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    <sectiondef kind="user-defined">
      <member refid="group__mfe__global__deprecated_1ga4cf00f0659e5f0480335d69e797f05b1" kind="function"><name>alifold</name></member>
      <member refid="group__mfe__global__deprecated_1gadbd3b0b1c144cbfb4efe704b2b260f96" kind="function"><name>circalifold</name></member>
      <member refid="group__mfe__global__deprecated_1ga72095e4554b5d577250ea14c42acc49e" kind="function"><name>free_alifold_arrays</name></member>
    </sectiondef>
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      <member refid="group__part__func__global__deprecated_1gab46954fb0ed3b6d5631e7f9b802978cd" kind="function"><name>alipf_fold_par</name></member>
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      <member refid="group__part__func__global__deprecated_1ga0c0498f35686e26b38ee460d3db1a661" kind="function"><name>free_alipf_arrays</name></member>
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      <member refid="group__part__func__global__deprecated_1ga5349960075b1847720a2e9df021e2675" kind="function"><name>get_alipf_arrays</name></member>
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        <name>DEPRECATED</name>
        <param><defname>func   </defname></param>
        <param><defname>msg</defname></param>
        <initializer>func</initializer>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/alifold.h" line="23" column="11" bodyfile="ViennaRNA/alifold.h" bodystart="23" bodyend="-1"/>
      </memberdef>
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    <sectiondef kind="var">
      <member refid="group__model__details_1gaf3cbac6ff5d706d6e414677841ddf94c" kind="variable"><name>cv_fact</name></member>
      <member refid="group__model__details_1ga502948a122a2af5b914355b1f3ea2f61" kind="variable"><name>nc_fact</name></member>
    </sectiondef>
    <sectiondef kind="func">
      <member refid="group__eval__deprecated_1ga1c48869c03b49a342bf4cbdd61900081" kind="function"><name>energy_of_alistruct</name></member>
      <memberdef kind="function" id="alifold_8h_1a867057bf4da81917bd34c356285e99d9" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>float</type>
        <definition>float energy_of_ali_gquad_structure</definition>
        <argsstring>(const char **sequences, const char *structure, int n_seq, float *energy)</argsstring>
        <name>energy_of_ali_gquad_structure</name>
        <param>
          <type>const char **</type>
          <declname>sequences</declname>
        </param>
        <param>
          <type>const char *</type>
          <declname>structure</declname>
        </param>
        <param>
          <type>int</type>
          <declname>n_seq</declname>
        </param>
        <param>
          <type>float *</type>
          <declname>energy</declname>
        </param>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/alifold.h" line="119" column="8" declfile="ViennaRNA/alifold.h" declline="119" declcolumn="8"/>
      </memberdef>
      <member refid="group__mfe__global__deprecated_1gac484c6bd429bafbd353b91044508d8e9" kind="function"><name>update_alifold_params</name></member>
    </sectiondef>
    <briefdescription>
<para>Functions for comparative structure prediction using RNA sequence alignments. </para>
    </briefdescription>
    <detaileddescription>
    </detaileddescription>
    <programlisting>
<codeline lineno="1"><highlight class="preprocessor">#ifndef<sp/>VIENNA_RNA_PACKAGE_ALIFOLD_H</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="2"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VIENNA_RNA_PACKAGE_ALIFOLD_H</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="3"><highlight class="normal"></highlight></codeline>
<codeline lineno="4"><highlight class="normal"></highlight><highlight class="preprocessor">#include<sp/>&lt;<ref refid="datastructures_2basic_8h" kindref="compound">ViennaRNA/datastructures/basic.h</ref>&gt;</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="5"><highlight class="normal"></highlight><highlight class="preprocessor">#include<sp/>&lt;<ref refid="params_2basic_8h" kindref="compound">ViennaRNA/params/basic.h</ref>&gt;</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="6"><highlight class="normal"></highlight><highlight class="preprocessor">#include<sp/>&lt;<ref refid="ribosum_8h" kindref="compound">ViennaRNA/params/ribosum.h</ref>&gt;</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="7"><highlight class="normal"></highlight><highlight class="preprocessor">#include<sp/>&lt;<ref refid="mfe_2global_8h" kindref="compound">ViennaRNA/mfe/global.h</ref>&gt;</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="8"><highlight class="normal"></highlight><highlight class="preprocessor">#include<sp/>&lt;<ref