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    <sectiondef kind="define">
      <memberdef kind="define" id="LPfold_8h_1aab347a3c03fbe8e7319551b9fa0cce4a" prot="public" static="no">
        <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/LPfold.h" line="31" column="11" bodyfile="ViennaRNA/LPfold.h" bodystart="31" bodyend="-1"/>
      </memberdef>
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    <sectiondef kind="func">
      <member refid="group__part__func__window__deprecated_1ga5a019014d37fe6105131dfc2fc447880" kind="function"><name>update_pf_paramsLP</name></member>
      <member refid="group__part__func__window__deprecated_1gab5aa36df48576d25cd42aea2c0bd021d" kind="function"><name>update_pf_paramsLP_par</name></member>
      <member refid="group__part__func__window__deprecated_1gaf6d77f10775c1d58c8199d5ec95d4228" kind="function"><name>pfl_fold</name></member>
      <member refid="group__part__func__window__deprecated_1gab34f3add76cd5b99441bcd983ff9db83" kind="function"><name>pfl_fold_par</name></member>
      <memberdef kind="function" id="LPfold_8h_1aedb90ad3f54a9bdd6b24f47155e431c3" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>void</type>
        <definition>void putoutpU_prob_par</definition>
        <argsstring>(double **pU, int length, int ulength, FILE *fp, int energies, vrna_exp_param_t *parameters)</argsstring>
        <name>putoutpU_prob_par</name>
        <param>
          <type>double **</type>
          <declname>pU</declname>
        </param>
        <param>
          <type>int</type>
          <declname>length</declname>
        </param>
        <param>
          <type>int</type>
          <declname>ulength</declname>
        </param>
        <param>
          <type>FILE *</type>
          <declname>fp</declname>
        </param>
        <param>
          <type>int</type>
          <declname>energies</declname>
        </param>
        <param>
          <type><ref refid="group__energy__parameters_1ga01d8b92fe734df8d79a6169482c7d8d8" kindref="member">vrna_exp_param_t</ref> *</type>
          <declname>parameters</declname>
        </param>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/LPfold.h" line="128" column="7" declfile="ViennaRNA/LPfold.h" declline="128" declcolumn="7"/>
      </memberdef>
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      <memberdef kind="function" id="LPfold_8h_1ae6f8303a20b9b7377837f4c845bbec04" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>void</type>
        <definition>void putoutpU_prob_bin_par</definition>
        <argsstring>(double **pU, int length, int ulength, FILE *fp, int energies, vrna_exp_param_t *parameters)</argsstring>
        <name>putoutpU_prob_bin_par</name>
        <param>
          <type>double **</type>
          <declname>pU</declname>
        </param>
        <param>
          <type>int</type>
          <declname>length</declname>
        </param>
        <param>
          <type>int</type>
          <declname>ulength</declname>
        </param>
        <param>
          <type>FILE *</type>
          <declname>fp</declname>
        </param>
        <param>
          <type>int</type>
          <declname>energies</declname>
        </param>
        <param>
          <type><ref refid="group__energy__parameters_1ga01d8b92fe734df8d79a6169482c7d8d8" kindref="member">vrna_exp_param_t</ref> *</type>
          <declname>parameters</declname>
        </param>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/LPfold.h" line="159" column="7" declfile="ViennaRNA/LPfold.h" declline="159" declcolumn="7"/>
      </memberdef>
      <member refid="group__part__func__window__deprecated_1ga9acb00ee10e96b1ca4ea394cd8bcec75" kind="function"><name>putoutpU_prob_bin</name></member>
      <memberdef kind="function" id="LPfold_8h_1ae85bf55053e9fb295208be322e0fa07a" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>void</type>
        <definition>void init_pf_foldLP</definition>
        <argsstring>(int length)</argsstring>
        <name>init_pf_foldLP</name>
        <param>
          <type>int</type>
          <declname>length</declname>
        </param>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
<para>Dunno if this function was ever used by external programs linking to RNAlib, but it was declared PUBLIC before. Anyway, never use this function as it will be removed soon and does nothing at all </para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/LPfold.h" line="190" column="7" declfile="ViennaRNA/LPfold.h" declline="190" declcolumn="7"/>
      </memberdef>
    </sectiondef>
    <briefdescription>
<para>Partition function and equilibrium probability implementation for the sliding window algorithm. </para>
    </briefdescription>
    <detaileddescription>
<para>This file contains the implementation for sliding window partition function and equilibrium probabilities. It also provides the unpaired probability implementation from  <verbatim>embed:rst:inline  :cite:t:`bernhart:2011` </verbatim> </para>
