WSTester updated to work plus hopefully all the other changes that need to go into...

[jabaws.git] / binaries / src / ViennaRNA / doc / RNAlib-2.1.2.tag

diff --git a/binaries/src/ViennaRNA/doc/RNAlib-2.1.2.tag b/binaries/src/ViennaRNA/doc/RNAlib-2.1.2.tag
new file mode 100644 (file)
index 0000000..68aee50
--- /dev/null
+++ b/binaries/src/ViennaRNA/doc/RNAlib-2.1.2.tag
@@ -0,0 +1,4392 @@
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+      <arglist>(const char **strings, char *structure, int maxdist)</arglist>
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+    <member kind="function">
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+      <anchor>a3e5ad89f451254b1fe366d77aa8ff7bd</anchor>
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+      <arglist>(int type, int si1, int sj1, int extLoop, paramT *P)</arglist>
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+      <arglist>(int type, int si1, int sj1, int extLoop, pf_paramT *P)</arglist>
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+    <member kind="function">
+      <type>void</type>
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+      <anchorfile>group__local__pf__fold.html</anchorfile>
+      <anchor>ga5a019014d37fe6105131dfc2fc447880</anchor>
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+    </member>
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+      <anchor>ga0bcb751860bbf34e3dfee8c2fbdb3ef3</anchor>
+      <arglist>(double **pU, int length, int ulength, FILE *fp, int energies)</arglist>
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+      <anchor>ga9acb00ee10e96b1ca4ea394cd8bcec75</anchor>
+      <arglist>(double **pU, int length, int ulength, FILE *fp, int energies)</arglist>
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+      <anchorfile>LPfold_8h.html</anchorfile>
+      <anchor>ae85bf55053e9fb295208be322e0fa07a</anchor>
+      <arglist>(int length)</arglist>
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+    <path>/home/mescalin/ronny/public_html/programs/ViennaRNA/H/</path>
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+    <member kind="function">
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+      <name>MEA</name>
+      <anchorfile>MEA_8h.html</anchorfile>
+      <anchor>a396ec6144c6a74fcbab4cea6b42d76c3</anchor>
+      <arglist>(plist *p, char *structure, double gamma)</arglist>
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+    <member kind="function">
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+      <arglist>(double temperature, model_detailsT md)</arglist>
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+      <anchorfile>group__energy__parameters.html</anchorfile>
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+      <arglist>(void)</arglist>
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+      <anchor>ga6fc2f3eef5a3024d44963ac59a42e39d</anchor>
+      <arglist>(double temperature, double betaScale, model_detailsT md, double pf_scale)</arglist>
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+      <anchorfile>group__energy__parameters.html</anchorfile>
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+      <arglist>(pf_paramT *parameters)</arglist>
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+      <anchorfile>group__energy__parameters.html</anchorfile>
+      <anchor>gaa6a4297a2b91d6f7ae47dd61ca1862a0</anchor>
+      <arglist>(unsigned int n_seq)</arglist>
+    </member>
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+      <anchorfile>group__energy__parameters.html</anchorfile>
+      <anchor>gaaa049a8c9f1c2ed4398cb1b5a3d65a66</anchor>
+      <arglist>(unsigned int n_seq, double temperature, double betaScale, model_detailsT md, double pf_scale)</arglist>
+    </member>
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+    <path>/home/mescalin/ronny/public_html/programs/ViennaRNA/H/</path>
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+      <name>pf_fold_par</name>
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+      <anchor>ga1839c61275760944b3a007c41d5c0823</anchor>
+      <arglist>(const char *sequence, char *structure, pf_paramT *parameters, int calculate_bppm, int is_constrained, int is_circular)</arglist>
+    </member>
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+      <name>pf_fold</name>
+      <anchorfile>group__pf__fold.html</anchorfile>
+      <anchor>gadc3db3d98742427e7001a7fd36ef28c2</anchor>
+      <arglist>(const char *sequence, char *structure)</arglist>
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+      <anchor>ga819ce5fca8984004ac81c4a3b04cb735</anchor>
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+      <anchorfile>group__subopt__stochbt.html</anchorfile>
+      <anchor>gac03ca6db186bb3bf0a2a326d7fb3ba03</anchor>
+      <arglist>(char *sequence)</arglist>
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+      <anchorfile>group__pf__fold.html</anchorfile>
+      <anchor>gae73db3f49a94f0f72e067ecd12681dbd</anchor>
+      <arglist>(void)</arglist>
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+      <anchor>ga384e927890f9c034ff09fa66da102d28</anchor>
+      <arglist>(int length)</arglist>
+    </member>
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+      <anchorfile>group__pf__fold.html</anchorfile>
+      <anchor>ga0733527a94de3b79eee3c3c03c99c1bc</anchor>
+      <arglist>(int length, pf_paramT *parameters)</arglist>
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+      <name>export_bppm</name>
+      <anchorfile>group__pf__fold.html</anchorfile>
+      <anchor>ga6d463707d5f64bdc4d21515b7dd9b115</anchor>
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+      <anchor>ga03e15e831a31b1154855ab47edbdb019</anchor>
+      <arglist>(plist **pl, double *probs, int length, double cutoff)</arglist>
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+      <anchorfile>group__pf__fold.html</anchorfile>