refid="backtrack_2global_8h" kindref="compound">ViennaRNA/backtrack/global.h</ref>&gt;</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="9"><highlight class="normal"></highlight><highlight class="preprocessor">#include<sp/>&lt;<ref refid="partfunc_2global_8h" kindref="compound">ViennaRNA/partfunc/global.h</ref>&gt;</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="10"><highlight class="normal"></highlight><highlight class="preprocessor">#include<sp/>&lt;ViennaRNA/sequences/alignments.h&gt;</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="11"><highlight class="normal"></highlight><highlight class="preprocessor">#include<sp/>&lt;<ref refid="problist_8h" kindref="compound">ViennaRNA/structures/problist.h</ref>&gt;</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="12"><highlight class="normal"></highlight><highlight class="preprocessor">#include<sp/>&lt;<ref refid="sampling_2basic_8h" kindref="compound">ViennaRNA/sampling/basic.h</ref>&gt;</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="13"><highlight class="normal"></highlight></codeline>
<codeline lineno="14"><highlight class="normal"></highlight><highlight class="preprocessor">#ifdef<sp/>VRNA_WARN_DEPRECATED</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="15"><highlight class="normal"></highlight><highlight class="preprocessor">#<sp/>if<sp/>defined(__clang__)</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="16"><highlight class="normal"></highlight><highlight class="preprocessor">#<sp/><sp/>define<sp/>DEPRECATED(func,<sp/>msg)<sp/>func<sp/>__attribute__<sp/>((deprecated(&quot;&quot;,<sp/>msg)))</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="17"><highlight class="normal"></highlight><highlight class="preprocessor">#<sp/>elif<sp/>defined(__GNUC__)</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="18"><highlight class="normal"></highlight><highlight class="preprocessor">#<sp/><sp/>define<sp/>DEPRECATED(func,<sp/>msg)<sp/>func<sp/>__attribute__<sp/>((deprecated(msg)))</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="19"><highlight class="normal"></highlight><highlight class="preprocessor">#<sp/>else</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="20"><highlight class="normal"></highlight><highlight class="preprocessor">#<sp/><sp/>define<sp/>DEPRECATED(func,<sp/>msg)<sp/>func</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="21"><highlight class="normal"></highlight><highlight class="preprocessor">#<sp/>endif</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="22"><highlight class="normal"></highlight><highlight class="preprocessor">#else</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="23"><highlight class="normal"></highlight><highlight class="preprocessor">#<sp/>define<sp/>DEPRECATED(func,<sp/>msg)<sp/>func</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="24"><highlight class="normal"></highlight><highlight class="preprocessor">#endif</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="25"><highlight class="normal"></highlight></codeline>
<codeline lineno="32"><highlight class="normal"></highlight></codeline>
<codeline lineno="33"><highlight class="normal"></highlight><highlight class="preprocessor">#ifndef<sp/>VRNA_DISABLE_BACKWARD_COMPATIBILITY</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="34"><highlight class="normal"></highlight></codeline>
<codeline lineno="35"><highlight class="normal"></highlight><highlight class="comment">/*</highlight></codeline>
<codeline lineno="36"><highlight class="comment">#################################################</highlight></codeline>
<codeline lineno="37"><highlight class="comment">#<sp/>DEPRECATED<sp/>FUNCTIONS<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>#</highlight></codeline>
<codeline lineno="38"><highlight class="comment">#################################################</highlight></codeline>
<codeline lineno="39"><highlight class="comment">*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="40"><highlight class="normal"></highlight></codeline>
<codeline lineno="45"><highlight class="normal"></highlight></codeline>
<codeline lineno="65"><highlight class="normal">DEPRECATED(</highlight><highlight class="keywordtype">float</highlight><highlight class="normal"><sp/><ref refid="group__mfe__global__deprecated_1ga4cf00f0659e5f0480335d69e797f05b1" kindref="member">alifold</ref>(<sp/></highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>**strings,<sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>*structure),</highlight></codeline>
<codeline lineno="66" refid="group__mfe__global__deprecated_1ga4cf00f0659e5f0480335d69e797f05b1" refkind="member"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;Use<sp/>vrna_alifold()<sp/>or<sp/>vrna_mfe()<sp/>instead&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="67"><highlight class="normal"></highlight></codeline>
