48869c03b49a342bf4cbdd61900081"><td class="memItemLeft" align="right" valign="top">float </td><td class="memItemRight" valign="bottom"><a class="el" href="group__consensus__fold.html#ga1c48869c03b49a342bf4cbdd61900081">energy_of_alistruct</a> (const char **sequences, const char *structure, int n_seq, float *energy)</td></tr>
+<tr class="memdesc:ga1c48869c03b49a342bf4cbdd61900081"><td class="mdescLeft"> </td><td class="mdescRight">Calculate the free energy of a consensus structure given a set of aligned sequences. <a href="group__consensus__fold.html#ga1c48869c03b49a342bf4cbdd61900081"></a><br/></td></tr>
+<tr class="memitem:gaa3e40277c837d6f7603afe319884c786"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__consensus__fold.html#gaa3e40277c837d6f7603afe319884c786">encode_ali_sequence</a> (const char *sequence, short *S, short *s5, short *s3, char *ss, unsigned short *as, int <a class="el" href="fold__vars_8h.html#af9202a1a09f5828dc731e2d9a10fa111">circ</a>)</td></tr>
+<tr class="memdesc:gaa3e40277c837d6f7603afe319884c786"><td class="mdescLeft"> </td><td class="mdescRight">Get arrays with encoded sequence of the alignment. <a href="group__consensus__fold.html#gaa3e40277c837d6f7603afe319884c786"></a><br/></td></tr>
+<tr class="memitem:ga8a560930f7f2582cc3967723a86cfdfa"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__consensus__fold.html#ga8a560930f7f2582cc3967723a86cfdfa">alloc_sequence_arrays</a> (const char **sequences, short ***S, short ***S5, short ***S3, unsigned short ***a2s, char ***Ss, int <a class="el" href="fold__vars_8h.html#af9202a1a09f5828dc731e2d9a10fa111">circ</a>)</td></tr>
+<tr class="memdesc:ga8a560930f7f2582cc3967723a86cfdfa"><td class="mdescLeft"> </td><td class="mdescRight">Allocate memory for sequence array used to deal with aligned sequences. <a href="group__consensus__fold.html#ga8a560930f7f2582cc3967723a86cfdfa"></a><br/></td></tr>
+<tr class="memitem:ga298a420a8c879202e2617b3f724fde38"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__consensus__fold.html#ga298a420a8c879202e2617b3f724fde38">free_sequence_arrays</a> (unsigned int n_seq, short ***S, short ***S5, short ***S3, unsigned short ***a2s, char ***Ss)</td></tr>
+<tr class="memdesc:ga298a420a8c879202e2617b3f724fde38"><td class="mdescLeft"> </td><td class="mdescRight">Free the memory of the sequence arrays used to deal with aligned sequences. <a href="group__consensus__fold.html#ga298a420a8c879202e2617b3f724fde38"></a><br/></td></tr>
+<tr class="memitem:ga4d2ff54d8210fc7cceeeff389d4dbd1d"><td class="memItemLeft" align="right" valign="top">float </td><td class="memItemRight" valign="bottom"><a class="el" href="group__consensus__pf__fold.html#ga4d2ff54d8210fc7cceeeff389d4dbd1d">alipf_fold_par</a> (const char **sequences, char *structure, <a class="el" href="structplist.html">plist</a> **pl, <a class="el" href="structpf__paramT.html">pf_paramT</a> *parameters, int calculate_bppm, int is_constrained, int is_circular)</td></tr>
+<tr class="memitem:gad32ded7d753ccaf211ab35782d1f42a9"><td class="memItemLeft" align="right" valign="top">float </td><td class="memItemRight" valign="bottom"><a class="el" href="group__consensus__pf__fold.html#gad32ded7d753ccaf211ab35782d1f42a9">alipf_fold</a> (const char **sequences, char *structure, <a class="el" href="structplist.html">plist</a> **pl)</td></tr>
+<tr class="memdesc:gad32ded7d753ccaf211ab35782d1f42a9"><td class="mdescLeft"> </td><td class="mdescRight">The partition function version of <a class="el" href="group__consensus__mfe__fold.html#ga4cf00f0659e5f0480335d69e797f05b1" title="Compute MFE and according consensus structure of an alignment of sequences.">alifold()</a> works in analogy to <a class="el" href="group__pf__fold.html#gadc3db3d98742427e7001a7fd36ef28c2" title="Compute the partition function of an RNA sequence.">pf_fold()</a>. Pair probabilities and information about sequence covariations are returned via the 'pi' variable as a list of <a class="el" href="structpair__info.html" title="A base pair info structure.">pair_info</a> structs. The list is terminated by the first entry with pi.i = 0. <a href="group__consensus__pf__fold.html#gad32ded7d753ccaf211ab35782d1f42a9"></a><br/></td></tr>