    </detaileddescription>
    <programlisting>
<codeline lineno="1"><highlight class="preprocessor">#ifndef<sp/>VIENNA_RNA_PACKAGE_LPFOLD_H</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="2"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VIENNA_RNA_PACKAGE_LPFOLD_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">#ifndef<sp/>VRNA_DISABLE_BACKWARD_COMPATIBILITY</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="5"><highlight class="normal"></highlight></codeline>
<codeline lineno="15"><highlight class="normal"></highlight></codeline>
<codeline lineno="16"><highlight class="normal"></highlight><highlight class="preprocessor">#include<sp/>&lt;stdio.h&gt;</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="17"><highlight class="normal"></highlight></codeline>
<codeline lineno="18"><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="19"><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="20"><highlight class="normal"></highlight><highlight class="preprocessor">#include<sp/>&lt;<ref refid="partfunc_2local_8h" kindref="compound">ViennaRNA/partfunc/local.h</ref>&gt;</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="21"><highlight class="normal"></highlight></codeline>
<codeline lineno="22"><highlight class="normal"></highlight><highlight class="preprocessor">#ifdef<sp/>VRNA_WARN_DEPRECATED</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="23"><highlight class="normal"></highlight><highlight class="preprocessor">#<sp/>if<sp/>defined(__clang__)</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="24"><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="25"><highlight class="normal"></highlight><highlight class="preprocessor">#<sp/>elif<sp/>defined(__GNUC__)</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="26"><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="27"><highlight class="normal"></highlight><highlight class="preprocessor">#<sp/>else</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="28"><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="29"><highlight class="normal"></highlight><highlight class="preprocessor">#<sp/>endif</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="30"><highlight class="normal"></highlight><highlight class="preprocessor">#else</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="31"><highlight class="normal"></highlight><highlight class="preprocessor">#<sp/>define<sp/>DEPRECATED(func,<sp/>msg)<sp/>func</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="32"><highlight class="normal"></highlight><highlight class="preprocessor">#endif</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="33"><highlight class="normal"></highlight></codeline>
<codeline lineno="41"><highlight class="normal">DEPRECATED(</highlight><highlight class="keywordtype">void</highlight><highlight class="normal"><sp/><ref refid="group__part__func__window__deprecated_1ga5a019014d37fe6105131dfc2fc447880" kindref="member">update_pf_paramsLP</ref>(</highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>length),</highlight></codeline>
<codeline lineno="42" refid="group__part__func__window__deprecated_1ga5a019014d37fe6105131dfc2fc447880" refkind="member"><highlight class="normal"></highlight><highlight class="stringliteral">&quot;This<sp/>function<sp/>is<sp/>obsolete&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="43"><highlight class="normal"></highlight></codeline>
<codeline lineno="44"><highlight class="normal"></highlight></codeline>
<codeline lineno="51"><highlight class="normal">DEPRECATED(</highlight><highlight class="keywordtype">void</highlight><highlight class="normal"><sp/>update_pf_paramsLP_par(</highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>length,</highlight></codeline>
<codeline lineno="52"><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/><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="53"><highlight class="normal"></highlight><highlight class="stringliteral">&quot;Use<sp/>the<sp/>new<sp/>API<sp/>with<sp/>vrna_folc_compound_t<sp/>instead&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="54"><highlight class="normal"></highlight></codeline>
<codeline lineno="55"><highlight class="normal"></highlight></codeline>
<codeline lineno="93"><highlight class="normal">DEPRECATED(<ref refid="group__struct__utils__plist_1gab9ac98ab55ded9fb90043b024b915aca" kindref="member">vrna_ep_t</ref><sp/>*<ref refid="group__part__func__window__deprecated_1gaf6d77f10775c1d58c8199d5ec95d4228" kindref="member">pfl_fold</ref>(</highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*sequence,</highlight></codeline>
<codeline lineno="94"><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>winSize,</highlight></codeline>
<codeline lineno="95"><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>pairSize,</highlight></codeline>