<codeline lineno="80"><highlight class="normal">DEPRECATED(</highlight><highlight class="keywordtype">float</highlight><highlight class="normal"><sp/><ref refid="group__mfe__global__deprecated_1gadbd3b0b1c144cbfb4efe704b2b260f96" kindref="member">circalifold</ref>(<sp/></highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>**strings,<sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>*structure),</highlight></codeline>
<codeline lineno="81" refid="group__mfe__global__deprecated_1gadbd3b0b1c144cbfb4efe704b2b260f96" refkind="member"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;Use<sp/>vrna_alicircfold()<sp/>or<sp/>vrna_mfe()<sp/>instead&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="82"><highlight class="normal"></highlight></codeline>
<codeline lineno="94"><highlight class="normal">DEPRECATED(</highlight><highlight class="keywordtype">void</highlight><highlight class="normal"><sp/><ref refid="group__mfe__global__deprecated_1ga72095e4554b5d577250ea14c42acc49e" kindref="member">free_alifold_arrays</ref>(</highlight><highlight class="keywordtype">void</highlight><highlight class="normal">),</highlight></codeline>
<codeline lineno="95" refid="group__mfe__global__deprecated_1ga72095e4554b5d577250ea14c42acc49e" refkind="member"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;This<sp/>function<sp/>is<sp/>obsolete&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="96"><highlight class="normal"></highlight></codeline>
<codeline lineno="97"><highlight class="normal"></highlight><highlight class="comment">/*<sp/>End<sp/>group<sp/>mfe_global_deprecated<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="99"><highlight class="normal"></highlight></codeline>
<codeline lineno="115"><highlight class="normal">DEPRECATED(</highlight><highlight class="keywordtype">float</highlight><highlight class="normal"><sp/><ref refid="group__eval__deprecated_1ga1c48869c03b49a342bf4cbdd61900081" kindref="member">energy_of_alistruct</ref>(</highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>**sequences,<sp/></highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>*structure,<sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>n_seq,<sp/></highlight><highlight class="keywordtype">float</highlight><highlight class="normal"><sp/>*energy),</highlight></codeline>
<codeline lineno="116" refid="group__eval__deprecated_1ga1c48869c03b49a342bf4cbdd61900081" refkind="member"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;Use<sp/>vrna_eval_structure()<sp/>and<sp/>vrna_eval_covar_structure()<sp/>instead&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="117"><highlight class="normal"></highlight></codeline>
<codeline lineno="118"><highlight class="normal">DEPRECATED(</highlight><highlight class="keywordtype">float</highlight><highlight class="normal"><sp/>energy_of_ali_gquad_structure(</highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>**sequences,<sp/></highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>*structure,<sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>n_seq,<sp/></highlight><highlight class="keywordtype">float</highlight><highlight class="normal"><sp/>*energy),</highlight></codeline>
<codeline lineno="119"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;Use<sp/>vrna_eval_structure()<sp/>and<sp/>vrna_eval_covar_structure()<sp/>instead&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="120"><highlight class="normal"></highlight></codeline>
<codeline lineno="131"><highlight class="normal">DEPRECATED(</highlight><highlight class="keyword">extern</highlight><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/><sp/><ref refid="group__model__details_1gaf3cbac6ff5d706d6e414677841ddf94c" kindref="member">cv_fact</ref>,</highlight></codeline>
<codeline lineno="132"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;Use<sp/>the<sp/>cv_fact<sp/>attribute<sp/>of<sp/>the<sp/>vrna_md_t<sp/>datastructure<sp/>instead&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="143"><highlight class="normal">DEPRECATED(</highlight><highlight class="keyword">extern</highlight><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/><sp/><ref refid="group__model__details_1ga502948a122a2af5b914355b1f3ea2f61" kindref="member">nc_fact</ref>,</highlight></codeline>
<codeline lineno="144"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;Use<sp/>the<sp/>nc_fact<sp/>attribute<sp/>of<sp/>the<sp/>vrna_md_t<sp/>datastructure<sp/>instead&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="145"><highlight class="normal"></highlight></codeline>
<codeline lineno="150"><highlight class="normal"></highlight></codeline>