+      <anchor>ga18607e79e106cad827f482eedd2f632e</anchor>
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+      <anchorfile>group__centroid__fold.html</anchorfile>
+      <anchor>gacdabece4aa1e20c9eaa97acb4c4dcc38</anchor>
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+      <anchorfile>group__pf__fold.html</anchorfile>
+      <anchor>ga79cbc375af65f11609feb6b055269e7d</anchor>
+      <arglist>(int length)</arglist>
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+      <anchorfile>group__pf__fold.html</anchorfile>
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+      <arglist>(int length, double *pr)</arglist>
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+      <anchorfile>part__func_8h.html</anchorfile>
+      <anchor>a1f562d463c14d4703d9656056200eb38</anchor>
+      <arglist>(char *structure, double *pr, unsigned int length)</arglist>
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+      <anchor>a49962ad6242b8c628de6ca16bb831c1d</anchor>
+      <arglist>(const float *x)</arglist>
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+      <arglist>(int length)</arglist>
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+      <anchorfile>part__func_8h.html</anchorfile>
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+      <arglist>(int u1, int u2, int type, int type2, short si1, short sj1, short sp1, short sq1)</arglist>
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+      <anchorfile>group__pf__cofold.html</anchorfile>
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+    <subgroup>local_pf_fold</subgroup>
+    <subgroup>kl_neighborhood_pf</subgroup>
+    <file>part_func.h</file>
+    <member kind="function">
+      <type>float</type>
+      <name>pf_fold_par</name>
+      <anchorfile>group__pf__fold.html</anchorfile>
+      <anchor>ga1839c61275760944b3a007c41d5c0823</anchor>
+      <arglist>(const char *sequence, char *structure, pf_paramT *parameters, int calculate_bppm, int is_constrained, int is_circular)</arglist>
+    </member>
+    <member kind="function">
+      <type>float</type>
+      <name>pf_fold</name>
+      <anchorfile>group__pf__fold.html</anchorfile>
+      <anchor>gadc3db3d98742427e7001a7fd36ef28c2</anchor>
+      <arglist>(const char *sequence, char *structure)</arglist>
+    </member>
+    <member kind="function">
+      <type>float</type>
+      <name>pf_circ_fold</name>
+      <anchorfile>group__pf__fold.html</anchorfile>
+      <anchor>ga819ce5fca8984004ac81c4a3b04cb735</anchor>
+      <arglist>(const char *sequence, char *structure)</arglist>
+    </member>
+    <member kind="function">
+      <type>void</type>
+      <name>free_pf_arrays</name>
+      <anchorfile>group__pf__fold.html</anchorfile>
+      <anchor>gae73db3f49a94f0f72e067ecd12681dbd</anchor>
+      <arglist>(void)</arglist>
+    </member>
+    <member kind="function">
+      <type>void</type>
+      <name>update_pf_params</name>
+      <anchorfile>group__pf__fold.html</anchorfile>
+      <anchor>ga384e927890f9c034ff09fa66da102d28</anchor>
+      <arglist>(int length)</arglist>
+    </member>
+    <member kind="function">
+      <type>void</type>
+      <name>update_pf_params_par</name>
+      <anchorfile>group__pf__fold.html</anchorfile>
+      <anchor>ga0733527a94de3b79eee3c3c03c99c1bc</anchor>
+      <arglist>(int length, pf_paramT *parameters)</arglist>
+    </member>
+    <member kind="function">
+      <type>double *</type>
+      <name>export_bppm</name>
+      <anchorfile>group__pf__fold.html</anchorfile>
+      <anchor>ga6d463707d5f64bdc4d21515b7dd9b115</anchor>
+      <arglist>(void)</arglist>
+    </member>
+    <member kind="function">
+      <type>void</type>
+      <name>assign_plist_from_pr</name>
+      <anchorfile>group__pf__fold.html</anchorfile>
+      <anchor>ga03e15e831a31b1154855ab47edbdb019</anchor>
+      <arglist>(plist **pl, double *probs, int length, double cutoff)</arglist>
+    </member>
+    <member kind="function">
+      <type>int</type>
+      <name>get_pf_arrays</name>
+      <anchorfile>group__pf__fold.html</anchorfile>
+      <anchor>ga18607e79e106cad827f482eedd2f632e</anchor>
+      <arglist>(short **S_p, short **S1_p, char **ptype_p, double **qb_p, double **qm_p, double **q1k_p, double **qln_p)</arglist>
+    </member>
+    <member kind="function">
+      <type>double</type>
+      <name>mean_bp_distance</name>
+      <anchorfile>group__pf__fold.html</anchorfile>
+      <anchor>ga79cbc375af65f11609feb6b055269e7d</anchor>
+      <arglist>(int length)</arglist>
+    </member>
+    <member kind="function">
+      <type>double</type>
+      <name>mean_bp_distance_pr</name>
+      <anchorfile>group__pf__fold.html</anchorfile>
+      <anchor>ga72d84525f0afd3a9d60d830a2f501fa5</anchor>
+      <arglist>(int length, double *pr)</arglist>
+    </member>
+  </compound>
+  <compound kind="group">
+    <name>mea_fold</name>
+    <title>Compute the structure with maximum expected accuracy (MEA)</title>
+    <filename>group__mea__fold.html</filename>
+  </compound>
+  <compound kind="group">
+    <name>centroid_fold</name>
+    <title>Compute the centroid structure</title>
+    <filename>group__centroid__fold.html</filename>
+    <member kind="function">
+      <type>char *</type>
+      <name>get_centroid_struct_pl</name>
+      <anchorfile>group__centroid__fold.html</anchorfile>
+      <anchor>ga9aba0ba1433a6d259331e0fe9fc4a9a6</anchor>
+      <arglist>(int length, double *dist, plist *pl)</arglist>
+    </member>
+    <member kind="function">
+      <type>char *</type>
+      <name>get_centroid_struct_pr</name>
+      <anchorfile>group__centroid__fold.html</anchorfile>
+      <anchor>gacdabece4aa1e20c9eaa97acb4c4dcc38</anchor>
+      <arglist>(int length, double *dist, double *pr)</arglist>
+    </member>
+  </compound>
+  <compound kind="group">