<codeline lineno="96"><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">float</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>cutoffb,</highlight></codeline>
<codeline lineno="97"><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>**pU,</highlight></codeline>
<codeline lineno="98"><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><ref refid="group__struct__utils__plist_1gab9ac98ab55ded9fb90043b024b915aca" kindref="member">vrna_ep_t</ref><sp/><sp/><sp/><sp/><sp/>**dpp2,</highlight></codeline>
<codeline lineno="99"><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>FILE<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*pUfp,</highlight></codeline>
<codeline lineno="100"><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>FILE<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*spup),</highlight></codeline>
<codeline lineno="101" refid="group__part__func__window__deprecated_1gaf6d77f10775c1d58c8199d5ec95d4228" refkind="member"><highlight class="normal"></highlight><highlight class="stringliteral">&quot;Use<sp/>vrna_pfl_fold(),<sp/>vrna_pfl_fold_cb(),<sp/>vrna_pfl_fold_up(),<sp/>or<sp/>vrna_pfl_fold_up_cb()<sp/>instead&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="102"><highlight class="normal"></highlight></codeline>
<codeline lineno="103"><highlight class="normal"></highlight></codeline>
<codeline lineno="110"><highlight class="normal">DEPRECATED(<ref refid="group__struct__utils__plist_1gab9ac98ab55ded9fb90043b024b915aca" kindref="member">vrna_ep_t</ref><sp/>*<ref refid="group__part__func__window__deprecated_1gab34f3add76cd5b99441bcd983ff9db83" kindref="member">pfl_fold_par</ref>(</highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*sequence,</highlight></codeline>
<codeline lineno="111"><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/><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>winSize,</highlight></codeline>
<codeline lineno="112"><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/><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>pairSize,</highlight></codeline>
<codeline lineno="113"><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">float</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>cutoffb,</highlight></codeline>
<codeline lineno="114"><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>**pU,</highlight></codeline>
<codeline lineno="115"><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/><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>**dpp2,</highlight></codeline>
<codeline lineno="116"><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>FILE<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*pUfp,</highlight></codeline>
<codeline lineno="117"><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>FILE<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*spup,</highlight></codeline>
<codeline lineno="118"><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/><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/><sp/>*parameters),</highlight></codeline>
<codeline lineno="119" refid="group__part__func__window__deprecated_1gab34f3add76cd5b99441bcd983ff9db83" refkind="member"><highlight class="normal"></highlight><highlight class="stringliteral">&quot;Use<sp/>the<sp/>new<sp/>API<sp/>and<sp/>vrna_probs_window()<sp/>instead&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="120"><highlight class="normal"></highlight></codeline>
<codeline lineno="121"><highlight class="normal"></highlight></codeline>
<codeline lineno="122"><highlight class="normal">DEPRECATED(</highlight><highlight class="keywordtype">void</highlight><highlight class="normal"><sp/>putoutpU_prob_par(</highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>**pU,</highlight></codeline>
<codeline lineno="123"><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>length,</highlight></codeline>
<codeline lineno="124"><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>ulength,</highlight></codeline>
<codeline lineno="125"><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>FILE<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*fp,</highlight></codeline>
<codeline lineno="126"><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>energies,</highlight></codeline>
<codeline lineno="127"><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/><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/><sp/>*parameters),</highlight></codeline>
<codeline lineno="128"><highlight class="normal"></highlight><highlight class="stringliteral">&quot;&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="129"><highlight class="normal"></highlight></codeline>
<codeline lineno="130"><highlight class="normal"></highlight></codeline>
<codeline lineno="145"><highlight class="normal">DEPRECATED(</highlight><highlight class="keywordtype">void</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><ref refid="group__part__func__window__deprecated_1ga0bcb751860bbf34e3dfee8c2fbdb3ef3" kindref="member">putoutpU_prob</ref>(</highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/>**pU,</highlight></codeline>