<codeline lineno="165"><highlight class="normal">DEPRECATED(</highlight><highlight class="keywordtype">float</highlight><highlight class="normal"><sp/><ref refid="group__part__func__global__deprecated_1gab46954fb0ed3b6d5631e7f9b802978cd" kindref="member">alipf_fold_par</ref>(<sp/></highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>**sequences,</highlight></codeline>
<codeline lineno="166"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>*structure,</highlight></codeline>
<codeline lineno="167"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><ref refid="group__struct__utils__plist_1gab9ac98ab55ded9fb90043b024b915aca" kindref="member">vrna_ep_t</ref><sp/>**pl,</highlight></codeline>
<codeline lineno="168"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><ref refid="group__energy__parameters_1ga01d8b92fe734df8d79a6169482c7d8d8" kindref="member">vrna_exp_param_t</ref><sp/>*parameters,</highlight></codeline>
<codeline lineno="169"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>calculate_bppm,</highlight></codeline>
<codeline lineno="170"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>is_constrained,</highlight></codeline>
<codeline lineno="171"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>is_circular),</highlight></codeline>
<codeline lineno="172" refid="group__part__func__global__deprecated_1gab46954fb0ed3b6d5631e7f9b802978cd" refkind="member"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;Use<sp/>vrna_pf_alifold()<sp/>or<sp/>vrna_pf()<sp/>instead&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="173"><highlight class="normal"></highlight></codeline>
<codeline lineno="190"><highlight class="normal">DEPRECATED(</highlight><highlight class="keywordtype">float</highlight><highlight class="normal"><sp/><ref refid="group__part__func__global__deprecated_1ga1a5f6cfb9d761fa862ce4edc7c369cd2" kindref="member">alipf_fold</ref>(<sp/></highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>**sequences,<sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>*structure,<sp/><ref refid="group__struct__utils__plist_1gab9ac98ab55ded9fb90043b024b915aca" kindref="member">vrna_ep_t</ref><sp/>**pl),</highlight></codeline>
<codeline lineno="191" refid="group__part__func__global__deprecated_1ga1a5f6cfb9d761fa862ce4edc7c369cd2" refkind="member"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;Use<sp/>vrna_pf_alifold()<sp/>or<sp/>vrna_pf()<sp/>instead&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="192"><highlight class="normal"></highlight></codeline>
<codeline lineno="203"><highlight class="normal">DEPRECATED(</highlight><highlight class="keywordtype">float</highlight><highlight class="normal"><sp/><ref refid="group__part__func__global__deprecated_1ga604a42ad64178279551ad3e4def3d603" kindref="member">alipf_circ_fold</ref>(</highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>**sequences,<sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>*structure,<sp/><ref refid="group__struct__utils__plist_1gab9ac98ab55ded9fb90043b024b915aca" kindref="member">vrna_ep_t</ref><sp/>**pl),</highlight></codeline>
<codeline lineno="204" refid="group__part__func__global__deprecated_1ga604a42ad64178279551ad3e4def3d603" refkind="member"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;Use<sp/>vrna_pf_circalifold()<sp/>or<sp/>vrna_pf()<sp/>instead&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="205"><highlight class="normal"></highlight></codeline>
<codeline lineno="206"><highlight class="normal"></highlight></codeline>
<codeline lineno="223"><highlight class="normal">DEPRECATED(<ref refid="group__data__structures_1ga31125aeace516926bf7f251f759b6126" kindref="member">FLT_OR_DBL</ref><sp/>*<ref refid="group__part__func__global__deprecated_1gaba5a18064258036b3753665e89da2072" kindref="member">export_ali_bppm</ref>(</highlight><highlight class="keywordtype">void</highlight><highlight class="normal">),</highlight></codeline>
<codeline lineno="224" refid="group__part__func__global__deprecated_1gaba5a18064258036b3753665e89da2072" refkind="member"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;Use<sp/>the<sp/>new<sp/>API<sp/>with<sp/>vrna_fold_compound_t<sp/>datastructure<sp/>instead&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="225"><highlight class="normal"></highlight></codeline>
<codeline lineno="236"><highlight class="normal">DEPRECATED(</highlight><highlight class="keywordtype">void</highlight><highlight class="normal"><sp/><sp/><ref refid="group__part__func__global__deprecated_1ga0c0498f35686e26b38ee460d3db1a661" kindref="member">free_alipf_arrays</ref>(</highlight><highlight class="keywordtype">void</highlight><highlight class="normal">),</highlight></codeline>
<codeline lineno="237" refid="group__part__func__global__deprecated_1ga0c0498f35686e26b38ee460d3db1a661" refkind="member"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;This<sp/>function<sp/>is<sp/>obsolete&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="238"><highlight class="normal"></highlight></codeline>