+    <name>subopt_fold</name>
+    <title>Enumerating Suboptimal Structures</title>
+    <filename>group__subopt__fold.html</filename>
+    <subgroup>subopt_zuker</subgroup>
+    <subgroup>subopt_wuchty</subgroup>
+    <subgroup>subopt_stochbt</subgroup>
+    <file>subopt.h</file>
+  </compound>
+  <compound kind="group">
+    <name>subopt_zuker</name>
+    <title>Suboptimal structures according to Zuker et al. 1989</title>
+    <filename>group__subopt__zuker.html</filename>
+    <member kind="function">
+      <type>SOLUTION *</type>
+      <name>zukersubopt</name>
+      <anchorfile>group__subopt__zuker.html</anchorfile>
+      <anchor>ga0d5104e3ecf119d8eabd40aa5fe47f90</anchor>
+      <arglist>(const char *string)</arglist>
+    </member>
+    <member kind="function">
+      <type>SOLUTION *</type>
+      <name>zukersubopt_par</name>
+      <anchorfile>group__subopt__zuker.html</anchorfile>
+      <anchor>ga6d98a9450d1affadf144ac79f543da8c</anchor>
+      <arglist>(const char *string, paramT *parameters)</arglist>
+    </member>
+  </compound>
+  <compound kind="group">
+    <name>subopt_wuchty</name>
+    <title>Suboptimal structures within an energy band arround the MFE</title>
+    <filename>group__subopt__wuchty.html</filename>
+    <member kind="function">
+      <type>SOLUTION *</type>
+      <name>subopt</name>
+      <anchorfile>group__subopt__wuchty.html</anchorfile>
+      <anchor>ga700f662506a233e42dd7fda74fafd40e</anchor>
+      <arglist>(char *seq, char *structure, int delta, FILE *fp)</arglist>
+    </member>
+    <member kind="function">
+      <type>SOLUTION *</type>
+      <name>subopt_par</name>
+      <anchorfile>group__subopt__wuchty.html</anchorfile>
+      <anchor>ga554dedfcdb249fdf151caade58666e4d</anchor>
+      <arglist>(char *seq, char *structure, paramT *parameters, int delta, int is_constrained, int is_circular, FILE *fp)</arglist>
+    </member>
+    <member kind="function">
+      <type>SOLUTION *</type>
+      <name>subopt_circ</name>
+      <anchorfile>group__subopt__wuchty.html</anchorfile>
+      <anchor>ga8634516e4740e0b6c9a46d2bae940340</anchor>
+      <arglist>(char *seq, char *sequence, int delta, FILE *fp)</arglist>
+    </member>
+    <member kind="variable">
+      <type>int</type>
+      <name>subopt_sorted</name>
+      <anchorfile>group__subopt__wuchty.html</anchorfile>
+      <anchor>ga873cf8ed69e0437f8efa8b1fec854a0e</anchor>
+      <arglist></arglist>
+    </member>
+    <member kind="variable">
+      <type>double</type>
+      <name>print_energy</name>
+      <anchorfile>group__subopt__wuchty.html</anchorfile>
+      <anchor>ga5e57d914bcb5feeecdf520e25313fcfe</anchor>
+      <arglist></arglist>
+    </member>
+  </compound>
+  <compound kind="group">
+    <name>subopt_stochbt</name>
+    <title>Stochastic backtracking in the Ensemble</title>
+    <filename>group__subopt__stochbt.html</filename>
+    <subgroup>consensus_stochbt</subgroup>
+    <subgroup>kl_neighborhood_stochbt</subgroup>
+    <member kind="function">
+      <type>char *</type>
+      <name>pbacktrack</name>
+      <anchorfile>group__subopt__stochbt.html</anchorfile>
+      <anchor>gac03ca6db186bb3bf0a2a326d7fb3ba03</anchor>
+      <arglist>(char *sequence)</arglist>
+    </member>
+    <member kind="function">
+      <type>char *</type>
+      <name>pbacktrack_circ</name>
+      <anchorfile>group__subopt__stochbt.html</anchorfile>
+      <anchor>ga00474051204ac9ad576b3e45174d03ff</anchor>
+      <arglist>(char *sequence)</arglist>
+    </member>
+    <member kind="variable">
+      <type>int</type>
+      <name>st_back</name>
+      <anchorfile>group__subopt__stochbt.html</anchorfile>
+      <anchor>gacd79b1a570e6ad9be24cb11fe8cae30a</anchor>
+      <arglist></arglist>
+    </member>
+  </compound>
+  <compound kind="group">
+    <name>cofold</name>
+    <title>Calculate Secondary Structures of two RNAs upon Dimerization</title>
+    <filename>group__cofold.html</filename>
+    <subgroup>mfe_cofold</subgroup>
+    <subgroup>pf_cofold</subgroup>
+    <subgroup>up_cofold</subgroup>
+  </compound>
+  <compound kind="group">
+    <name>mfe_cofold</name>
+    <title>MFE Structures of two hybridized Sequences</title>
+    <filename>group__mfe__cofold.html</filename>
+    <file>cofold.h</file>
+    <member kind="function">
+      <type>float</type>
+      <name>cofold</name>
+      <anchorfile>group__mfe__cofold.html</anchorfile>
+      <anchor>gabc8517f22cfe70595ee81fc837910d52</anchor>
+      <arglist>(const char *sequence, char *structure)</arglist>
+    </member>
+    <member kind="function">
+      <type>float</type>
+      <name>cofold_par</name>
+      <anchorfile>group__mfe__cofold.html</anchorfile>
+      <anchor>gafe430060533f14b11fc611f60b3f1f6f</anchor>
+      <arglist>(const char *string, char *structure, paramT *parameters, int is_constrained)</arglist>
+    </member>
+    <member kind="function">
+      <type>void</type>
+      <name>free_co_arrays</name>
+      <anchorfile>group__mfe__cofold.html</anchorfile>
+      <anchor>gaafb33d7473eb9af9d1b168ca8761c41a</anchor>
+      <arglist>(void)</arglist>
+    </member>
+    <member kind="function">
+      <type>void</type>
+      <name>update_cofold_params</name>
+      <anchorfile>group__mfe__cofold.html</anchorfile>
+      <anchor>ga4fcbf34e77b99bfbb2333d2ab0c41a57</anchor>
+      <arglist>(void)</arglist>
+    </member>
+    <member kind="function">
+      <type>void</type>
+      <name>export_cofold_arrays_gq</name>
+      <anchorfile>group__mfe__cofold.html</anchorfile>
+      <anchor>ga5f5bf4df35d0554f6ace9579f8744c48</anchor>
+      <arglist>(int **f5_p, int **c_p, int **fML_p, int **fM1_p, int **fc_p, int **ggg_p, int **indx_p, char **ptype_p)</arglist>
+    </member>
+    <member kind="function">
+      <type>void</type>
+      <name>export_cofold_arrays</name>
+      <anchorfile>group__mfe__cofold.html</anchorfile>
