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- <li><a href="annotated.html"><span>Data Structures</span></a></li>
+ <li><a href="annotated.html"><span>Data Structures</span></a></li>
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-<div class="title">Deprecated List </div> </div>
-</div><!--header-->
<div class="contents">
-<div class="textblock"><dl class="reflist">
-<dt><a class="anchor" id="_deprecated000008"></a>Global <a class="el" href="fold__vars_8h.html#a0244a629b5ab4f58b77590c3dfd130dc">base_pair</a> </dt>
-<dd>Do not use this variable anymore! </dd>
-<dt><a class="anchor" id="_deprecated000012"></a>Global <a class="el" href="part__func_8h.html#ae89a63bd83e75a80b2ba36d20b31ce81">centroid</a> (int length, double *dist)</dt>
-<dd>This function is deprecated and should not be used anymore as it is not threadsafe! </dd>
-<dt><a class="anchor" id="_deprecated000007"></a>Global <a class="el" href="fold_8h.html#a657222e2758c46bf13b416ef3032e417">energy_of_circ_struct</a> (const char *string, const char *structure)</dt>
-<dd>This function is deprecated and should not be used in future programs Use <a class="el" href="group__eval.html#gaeb14f3664aec67fc03268ac75253f0f8">energy_of_circ_structure()</a> instead! </dd>
-<dt><a class="anchor" id="_deprecated000005"></a>Global <a class="el" href="fold_8h.html#ac2b37fea2145c94d925a3f33378ef87b">energy_of_struct</a> (const char *string, const char *structure)</dt>
-<dd>This function is deprecated and should not be used in future programs! Use <a class="el" href="group__eval.html#gaf93986cb3cb29770ec9cca69c9fab8cf">energy_of_structure()</a> instead! </dd>
-<dt><a class="anchor" id="_deprecated000006"></a>Global <a class="el" href="fold_8h.html#a27ce6f68512d43bf1fe14a06c9d76d5c">energy_of_struct_pt</a> (const char *string, short *ptable, short *s, short *s1)</dt>
-<dd>This function is deprecated and should not be used in future programs! Use <a class="el" href="group__eval.html#ga8831445966b761417e713360791299d8">energy_of_structure_pt()</a> instead! </dd>
-<dt><a class="anchor" id="_deprecated000015"></a>Global <a class="el" href="part__func_8h.html#a7b6ab474cc80accc48010ccfcc59f96b">expHairpinEnergy</a> (int u, int type, short si1, short sj1, const char *string)</dt>
-<dd>Use <a class="el" href="loop__energies_8h.html#a0e128184bb097dc2da33706f33b555a6">exp_E_Hairpin()</a> from <a class="el" href="loop__energies_8h.html" title="Energy evaluation for MFE and partition function calculations.">loop_energies.h</a> instead </dd>
-<dt><a class="anchor" id="_deprecated000014"></a>Global <a class="el" href="part__func_8h.html#a68ba6f3a48e08ca131ab54621ce3a2d7">expLoopEnergy</a> (int u1, int u2, int type, int type2, short si1, short sj1, short sp1, short sq1)</dt>
-<dd>Use <a class="el" href="loop__energies_8h.html#aa5e98e524e2a41e290b942b09544bc9e">exp_E_IntLoop()</a> from <a class="el" href="loop__energies_8h.html" title="Energy evaluation for MFE and partition function calculations.">loop_energies.h</a> instead </dd>
-<dt><a class="anchor" id="_deprecated000016"></a>Global <a class="el" href="part__func__co_8h.html#a334de3c96e2186abfbdc0eaea6d08b14">get_plist</a> (struct plist *pl, int length, double cut_off)</dt>