<codeline lineno="247"><highlight class="normal">DEPRECATED(</highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/><sp/>*<ref refid="group__part__func__global__deprecated_1ga955a7e2f25d6a1a00a3c92c6229fc44d" kindref="member">alipbacktrack</ref>(</highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/>*prob),</highlight></codeline>
<codeline lineno="248" refid="group__part__func__global__deprecated_1ga955a7e2f25d6a1a00a3c92c6229fc44d" refkind="member"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;Use<sp/>the<sp/>new<sp/>API<sp/>and<sp/>vrna_pbacktrack()<sp/>instead&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="249"><highlight class="normal"></highlight></codeline>
<codeline lineno="273"><highlight class="normal">DEPRECATED(</highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><ref refid="group__part__func__global__deprecated_1ga5349960075b1847720a2e9df021e2675" kindref="member">get_alipf_arrays</ref>(</highlight><highlight class="keywordtype">short</highlight><highlight class="normal"><sp/>***S_p,</highlight></codeline>
<codeline lineno="274"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">short</highlight><highlight class="normal"><sp/>***S5_p,</highlight></codeline>
<codeline lineno="275"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">short</highlight><highlight class="normal"><sp/>***S3_p,</highlight></codeline>
<codeline lineno="276"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">unsigned</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">short</highlight><highlight class="normal"><sp/>***a2s_p,</highlight></codeline>
<codeline lineno="277"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>***Ss_p,</highlight></codeline>
<codeline lineno="278"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><ref refid="group__data__structures_1ga31125aeace516926bf7f251f759b6126" kindref="member">FLT_OR_DBL</ref><sp/>**qb_p,</highlight></codeline>
<codeline lineno="279"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><ref refid="group__data__structures_1ga31125aeace516926bf7f251f759b6126" kindref="member">FLT_OR_DBL</ref><sp/>**qm_p,</highlight></codeline>
<codeline lineno="280"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><ref refid="group__data__structures_1ga31125aeace516926bf7f251f759b6126" kindref="member">FLT_OR_DBL</ref><sp/>**q1k_p,</highlight></codeline>
<codeline lineno="281"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><ref refid="group__data__structures_1ga31125aeace516926bf7f251f759b6126" kindref="member">FLT_OR_DBL</ref><sp/>**qln_p,</highlight></codeline>
<codeline lineno="282"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">short</highlight><highlight class="normal"><sp/>**pscore),</highlight></codeline>
<codeline lineno="283" refid="group__part__func__global__deprecated_1ga5349960075b1847720a2e9df021e2675" refkind="member"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;Use<sp/>the<sp/>new<sp/>API<sp/>with<sp/>vrna_fold_compound_t<sp/>datastructure<sp/>instead&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="284"><highlight class="normal"></highlight></codeline>
<codeline lineno="285"><highlight class="normal"></highlight></codeline>
<codeline lineno="286"><highlight class="normal"></highlight><highlight class="comment">/*<sp/>End<sp/>group<sp/>part_func_global_deprecated<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="288"><highlight class="normal"></highlight></codeline>
<codeline lineno="300"><highlight class="normal">DEPRECATED(</highlight><highlight class="keywordtype">void</highlight><highlight class="normal"><sp/><ref refid="group__mfe__global__deprecated_1gac484c6bd429bafbd353b91044508d8e9" kindref="member">update_alifold_params</ref>(</highlight><highlight class="keywordtype">void</highlight><highlight class="normal">),</highlight></codeline>
<codeline lineno="301" refid="group__mfe__global__deprecated_1gac484c6bd429bafbd353b91044508d8e9" refkind="member"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;Use<sp/>the<sp/>new<sp/>API<sp/>with<sp/>vrna_fold_compound_t<sp/>datastructure<sp/>instead&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="302"><highlight class="normal"></highlight></codeline>
<codeline lineno="303"><highlight class="normal"></highlight><highlight class="preprocessor">#endif</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="304"><highlight class="normal"></highlight></codeline>
<codeline lineno="305"><highlight class="normal"></highlight></codeline>
<codeline lineno="306"><highlight class="normal"></highlight><highlight class="preprocessor">#endif</highlight></codeline>
    </programlisting>
    <location file="ViennaRNA/alifold.h"/>
  </compounddef>
</doxygen>