+      <anchor>ga5cb6b59983f1f74ccc00b9b9c4e84482</anchor>
+      <arglist>(int **f5_p, int **c_p, int **fML_p, int **fM1_p, int **fc_p, int **indx_p, char **ptype_p)</arglist>
+    </member>
+  </compound>
+  <compound kind="group">
+    <name>pf_cofold</name>
+    <title>Partition Function for two hybridized Sequences</title>
+    <filename>group__pf__cofold.html</filename>
+    <file>part_func_co.h</file>
+    <member kind="function">
+      <type>cofoldF</type>
+      <name>co_pf_fold</name>
+      <anchorfile>group__pf__cofold.html</anchorfile>
+      <anchor>gaa86a5f998789ed71813d23d7307a791b</anchor>
+      <arglist>(char *sequence, char *structure)</arglist>
+    </member>
+    <member kind="function">
+      <type>cofoldF</type>
+      <name>co_pf_fold_par</name>
+      <anchorfile>group__pf__cofold.html</anchorfile>
+      <anchor>gabd873b450832ab5f21101fc5ab354d21</anchor>
+      <arglist>(char *sequence, char *structure, pf_paramT *parameters, int calculate_bppm, int is_constrained)</arglist>
+    </member>
+    <member kind="function">
+      <type>double *</type>
+      <name>export_co_bppm</name>
+      <anchorfile>group__pf__cofold.html</anchorfile>
+      <anchor>ga11f0252c1d2c4697253ff4b5bd392d3c</anchor>
+      <arglist>(void)</arglist>
+    </member>
+    <member kind="function">
+      <type>void</type>
+      <name>free_co_pf_arrays</name>
+      <anchorfile>group__pf__cofold.html</anchorfile>
+      <anchor>gade3ce34ae8214811374b1d28a40dc247</anchor>
+      <arglist>(void)</arglist>
+    </member>
+    <member kind="function">
+      <type>void</type>
+      <name>update_co_pf_params</name>
+      <anchorfile>group__pf__cofold.html</anchorfile>
+      <anchor>ga6e0f36c1f9b7d9dd4bfbad914c1119e5</anchor>
+      <arglist>(int length)</arglist>
+    </member>
+    <member kind="function">
+      <type>void</type>
+      <name>update_co_pf_params_par</name>
+      <anchorfile>group__pf__cofold.html</anchorfile>
+      <anchor>ga117d880df45bef444d5e2785ffa40a53</anchor>
+      <arglist>(int length, pf_paramT *parameters)</arglist>
+    </member>
+    <member kind="function">
+      <type>void</type>
+      <name>compute_probabilities</name>
+      <anchorfile>group__pf__cofold.html</anchorfile>
+      <anchor>ga15ae04ac5ab84e876dcf0093120cb617</anchor>
+      <arglist>(double FAB, double FEA, double FEB, struct plist *prAB, struct plist *prA, struct plist *prB, int Alength)</arglist>
+    </member>
+    <member kind="function">
+      <type>ConcEnt *</type>
+      <name>get_concentrations</name>
+      <anchorfile>group__pf__cofold.html</anchorfile>
+      <anchor>ga5545cb936ac4ff93c7d699d46e72e8c7</anchor>
+      <arglist>(double FEAB, double FEAA, double FEBB, double FEA, double FEB, double *startconc)</arglist>
+    </member>
+    <member kind="variable">
+      <type>int</type>
+      <name>mirnatog</name>
+      <anchorfile>group__pf__cofold.html</anchorfile>
+      <anchor>gaff27888c4088cc1f60fd59cbd589474c</anchor>
+      <arglist></arglist>
+    </member>
+    <member kind="variable">
+      <type>double</type>
+      <name>F_monomer</name>
+      <anchorfile>group__pf__cofold.html</anchorfile>
+      <anchor>gac2d1851a710a8561390861155ca988fe</anchor>
+      <arglist>[2]</arglist>
+    </member>
+  </compound>
+  <compound kind="group">
+    <name>up_cofold</name>
+    <title>Partition Function for two hybridized Sequences as a stepwise Process</title>
+    <filename>group__up__cofold.html</filename>
+    <file>part_func_up.h</file>
+    <member kind="function">
+      <type>pu_contrib *</type>
+      <name>pf_unstru</name>
+      <anchorfile>group__up__cofold.html</anchorfile>
+      <anchor>ga5b4ee40e190d2f633cd01cf0d2fe93cf</anchor>
+      <arglist>(char *sequence, int max_w)</arglist>
+    </member>
+    <member kind="function">
+      <type>interact *</type>
+      <name>pf_interact</name>
+      <anchorfile>group__up__cofold.html</anchorfile>
+      <anchor>ga1aa0aa02bc3a724f87360c03097afd00</anchor>
+      <arglist>(const char *s1, const char *s2, pu_contrib *p_c, pu_contrib *p_c2, int max_w, char *cstruc, int incr3, int incr5)</arglist>
+    </member>
+    <member kind="function">
+      <type>void</type>
+      <name>free_interact</name>
+      <anchorfile>group__up__cofold.html</anchorfile>
+      <anchor>gadde308fd5f696dc271b1532aa96fd12f</anchor>
+      <arglist>(interact *pin)</arglist>
+    </member>
+    <member kind="function">
+      <type>void</type>
+      <name>free_pu_contrib_struct</name>
+      <anchorfile>group__up__cofold.html</anchorfile>
+      <anchor>gac20bd61824981d45ce0dc9934aa56df8</anchor>
+      <arglist>(pu_contrib *pu)</arglist>
+    </member>
+  </compound>
+  <compound kind="group">
+    <name>consensus_fold</name>
+    <title>Predicting Consensus Structures from Alignment(s)</title>
+    <filename>group__consensus__fold.html</filename>
+    <subgroup>consensus_mfe_fold</subgroup>
+    <subgroup>consensus_pf_fold</subgroup>
+    <subgroup>consensus_stochbt</subgroup>
+    <subgroup>local_consensus_fold</subgroup>
+    <file>alifold.h</file>
+    <member kind="function">
+      <type>int</type>
+      <name>get_mpi</name>
+      <anchorfile>group__consensus__fold.html</anchorfile>
+      <anchor>gaa2d600be90844094ec145ea14a314d2f</anchor>
+      <arglist>(char *Alseq[], int n_seq, int length, int *mini)</arglist>
+    </member>
+    <member kind="function">
+      <type>float **</type>
+      <name>readribosum</name>
+      <anchorfile>group__consensus__fold.html</anchorfile>
+      <anchor>ga5e125c9586fcd4e2e1559fe76f7289cc</anchor>
+      <arglist>(char *name)</arglist>
+    </member>
+    <member kind="function">
+      <type>float</type>
+      <name>energy_of_alistruct</name>
+      <anchorfile>group__consensus__fold.html</anchorfile>
+      <anchor>ga1c48869c03b49a342bf4cbdd61900081</anchor>