-<dd>{ This function is deprecated and will be removed soon!} use <a class="el" href="group__pf__fold.html#ga03e15e831a31b1154855ab47edbdb019">assign_plist_from_pr()</a> instead! </dd>
-<dt><a class="anchor" id="_deprecated000003"></a>Global <a class="el" href="fold_8h.html#ab327ce11972f5ac069d52c8dedfdb700">HairpinE</a> (int size, int type, int si1, int sj1, const char *string)</dt>
-<dd>{This function is deprecated and will be removed soon. Use <a class="el" href="loop__energies_8h.html#aa362183cf6db89a10cdb0f5c4bd180c6">E_Hairpin()</a> instead!} </dd>
-<dt><a class="anchor" id="_deprecated000010"></a>Global <a class="el" href="fold__vars_8h.html#a92089ae3a51b5d75a14ce9cc29cc8317">iindx</a> </dt>
-<dd>Do not use this variable anymore! </dd>
-<dt><a class="anchor" id="_deprecated000017"></a>Global <a class="el" href="part__func__co_8h.html#aa12dda9dd6179cdd22bcce87c0682c07">init_co_pf_fold</a> (int length)</dt>
-<dd>{ This function is deprecated and will be removed soon!} </dd>
-<dt><a class="anchor" id="_deprecated000011"></a>Global <a class="el" href="part__func_8h.html#a15176e23eceeff8c7d14eabcfec8a2af">init_pf_fold</a> (int length)</dt>
-<dd>This function is obsolete and will be removed soon! </dd>
-<dt><a class="anchor" id="_deprecated000001"></a>Global <a class="el" href="cofold_8h.html#afee0c32208aa2ac97338b6e3fbad7fa5">initialize_cofold</a> (int length)</dt>
-<dd>{This function is obsolete and will be removed soon!} </dd>
-<dt><a class="anchor" id="_deprecated000004"></a>Global <a class="el" href="fold_8h.html#ac3f0a28d9cb609d388b155445073fd20">initialize_fold</a> (int length)</dt>
-<dd>{This function is deprecated and will be removed soon!} </dd>
-<dt><a class="anchor" id="_deprecated000002"></a>Global <a class="el" href="fold_8h.html#a2163034a25c6115d894b199e97e03f6c">LoopEnergy</a> (int n1, int n2, int type, int type_2, int si1, int sj1, int sp1, int sq1)</dt>
-<dd>{This function is deprecated and will be removed soon. Use <a class="el" href="loop__energies_8h.html#a3e5ad89f451254b1fe366d77aa8ff7bd">E_IntLoop()</a> instead!} </dd>
-<dt><a class="anchor" id="_deprecated000018"></a>Global <a class="el" href="profiledist_8h.html#a904c7eaf4a2413567c00ac4891749d18">Make_bp_profile</a> (int length)</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>
-<dt><a class="anchor" id="_deprecated000013"></a>Global <a class="el" href="part__func_8h.html#ae9556ba7ded44fe2321b6f67c3fc02a3">mean_bp_dist</a> (int length)</dt>
-<dd>This function is not threadsafe and should not be used anymore. Use <a class="el" href="group__pf__fold.html#ga79cbc375af65f11609feb6b055269e7d">mean_bp_distance()</a> instead! </dd>
-<dt><a class="anchor" id="_deprecated000009"></a>Global <a class="el" href="fold__vars_8h.html#a0f5757427fd5f2f79d6fca0081cd5a52">pr</a> </dt>
-<dd>Do not use this variable anymore! </dd>
-<dt><a class="anchor" id="_deprecated000019"></a>Global <a class="el" href="PS__dot_8h.html#a689a97a7e3b8a2df14728b8204d9d57b">PS_dot_plot</a> (char *string, char *file)</dt>
+
+
+<h1><a class="anchor" id="deprecated">Deprecated List </a></h1><p><a class="anchor" id="_deprecated000008"></a> </p>
+<dl>
+<dt>Global <a class="el" href="fold__vars_8h.html#a0244a629b5ab4f58b77590c3dfd130dc">base_pair</a> </dt>