+<tr class="memitem:ga6b4dde1d43b79ab3753508c46cf50363"><td class="memItemLeft" align="right" valign="top">float </td><td class="memItemRight" valign="bottom"><a class="el" href="group__consensus__pf__fold.html#ga6b4dde1d43b79ab3753508c46cf50363">alipf_circ_fold</a> (const char **sequences, char *structure, <a class="el" href="structplist.html">plist</a> **pl)</td></tr>
+<tr class="memitem:gadaaf83394216413505e48d913dbc1b4e"><td class="memItemLeft" align="right" valign="top">double * </td><td class="memItemRight" valign="bottom"><a class="el" href="group__consensus__pf__fold.html#gadaaf83394216413505e48d913dbc1b4e">export_ali_bppm</a> (void)</td></tr>
+<tr class="memdesc:gadaaf83394216413505e48d913dbc1b4e"><td class="mdescLeft"> </td><td class="mdescRight">Get a pointer to the base pair probability array. <a href="group__consensus__pf__fold.html#gadaaf83394216413505e48d913dbc1b4e"></a><br/></td></tr>
+<tr class="memitem:ga0df40248788f0fb17ebdc59d74116d1c"><td class="memItemLeft" align="right" valign="top">char * </td><td class="memItemRight" valign="bottom"><a class="el" href="group__consensus__stochbt.html#ga0df40248788f0fb17ebdc59d74116d1c">alipbacktrack</a> (double *prob)</td></tr>
+<tr class="memdesc:ga0df40248788f0fb17ebdc59d74116d1c"><td class="mdescLeft"> </td><td class="mdescRight">Sample a consensus secondary structure from the Boltzmann ensemble according its probability<br/>
+. <a href="group__consensus__stochbt.html#ga0df40248788f0fb17ebdc59d74116d1c"></a><br/></td></tr>
+<tr class="memitem:ga0cc49457fd79eeb04d4a7f97c868b09b"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="group__consensus__fold.html#ga0cc49457fd79eeb04d4a7f97c868b09b">get_alipf_arrays</a> (short ***S_p, short ***S5_p, short ***S3_p, unsigned short ***a2s_p, char ***Ss_p, double **qb_p, double **qm_p, double **q1k_p, double **qln_p, short **pscore)</td></tr>
+<tr class="memdesc:ga0cc49457fd79eeb04d4a7f97c868b09b"><td class="mdescLeft"> </td><td class="mdescRight">Get pointers to (almost) all relavant arrays used in alifold's partition function computation. <a href="group__consensus__fold.html#ga0cc49457fd79eeb04d4a7f97c868b09b"></a><br/></td></tr>
+</table><table class="memberdecls">
+<tr class="heading"><td colspan="2"><h2><a name="var-members"></a>
+Variables</h2></td></tr>
+<tr class="memitem:gaf3cbac6ff5d706d6e414677841ddf94c"><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="group__consensus__fold.html#gaf3cbac6ff5d706d6e414677841ddf94c">cv_fact</a></td></tr>
+<tr class="memdesc:gaf3cbac6ff5d706d6e414677841ddf94c"><td class="mdescLeft"> </td><td class="mdescRight">This variable controls the weight of the covariance term in the energy function of alignment folding algorithms. <a href="group__consensus__fold.html#gaf3cbac6ff5d706d6e414677841ddf94c"></a><br/></td></tr>
+<tr class="memitem:ga502948a122a2af5b914355b1f3ea2f61"><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="group__consensus__fold.html#ga502948a122a2af5b914355b1f3ea2f61">nc_fact</a></td></tr>
+<tr class="memdesc:ga502948a122a2af5b914355b1f3ea2f61"><td class="mdescLeft"> </td><td class="mdescRight">This variable controls the magnitude of the penalty for non-compatible sequences in the covariance term of alignment folding algorithms. <a href="group__consensus__fold.html#ga502948a122a2af5b914355b1f3ea2f61"></a><br/></td></tr>
+</table>
+<hr/><a name="details" id="details"></a><h2>Detailed Description</h2>
+<div class="textblock"><p>compute various properties (consensus MFE structures, partition function, Boltzmann distributed stochastic samples, ...) for RNA sequence alignments </p>
+</div><hr/><h2>Function Documentation</h2>
+<a class="anchor" id="ac484c6bd429bafbd353b91044508d8e9"></a>
+<div class="memitem">
+<div class="memproto">
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+ <td class="memname">void update_alifold_params </td>
+ <td>(</td>
+ <td class="paramtype">void </td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+
+<p>Update the energy parameters for alifold function. </p>
+<p>Call this to recalculate the pair matrix and energy parameters after a change in folding parameters like <a class="el" href="fold__vars_8h.html#ab4b11c8d9c758430960896bc3fe82ead" title="Rescale energy parameters to a temperature in degC.">temperature</a> </p>
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