+      <arglist>(const char **sequences, const char *structure, int n_seq, float *energy)</arglist>
+    </member>
+    <member kind="function">
+      <type>void</type>
+      <name>encode_ali_sequence</name>
+      <anchorfile>group__consensus__fold.html</anchorfile>
+      <anchor>gaa3e40277c837d6f7603afe319884c786</anchor>
+      <arglist>(const char *sequence, short *S, short *s5, short *s3, char *ss, unsigned short *as, int circ)</arglist>
+    </member>
+    <member kind="function">
+      <type>void</type>
+      <name>alloc_sequence_arrays</name>
+      <anchorfile>group__consensus__fold.html</anchorfile>
+      <anchor>ga8a560930f7f2582cc3967723a86cfdfa</anchor>
+      <arglist>(const char **sequences, short ***S, short ***S5, short ***S3, unsigned short ***a2s, char ***Ss, int circ)</arglist>
+    </member>
+    <member kind="function">
+      <type>void</type>
+      <name>free_sequence_arrays</name>
+      <anchorfile>group__consensus__fold.html</anchorfile>
+      <anchor>ga298a420a8c879202e2617b3f724fde38</anchor>
+      <arglist>(unsigned int n_seq, short ***S, short ***S5, short ***S3, unsigned short ***a2s, char ***Ss)</arglist>
+    </member>
+    <member kind="function">
+      <type>int</type>
+      <name>get_alipf_arrays</name>
+      <anchorfile>group__consensus__fold.html</anchorfile>
+      <anchor>ga0cc49457fd79eeb04d4a7f97c868b09b</anchor>
+      <arglist>(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)</arglist>
+    </member>
+    <member kind="variable">
+      <type>double</type>
+      <name>cv_fact</name>
+      <anchorfile>group__consensus__fold.html</anchorfile>
+      <anchor>gaf3cbac6ff5d706d6e414677841ddf94c</anchor>
+      <arglist></arglist>
+    </member>
+    <member kind="variable">
+      <type>double</type>
+      <name>nc_fact</name>
+      <anchorfile>group__consensus__fold.html</anchorfile>
+      <anchor>ga502948a122a2af5b914355b1f3ea2f61</anchor>
+      <arglist></arglist>
+    </member>
+  </compound>
+  <compound kind="group">
+    <name>consensus_mfe_fold</name>
+    <title>MFE Consensus Structures for Sequence Alignment(s)</title>
+    <filename>group__consensus__mfe__fold.html</filename>
+    <member kind="function">
+      <type>float</type>
+      <name>alifold</name>
+      <anchorfile>group__consensus__mfe__fold.html</anchorfile>
+      <anchor>ga4cf00f0659e5f0480335d69e797f05b1</anchor>
+      <arglist>(const char **strings, char *structure)</arglist>
+    </member>
+    <member kind="function">
+      <type>float</type>
+      <name>circalifold</name>
+      <anchorfile>group__consensus__mfe__fold.html</anchorfile>
+      <anchor>gadbd3b0b1c144cbfb4efe704b2b260f96</anchor>
+      <arglist>(const char **strings, char *structure)</arglist>
+    </member>
+    <member kind="function">
+      <type>void</type>
+      <name>free_alifold_arrays</name>
+      <anchorfile>group__consensus__mfe__fold.html</anchorfile>
+      <anchor>ga72095e4554b5d577250ea14c42acc49e</anchor>
+      <arglist>(void)</arglist>
+    </member>
+  </compound>
+  <compound kind="group">
+    <name>consensus_pf_fold</name>
+    <title>Partition Function and Base Pair Probabilities for Sequence Alignment(s)</title>
+    <filename>group__consensus__pf__fold.html</filename>
+    <member kind="function">
+      <type>float</type>
+      <name>alipf_fold_par</name>
+      <anchorfile>group__consensus__pf__fold.html</anchorfile>
+      <anchor>ga4d2ff54d8210fc7cceeeff389d4dbd1d</anchor>
+      <arglist>(const char **sequences, char *structure, plist **pl, pf_paramT *parameters, int calculate_bppm, int is_constrained, int is_circular)</arglist>
+    </member>
+    <member kind="function">
+      <type>float</type>
+      <name>alipf_fold</name>
+      <anchorfile>group__consensus__pf__fold.html</anchorfile>
+      <anchor>gad32ded7d753ccaf211ab35782d1f42a9</anchor>
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+    <title>Stochastic Backtracking of Consensus Structures from Sequence Alignment(s)</title>
+    <filename>group__consensus__stochbt.html</filename>
+    <member kind="function">
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+      <name>alipbacktrack</name>
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+      <anchor>ga0df40248788f0fb17ebdc59d74116d1c</anchor>
+      <arglist>(double *prob)</arglist>
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+    <title>Predicting Locally stable structures of large sequences</title>
+    <filename>group__local__fold.html</filename>
+    <subgroup>local_mfe_fold</subgroup>
+    <subgroup>local_pf_fold</subgroup>
+    <subgroup>local_consensus_fold</subgroup>
+    <file>Lfold.h</file>
+  </compound>
+  <compound kind="group">
+    <name>local_mfe_fold</name>
+    <title>Local MFE structure Prediction and Z-scores</title>
+    <filename>group__local__mfe__fold.html</filename>
+    <member kind="function">
+      <type>float</type>
+      <name>Lfold</name>
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+      <anchor>ga16e5a70e60835bb969eaecbe6482f1be</anchor>
+      <arglist>(const char *string, char *structure, int maxdist)</arglist>
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+      <arglist>(const char *string, char *structure, int maxdist, int zsc, double min_z)</arglist>
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+    <title>Partition functions for locally stable secondary structures</title>
+    <filename>group__local__pf__fold.html</filename>
+    <file>LPfold.h</file>
+    <member kind="function">
+      <type>void</type>
+      <name>update_pf_paramsLP</name>
+      <anchorfile>group__local__pf__fold.html</anchorfile>
+      <anchor>ga5a019014d37fe6105131dfc2fc447880</anchor>
+      <arglist>(int length)</arglist>
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+      <anchor>gaa1ecd401617ebc748a0220026543c777</anchor>