+<dd>Do not use this variable anymore! </dd>
+</dl>
+<p><a class="anchor" id="_deprecated000012"></a> </p>
+<dl>
+<dt>Global <a class="el" href="part__func_8h.html#ae89a63bd83e75a80b2ba36d20b31ce81">centroid</a> </dt>
+<dd>This function is deprecated and should not be used anymore as it is not threadsafe! </dd>
+</dl>
+<p><a class="anchor" id="_deprecated000007"></a> </p>
+<dl>
+<dt>Global <a class="el" href="fold_8h.html#a657222e2758c46bf13b416ef3032e417">energy_of_circ_struct</a> </dt>
+<dd><p class="startdd">This function is deprecated and should not be used in future programs Use <a class="el" href="group__eval.html#gaeb14f3664aec67fc03268ac75253f0f8">energy_of_circ_structure()</a> instead!</p>
+<p class="enddd"></p>
+</dd>
+</dl>
+<p><a class="anchor" id="_deprecated000005"></a> </p>
+<dl>
+<dt>Global <a class="el" href="fold_8h.html#ac2b37fea2145c94d925a3f33378ef87b">energy_of_struct</a> </dt>
+<dd><p class="startdd">This function is deprecated and should not be used in future programs! Use <a class="el" href="group__eval.html#gaf93986cb3cb29770ec9cca69c9fab8cf">energy_of_structure()</a> instead!</p>
+<p class="enddd"></p>
+</dd>
+</dl>
+<p><a class="anchor" id="_deprecated000006"></a> </p>
+<dl>
+<dt>Global <a class="el" href="fold_8h.html#a27ce6f68512d43bf1fe14a06c9d76d5c">energy_of_struct_pt</a> </dt>
+<dd><p class="startdd">This function is deprecated and should not be used in future programs! Use <a class="el" href="group__eval.html#ga8831445966b761417e713360791299d8">energy_of_structure_pt()</a> instead!</p>
+<p class="enddd"></p>
+</dd>
+</dl>
+<p><a class="anchor" id="_deprecated000015"></a> </p>
+<dl>
+<dt>Global <a class="el" href="part__func_8h.html#a7b6ab474cc80accc48010ccfcc59f96b">expHairpinEnergy</a> </dt>
+<dd>Use <a class="el" href="loop__energies_8h.html#a0e128184bb097dc2da33706f33b555a6">exp_E_Hairpin()</a> from <a class="el" href="loop__energies_8h.html" title="Energy evaluation for MFE and partition function calculations.">loop_energies.h</a> instead </dd>
+</dl>
+<p><a class="anchor" id="_deprecated000014"></a> </p>
+<dl>
+<dt>Global <a class="el" href="part__func_8h.html#a68ba6f3a48e08ca131ab54621ce3a2d7">expLoopEnergy</a> </dt>
+<dd>Use <a class="el" href="loop__energies_8h.html#aa5e98e524e2a41e290b942b09544bc9e">exp_E_IntLoop()</a> from <a class="el" href="loop__energies_8h.html" title="Energy evaluation for MFE and partition function calculations.">loop_energies.h</a> instead </dd>
+</dl>
+<p><a class="anchor" id="_deprecated000016"></a> </p>
+<dl>
+<dt>Global <a class="el" href="part__func__co_8h.html#a334de3c96e2186abfbdc0eaea6d08b14">get_plist</a> </dt>
+<dd>{ This function is deprecated and will be removed soon!} use <a class="el" href="group__pf__fold.html#ga03e15e831a31b1154855ab47edbdb019">assign_plist_from_pr()</a> instead! </dd>
+</dl>
+<p><a class="anchor" id="_deprecated000003"></a> </p>
+<dl>
+<dt>Global <a class="el" href="fold_8h.html#ab327ce11972f5ac069d52c8dedfdb700">HairpinE</a> </dt>
+<dd>{This function is deprecated and will be removed soon. Use <a class="el" href="loop__energies_8h.html#aa362183cf6db89a10cdb0f5c4bd180c6">E_Hairpin()</a> instead!} </dd>
+</dl>