<codeline lineno="146"><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/>length,</highlight></codeline>
<codeline lineno="147"><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/>ulength,</highlight></codeline>
<codeline lineno="148"><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>FILE<sp/><sp/><sp/>*fp,</highlight></codeline>
<codeline lineno="149"><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/>energies),</highlight></codeline>
<codeline lineno="150" refid="group__part__func__window__deprecated_1ga0bcb751860bbf34e3dfee8c2fbdb3ef3" refkind="member"><highlight class="normal"></highlight><highlight class="stringliteral">&quot;&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="151"><highlight class="normal"></highlight></codeline>
<codeline lineno="152"><highlight class="normal"></highlight></codeline>
<codeline lineno="153"><highlight class="normal">DEPRECATED(</highlight><highlight class="keywordtype">void</highlight><highlight class="normal"><sp/>putoutpU_prob_bin_par(</highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>**pU,</highlight></codeline>
<codeline lineno="154"><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/><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>length,</highlight></codeline>
<codeline lineno="155"><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/><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>ulength,</highlight></codeline>
<codeline lineno="156"><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>FILE<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*fp,</highlight></codeline>
<codeline lineno="157"><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/><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>energies,</highlight></codeline>
<codeline lineno="158"><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/><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/><sp/>*parameters),</highlight></codeline>
<codeline lineno="159"><highlight class="normal"></highlight><highlight class="stringliteral">&quot;&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="160"><highlight class="normal"></highlight></codeline>
<codeline lineno="161"><highlight class="normal"></highlight></codeline>
<codeline lineno="176"><highlight class="normal">DEPRECATED(</highlight><highlight class="keywordtype">void</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><ref refid="group__part__func__window__deprecated_1ga9acb00ee10e96b1ca4ea394cd8bcec75" kindref="member">putoutpU_prob_bin</ref>(</highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/>**pU,</highlight></codeline>
<codeline lineno="177"><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/><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/><sp/><sp/><sp/>length,</highlight></codeline>
<codeline lineno="178"><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/><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/><sp/><sp/><sp/>ulength,</highlight></codeline>
<codeline lineno="179"><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>FILE<sp/><sp/><sp/>*fp,</highlight></codeline>
<codeline lineno="180"><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/><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/><sp/><sp/><sp/>energies),</highlight></codeline>
<codeline lineno="181" refid="group__part__func__window__deprecated_1ga9acb00ee10e96b1ca4ea394cd8bcec75" refkind="member"><highlight class="normal"></highlight><highlight class="stringliteral">&quot;&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="182"><highlight class="normal"></highlight></codeline>
<codeline lineno="183"><highlight class="normal"></highlight></codeline>
<codeline lineno="189"><highlight class="normal">DEPRECATED(</highlight><highlight class="keywordtype">void</highlight><highlight class="normal"><sp/><ref refid="LPfold_8h_1ae85bf55053e9fb295208be322e0fa07a" kindref="member">init_pf_foldLP</ref>(</highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>length),</highlight></codeline>
<codeline lineno="190" refid="LPfold_8h_1ae85bf55053e9fb295208be322e0fa07a" refkind="member"><highlight class="normal"></highlight><highlight class="stringliteral">&quot;This<sp/>function<sp/>is<sp/>obsolete&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="191"><highlight class="normal"></highlight></codeline>
<codeline lineno="192"><highlight class="normal"></highlight><highlight class="preprocessor">#endif</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="193"><highlight class="normal"></highlight></codeline>
<codeline lineno="194"><highlight class="normal"></highlight><highlight class="preprocessor">#endif</highlight></codeline>
    </programlisting>
    <location file="ViennaRNA/LPfold.h"/>
  </compounddef>
</doxygen>