+      <arglist>(char *sequence, int winSize, int pairSize, float cutoffb, double **pU, struct plist **dpp2, FILE *pUfp, FILE *spup)</arglist>
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+      <anchor>gab354507e8028f3e1c52ef96bb1eb9df8</anchor>
+      <arglist>(char *sequence, int winSize, int pairSize, float cutoffb, double **pU, struct plist **dpp2, FILE *pUfp, FILE *spup, pf_paramT *parameters)</arglist>
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+    <member kind="function">
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+      <anchorfile>group__local__pf__fold.html</anchorfile>
+      <anchor>ga0bcb751860bbf34e3dfee8c2fbdb3ef3</anchor>
+      <arglist>(double **pU, int length, int ulength, FILE *fp, int energies)</arglist>
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+      <anchor>ga9acb00ee10e96b1ca4ea394cd8bcec75</anchor>
+      <arglist>(double **pU, int length, int ulength, FILE *fp, int energies)</arglist>
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+  <compound kind="group">
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+    <title>Local MFE consensus structures for Sequence Alignments</title>
+    <filename>group__local__consensus__fold.html</filename>
+    <member kind="function">
+      <type>float</type>
+      <name>aliLfold</name>
+      <anchorfile>group__local__consensus__fold.html</anchorfile>
+      <anchor>ga20a173a3cdb83f5d1778e36c1a6b1f2b</anchor>
+      <arglist>(const char **strings, char *structure, int maxdist)</arglist>
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+    <title>Change and Precalculate Energy Parameter Sets and Boltzmann Factors</title>
+    <filename>group__energy__parameters.html</filename>
+    <subgroup>energy_parameters_rw</subgroup>
+    <file>params.h</file>
+    <member kind="function">
+      <type>paramT *</type>
+      <name>scale_parameters</name>
+      <anchorfile>group__energy__parameters.html</anchorfile>
+      <anchor>ga527ef619cd8210b84d5d53be1e0e29b6</anchor>
+      <arglist>(void)</arglist>
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+      <anchorfile>group__energy__parameters.html</anchorfile>
+      <anchor>gac2f3ca440b7eaf4d999fb27da949fe72</anchor>
+      <arglist>(double temperature, model_detailsT md)</arglist>
+    </member>
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+      <type>pf_paramT *</type>
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+      <anchorfile>group__energy__parameters.html</anchorfile>
+      <anchor>gab85f6b6da051f380371deb0d8921bdba</anchor>
+      <arglist>(void)</arglist>
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+    <member kind="function">
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+      <anchorfile>group__energy__parameters.html</anchorfile>
+      <anchor>ga6fc2f3eef5a3024d44963ac59a42e39d</anchor>
+      <arglist>(double temperature, double betaScale, model_detailsT md, double pf_scale)</arglist>
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+      <type>pf_paramT *</type>
+      <name>get_boltzmann_factor_copy</name>
+      <anchorfile>group__energy__parameters.html</anchorfile>
+      <anchor>gacba212326a051734797e65987260fdd0</anchor>
+      <arglist>(pf_paramT *parameters)</arglist>
+    </member>
+    <member kind="function">
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+      <anchorfile>group__energy__parameters.html</anchorfile>
+      <anchor>gaa6a4297a2b91d6f7ae47dd61ca1862a0</anchor>
+      <arglist>(unsigned int n_seq)</arglist>
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+      <anchorfile>group__energy__parameters.html</anchorfile>
+      <anchor>gaaa049a8c9f1c2ed4398cb1b5a3d65a66</anchor>
+      <arglist>(unsigned int n_seq, double temperature, double betaScale, model_detailsT md, double pf_scale)</arglist>
+    </member>
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+    <name>energy_parameters_rw</name>
+    <title>Reading/Writing energy parameter sets from/to File</title>
+    <filename>group__energy__parameters__rw.html</filename>
+    <subgroup>energy_parameters_convert</subgroup>
+    <file>read_epars.h</file>
+    <member kind="function">
+      <type>void</type>
+      <name>read_parameter_file</name>
+      <anchorfile>group__energy__parameters__rw.html</anchorfile>
+      <anchor>ga165a142a3c68fb6655c69ef4ab7cd749</anchor>
+      <arglist>(const char fname[])</arglist>
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+    <member kind="function">
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+      <anchorfile>group__energy__parameters__rw.html</anchorfile>
+      <anchor>ga8a43459be386a7489feeab68dc2c6c76</anchor>
+      <arglist>(const char fname[])</arglist>
+    </member>
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+    <name>energy_parameters_convert</name>
+    <title>Converting energy parameter files</title>
+    <filename>group__energy__parameters__convert.html</filename>
+    <file>convert_epars.h</file>
+    <member kind="define">
+      <type>#define</type>
+      <name>VRNA_CONVERT_OUTPUT_ALL</name>
+      <anchorfile>group__energy__parameters__convert.html</anchorfile>
+      <anchor>ga8dc6aee5a806c49b71557152f9616bc4</anchor>
+      <arglist></arglist>
+    </member>
+    <member kind="define">
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+      <anchorfile>group__energy__parameters__convert.html</anchorfile>
+      <anchor>gaf66fe2cb11dfcfd32d791049c254a8a4</anchor>
+      <arglist></arglist>
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+      <anchorfile>group__energy__parameters__convert.html</anchorfile>
+      <anchor>gad23522d63f8d4c50d5a5deee9bee3ef2</anchor>
+      <arglist></arglist>
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+    <member kind="define">
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+      <name>VRNA_CONVERT_OUTPUT_MM_HP</name>