+<p><a class="anchor" id="_deprecated000010"></a> </p>
+<dl>
+<dt>Global <a class="el" href="fold__vars_8h.html#a92089ae3a51b5d75a14ce9cc29cc8317">iindx</a> </dt>
+<dd>Do not use this variable anymore! </dd>
+</dl>
+<p><a class="anchor" id="_deprecated000017"></a> </p>
+<dl>
+<dt>Global <a class="el" href="part__func__co_8h.html#aa12dda9dd6179cdd22bcce87c0682c07">init_co_pf_fold</a> </dt>
+<dd>{ This function is deprecated and will be removed soon!} </dd>
+</dl>
+<p><a class="anchor" id="_deprecated000011"></a> </p>
+<dl>
+<dt>Global <a class="el" href="part__func_8h.html#a15176e23eceeff8c7d14eabcfec8a2af">init_pf_fold</a> </dt>
+<dd>This function is obsolete and will be removed soon! </dd>
+</dl>
+<p><a class="anchor" id="_deprecated000001"></a> </p>
+<dl>
+<dt>Global <a class="el" href="cofold_8h.html#afee0c32208aa2ac97338b6e3fbad7fa5">initialize_cofold</a> </dt>
+<dd>{This function is obsolete and will be removed soon!} </dd>
+</dl>
+<p><a class="anchor" id="_deprecated000004"></a> </p>
+<dl>
+<dt>Global <a class="el" href="fold_8h.html#ac3f0a28d9cb609d388b155445073fd20">initialize_fold</a> </dt>
+<dd><p class="startdd">{This function is deprecated and will be removed soon!}</p>
+<p class="enddd"></p>
+</dd>
+</dl>
+<p><a class="anchor" id="_deprecated000002"></a> </p>
+<dl>
+<dt>Global <a class="el" href="fold_8h.html#a2163034a25c6115d894b199e97e03f6c">LoopEnergy</a> </dt>
+<dd>{This function is deprecated and will be removed soon. Use <a class="el" href="loop__energies_8h.html#a3e5ad89f451254b1fe366d77aa8ff7bd">E_IntLoop()</a> instead!} </dd>
+</dl>
+<p><a class="anchor" id="_deprecated000018"></a> </p>
+<dl>
+<dt>Global <a class="el" href="profiledist_8h.html#a904c7eaf4a2413567c00ac4891749d18">Make_bp_profile</a> </dt>
+<dd><p class="startdd">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</p>
+<p class="enddd"></p>
+</dd>
+</dl>
+<p><a class="anchor" id="_deprecated000013"></a> </p>
+<dl>
+<dt>Global <a class="el" href="part__func_8h.html#ae9556ba7ded44fe2321b6f67c3fc02a3">mean_bp_dist</a> </dt>
+<dd>This function is not threadsafe and should not be used anymore. Use <a class="el" href="group__pf__fold.html#ga79cbc375af65f11609feb6b055269e7d">mean_bp_distance()</a> instead! </dd>
+</dl>
+<p><a class="anchor" id="_deprecated000009"></a> </p>
+<dl>
+<dt>Global <a class="el" href="fold__vars_8h.html#a0f5757427fd5f2f79d6fca0081cd5a52">pr</a> </dt>
+<dd>Do not use this variable anymore! </dd>
+</dl>
+<p><a class="anchor" id="_deprecated000019"></a> </p>
+<dl>
+<dt>Global <a class="el" href="PS__dot_8h.html#a689a97a7e3b8a2df14728b8204d9d57b">PS_dot_plot</a> </dt>
<dd>This function is deprecated and will be removed soon! Use <a class="el" href="PS__dot_8h.html#a00ea223b5cf02eb2faae5ff29f0d5e12">PS_dot_plot_list()</a> instead! </dd>
</dl>
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- <a href="http://www.doxygen.org/index.html">
- <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.1.1 </li>
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</div>
+<hr size="1"/><address style="text-align: right;"><small>Generated on 11 Apr 2017 for RNAlib-2.1.2 by
+<a href="http://www.doxygen.org/index.html">
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