+      <anchorfile>group__energy__parameters__convert.html</anchorfile>
+      <anchor>gaa892c7b4957459090f3e08da298cc347</anchor>
+      <arglist></arglist>
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+      <anchorfile>group__energy__parameters__convert.html</anchorfile>
+      <anchor>ga4ff223fb1f9c62cd92d9ab811ad03d55</anchor>
+      <arglist></arglist>
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+    <member kind="define">
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+      <name>VRNA_CONVERT_OUTPUT_MM_INT_1N</name>
+      <anchorfile>group__energy__parameters__convert.html</anchorfile>
+      <anchor>gaf5d3743219f83c6348155cd81e755bbb</anchor>
+      <arglist></arglist>
+    </member>
+    <member kind="define">
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+      <name>VRNA_CONVERT_OUTPUT_MM_INT_23</name>
+      <anchorfile>group__energy__parameters__convert.html</anchorfile>
+      <anchor>ga78382ec622ba99e0ac2262317bdd7316</anchor>
+      <arglist></arglist>
+    </member>
+    <member kind="define">
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+      <anchorfile>group__energy__parameters__convert.html</anchorfile>
+      <anchor>gae67af9f1cdf7baf2865481282a5d1034</anchor>
+      <arglist></arglist>
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+    <member kind="define">
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+      <anchorfile>group__energy__parameters__convert.html</anchorfile>
+      <anchor>gaf14ead7ef1fdbe725ade653750fc51e3</anchor>
+      <arglist></arglist>
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+      <name>VRNA_CONVERT_OUTPUT_DANGLE5</name>
+      <anchorfile>group__energy__parameters__convert.html</anchorfile>
+      <anchor>ga036ffd996d8c8a9acf631760dd1da24b</anchor>
+      <arglist></arglist>
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+    <member kind="define">
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+      <name>VRNA_CONVERT_OUTPUT_DANGLE3</name>
+      <anchorfile>group__energy__parameters__convert.html</anchorfile>
+      <anchor>ga34a8a5479ef885834ef32f3fb43d79bc</anchor>
+      <arglist></arglist>
+    </member>
+    <member kind="define">
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+      <name>VRNA_CONVERT_OUTPUT_INT_11</name>
+      <anchorfile>group__energy__parameters__convert.html</anchorfile>
+      <anchor>ga079aafefd5f8ab57ee5120099a34bd25</anchor>
+      <arglist></arglist>
+    </member>
+    <member kind="define">
+      <type>#define</type>
+      <name>VRNA_CONVERT_OUTPUT_INT_21</name>
+      <anchorfile>group__energy__parameters__convert.html</anchorfile>
+      <anchor>gacf770881d9034431ebe741642342a1f9</anchor>
+      <arglist></arglist>
+    </member>
+    <member kind="define">
+      <type>#define</type>
+      <name>VRNA_CONVERT_OUTPUT_INT_22</name>
+      <anchorfile>group__energy__parameters__convert.html</anchorfile>
+      <anchor>gaa307671e2631cdacad9cbe4c6583b05f</anchor>
+      <arglist></arglist>
+    </member>
+    <member kind="define">
+      <type>#define</type>
+      <name>VRNA_CONVERT_OUTPUT_BULGE</name>
+      <anchorfile>group__energy__parameters__convert.html</anchorfile>
+      <anchor>ga7092fe0be4de6f02cc0bf08e81af726a</anchor>
+      <arglist></arglist>
+    </member>
+    <member kind="define">
+      <type>#define</type>
+      <name>VRNA_CONVERT_OUTPUT_INT</name>
+      <anchorfile>group__energy__parameters__convert.html</anchorfile>
+      <anchor>gac5c2289fdf8ff1b980976d1613ff943a</anchor>
+      <arglist></arglist>
+    </member>
+    <member kind="define">
+      <type>#define</type>
+      <name>VRNA_CONVERT_OUTPUT_ML</name>
+      <anchorfile>group__energy__parameters__convert.html</anchorfile>
+      <anchor>gaf2c8755d64eff3852aa45df9ac80a4fe</anchor>
+      <arglist></arglist>
+    </member>
+    <member kind="define">
+      <type>#define</type>
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+      <anchorfile>group__energy__parameters__convert.html</anchorfile>
+      <anchor>ga46d5b1535ae86060b6317565b7c6b40b</anchor>
+      <arglist></arglist>
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+    <member kind="define">
+      <type>#define</type>
+      <name>VRNA_CONVERT_OUTPUT_SPECIAL_HP</name>
+      <anchorfile>group__energy__parameters__convert.html</anchorfile>
+      <anchor>gaa1ff48a79642d69579d1766561ec6db6</anchor>
+      <arglist></arglist>
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+    <member kind="define">
+      <type>#define</type>
+      <name>VRNA_CONVERT_OUTPUT_VANILLA</name>
+      <anchorfile>group__energy__parameters__convert.html</anchorfile>
+      <anchor>ga0d4e8a836bb4864ab5129c085dbf592d</anchor>
+      <arglist></arglist>
+    </member>
+    <member kind="define">
+      <type>#define</type>
+      <name>VRNA_CONVERT_OUTPUT_NINIO</name>
+      <anchorfile>group__energy__parameters__convert.html</anchorfile>
+      <anchor>ga2eb0462f16939ddacdaf751a88d675ce</anchor>
+      <arglist></arglist>
+    </member>
+    <member kind="define">
+      <type>#define</type>
+      <name>VRNA_CONVERT_OUTPUT_DUMP</name>
+      <anchorfile>group__energy__parameters__convert.html</anchorfile>
+      <anchor>gac86976e9c2a55b3a6481ea60044f6098</anchor>
+      <arglist></arglist>
+    </member>
+    <member kind="function">
+      <type>void</type>
+      <name>convert_parameter_file</name>
+      <anchorfile>group__energy__parameters__convert.html</anchorfile>
+      <anchor>gafbe538bc4eb2cf2a33326e1010005f8a</anchor>
+      <arglist>(const char *iname, const char *oname, unsigned int options)</arglist>
+    </member>
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+    <name>eval</name>
+    <title>Energy evaluation</title>
+    <filename>group__eval.html</filename>
+    <member kind="function">
+      <type>float</type>
+      <name>energy_of_structure</name>
+      <anchorfile>group__eval.html</anchorfile>
+      <anchor>gaf93986cb3cb29770ec9cca69c9fab8cf</anchor>
+      <arglist>(const char *string, const char *structure, int verbosity_level)</arglist>
+    </member>
+    <member kind="function">
+      <type>float</type>
+      <name>energy_of_struct_par</name>
+      <anchorfile>group__eval.html</anchorfile>
+      <anchor>gab5169ea4f72f250e43811463a33f4e40</anchor>
+      <arglist>(const char *string, const char *structure, paramT *parameters, int verbosity_level)</arglist>
+    </member>
+    <member kind="function">
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+      <name>energy_of_circ_structure</name>
+      <anchorfile>group__eval.html</anchorfile>
+      <anchor>gaeb14f3664aec67fc03268ac75253f0f8</anchor>
+      <arglist>(const char *string, const char *structure, int verbosity_level)</arglist>
+    </member>
+    <member kind="function">
+      <type>float</type>
+      <name>energy_of_circ_struct_par</name>
+      <anchorfile>group__eval.html</anchorfile>
+      <anchor>ga75dc765ee4a1177832bc817c94cf88e5</anchor>
+      <arglist>(const char *string, const char *structure, paramT *parameters, int verbosity_level)</arglist>
+    </member>
+    <member kind="function">
+      <type>int</type>
+      <name>energy_of_structure_pt</name>
+      <anchorfile>group__eval.html</anchorfile>
+      <anchor>ga8831445966b761417e713360791299d8</anchor>
+      <arglist>(const char *string, short *ptable, short *s, short *s1, int verbosity_level)</arglist>
+    </member>
+    <member kind="function">
+      <type>int</type>
+      <name>energy_of_struct_pt_par</name>
+      <anchorfile>group__eval.html</anchorfile>
+      <anchor>gada4701dd7519b29da75ceac147601f4e</anchor>
+      <arglist>(const char *string, short *ptable, short *s, short *s1, paramT *parameters, int verbosity_level)</arglist>
+    </member>
+    <member kind="variable">
+      <type>int</type>
+      <name>eos_debug</name>
+      <anchorfile>group__eval.html</anchorfile>
+      <anchor>ga567530678f6260a1a649a5beca5da4c5</anchor>
+      <arglist></arglist>
+    </member>
+  </compound>
+  <compound kind="group">
+    <name>inverse_fold</name>
+    <title>Searching Sequences for Predefined Structures</title>
+    <filename>group__inverse__fold.html</filename>
+    <file>inverse.h</file>
+    <member kind="function">
+      <type>float</type>
+      <name>inverse_fold</name>
+      <anchorfile>group__inverse__fold.html</anchorfile>
+      <anchor>ga7af026de55d4babad879f2c92559cbbc</anchor>
+      <arglist>(char *start, const char *target)</arglist>
+    </member>
+    <member kind="function">
+      <type>float</type>
+      <name>inverse_pf_fold</name>
+      <anchorfile>group__inverse__fold.html</anchorfile>
+      <anchor>gaeef52ecbf2a2450ad585a344f9826806</anchor>
+      <arglist>(char *start, const char *target)</arglist>
+    </member>
+    <member kind="variable">
+      <type>char *</type>
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+      <anchorfile>group__inverse__fold.html</anchorfile>
+      <anchor>ga8f791e7740a5a28b9f6fafb4e60301d9</anchor>
+      <arglist></arglist>
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+    <member kind="variable">
+      <type>float</type>
+      <name>final_cost</name>
+      <anchorfile>group__inverse__fold.html</anchorfile>
+      <anchor>ga7f17d3b169af048d32bb185039a9c09c</anchor>
+      <arglist></arglist>
+    </member>
+    <member kind="variable">
+      <type>int</type>
+      <name>give_up</name>
+      <anchorfile>group__inverse__fold.html</anchorfile>
+      <anchor>ga7ec4ba51f86e1717a1e174264e4a75ce</anchor>
+      <arglist></arglist>
+    </member>
+    <member kind="variable">
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+      <anchorfile>group__inverse__fold.html</anchorfile>
+      <anchor>gafcfc65fba01b9cca5946726ed9057a63</anchor>
+      <arglist></arglist>
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+    <title>Classified Dynamic Programming</title>
+    <filename>group__class__fold.html</filename>
+    <subgroup>kl_neighborhood</subgroup>
+    <subgroup>dos</subgroup>
+  </compound>
+  <compound kind="group">
+    <name>kl_neighborhood</name>
+    <title>Distance based partitioning of the Secondary Structure Space</title>
+    <filename>group__kl__neighborhood.html</filename>
+    <subgroup>kl_neighborhood_mfe</subgroup>
+    <subgroup>kl_neighborhood_pf</subgroup>
+    <subgroup>kl_neighborhood_stochbt</subgroup>
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+  <compound kind="group">
+    <name>kl_neighborhood_mfe</name>
+    <title>Calculating MFE representatives of a Distance Based Partitioning</title>
+    <filename>group__kl__neighborhood__mfe.html</filename>
+    <file>2Dfold.h</file>
+    <member kind="function">
+      <type>TwoDfold_vars *</type>
+      <name>get_TwoDfold_variables</name>
+      <anchorfile>group__kl__neighborhood__mfe.html</anchorfile>
+      <anchor>gac9284f132cf0eaa0a2f43590eda05488</anchor>
+      <arglist>(const char *seq, const char *structure1, const char *structure2, int circ)</arglist>
+    </member>
+    <member kind="function">
+      <type>void</type>
+      <name>destroy_TwoDfold_variables</name>
+      <anchorfile>group__kl__neighborhood__mfe.html</anchorfile>
+      <anchor>ga05bf4f31d216b1b160fd2d3d68e9b487</anchor>
+      <arglist>(TwoDfold_vars *our_variables)</arglist>
+    </member>
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+      <type>TwoDfold_solution *</type>
+      <name>TwoDfoldList</name>
+      <anchorfile>group__kl__neighborhood__mfe.html</anchorfile>
+      <anchor>ga47da790166020558d27323aef489703e</anchor>
+      <arglist>(TwoDfold_vars *vars, int distance1, int distance2)</arglist>
+    </member>
+    <member kind="function">
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