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    <sectiondef kind="define">
      <memberdef kind="define" id="part__func__up_8h_1a8b383725f0e93e50f7e7a99bb2b1ef95" prot="public" static="no">
        <name>RNA_UP_MODE_1</name>
        <initializer>1U</initializer>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/part_func_up.h" line="8" column="11" bodyfile="ViennaRNA/part_func_up.h" bodystart="8" bodyend="-1"/>
      </memberdef>
      <memberdef kind="define" id="part__func__up_8h_1a90f0bbbea731d219b38368aa5f352a21" prot="public" static="no">
        <name>RNA_UP_MODE_2</name>
        <initializer>2U</initializer>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/part_func_up.h" line="9" column="11" bodyfile="ViennaRNA/part_func_up.h" bodystart="9" bodyend="-1"/>
      </memberdef>
      <memberdef kind="define" id="part__func__up_8h_1a90579142befc7aab9db8790ee6753fa9" prot="public" static="no">
        <name>RNA_UP_MODE_3</name>
        <initializer>4U</initializer>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/part_func_up.h" line="10" column="11" bodyfile="ViennaRNA/part_func_up.h" bodystart="10" bodyend="-1"/>
      </memberdef>
    </sectiondef>
    <sectiondef kind="func">
      <member refid="group__up__cofold_1ga2a7fb78dfbfb00eccf8d79f38e3384c3" kind="function"><name>pf_unstru</name></member>
      <member refid="group__up__cofold_1ga5adcc9222fe42d943e407e79a3f4558d" kind="function"><name>pf_interact</name></member>
      <member refid="group__up__cofold_1gadde308fd5f696dc271b1532aa96fd12f" kind="function"><name>free_interact</name></member>
      <member refid="group__up__cofold_1ga73efd2918cbbb2cdf44422653f996852" kind="function"><name>Up_plot</name></member>
      <member refid="group__up__cofold_1gac827201da2538b2eb37e1797031b036e" kind="function"><name>get_pu_contrib_struct</name></member>
      <member refid="group__up__cofold_1gac20bd61824981d45ce0dc9934aa56df8" kind="function"><name>free_pu_contrib_struct</name></member>
      <member refid="group__up__cofold_1gae1b3579727cf7a27eea93594d0e6d831" kind="function"><name>free_pu_contrib</name></member>
    </sectiondef>
    <briefdescription>
<para>Implementations for accessibility and RNA-RNA interaction as a stepwise process. </para>
    </briefdescription>
    <detaileddescription>
    </detaileddescription>
    <programlisting>
<codeline lineno="1"><highlight class="preprocessor">#ifndef<sp/>VIENNA_RNA_PACKAGE_PART_FUNC_UP_H</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="2"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VIENNA_RNA_PACKAGE_PART_FUNC_UP_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></codeline>
<codeline lineno="6"><highlight class="normal"></highlight><highlight class="preprocessor">#ifndef<sp/>VRNA_DISABLE_BACKWARD_COMPATIBILITY</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="7"><highlight class="normal"></highlight></codeline>
<codeline lineno="8"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/><sp/><sp/>RNA_UP_MODE_1<sp/><sp/><sp/>1U</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="9"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/><sp/><sp/>RNA_UP_MODE_2<sp/><sp/><sp/>2U</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="10"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/><sp/><sp/>RNA_UP_MODE_3<sp/><sp/><sp/>4U</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="11"><highlight class="normal"></highlight></codeline>
<codeline lineno="17"><highlight class="normal"></highlight></codeline>
<codeline lineno="22"><highlight class="normal"></highlight></codeline>
<codeline lineno="49" refid="group__up__cofold_1ga2a7fb78dfbfb00eccf8d79f38e3384c3" refkind="member"><highlight class="normal"><ref refid="structpu__contrib" kindref="compound">pu_contrib</ref><sp/>*<ref refid="group__up__cofold_1ga2a7fb78dfbfb00eccf8d79f38e3384c3" kindref="member">pf_unstru</ref>(</highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>*sequence,</highlight></codeline>
<codeline lineno="50"><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/>max_w);</highlight></codeline>
<codeline lineno="51"><highlight class="normal"></highlight></codeline>
<codeline lineno="94" refid="group__up__cofold_1ga5adcc9222fe42d943e407e79a3f4558d" refkind="member"><highlight class="normal"><ref refid="structinteract" kindref="compound">interact</ref><sp/>*<ref refid="group__up__cofold_1ga5adcc9222fe42d943e407e79a3f4558d" kindref="member">pf_interact</ref>(</highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>*s1,</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/></highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>*s2,</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/><ref refid="structpu__contrib" kindref="compound">pu_contrib</ref><sp/>*p_c,</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/><ref refid="structpu__contrib" kindref="compound">pu_contrib</ref><sp/>*p_c2,</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/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>max_w,</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/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>*cstruc,</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/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>incr3,</highlight></codeline>
<codeline lineno="101"><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/>incr5);</highlight></codeline>
<codeline lineno="102"><highlight class="normal"></highlight></codeline>
<codeline lineno="106" refid="group__up__cofold_1gadde308fd5f696dc271b1532aa96fd12f" refkind="member"><highlight class="normal"></highlight><highlight class="keywordtype">void</highlight><highlight class="normal"><sp/><ref refid="group__up__cofold_1gadde308fd5f696dc271b1532aa96fd12f" kindref="member">free_interact</ref>(<ref refid="structinteract" kindref="compound">interact</ref><sp/>*pin);</highlight></codeline>
<codeline lineno="107"><highlight class="normal"></highlight></codeline>
<codeline lineno="111"><highlight class="normal"></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>Up_plot(<ref refid="structpu__contrib" kindref="compound">pu_contrib</ref><sp/>*p_c,</highlight></codeline>
<codeline lineno="112"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><ref refid="structpu__contrib" kindref="compound">pu_contrib</ref><sp/>*p_c_sh,</highlight></codeline>
<codeline lineno="113"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><ref refid="structinteract" kindref="compound">interact</ref><sp/>*pint,</highlight></codeline>
<codeline lineno="114"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>*ofile,</highlight></codeline>
<codeline lineno="115"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>**unpaired_values,</highlight></codeline>
<codeline lineno="116"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>*select_contrib,</highlight></codeline>
<codeline lineno="117"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>*head,</highlight></codeline>
<codeline lineno="118"><highlight class="normal"><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">int</highlight><highlight class="normal"><sp/>mode);</highlight></codeline>
<codeline lineno="119"><highlight class="normal"></highlight></codeline>
<codeline lineno="123"><highlight class="normal"><ref refid="structpu__contrib" kindref="compound">pu_contrib</ref><sp/><sp/>*get_pu_contrib_struct(<sp/></highlight><highlight class="keywordtype">unsigned</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>n,</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/><sp/><sp/></highlight><highlight class="keywordtype">unsigned</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>w);</highlight></codeline>
<codeline lineno="125"><highlight class="normal"></highlight></codeline>
<codeline lineno="129" refid="group__up__cofold_1gac20bd61824981d45ce0dc9934aa56df8" refkind="member"><highlight class="normal"></highlight><highlight class="keywordtype">void</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><ref refid="group__up__cofold_1gac20bd61824981d45ce0dc9934aa56df8" kindref="member">free_pu_contrib_struct</ref>(<ref refid="structpu__contrib" kindref="compound">pu_contrib</ref><sp/>*pu);</highlight></codeline>
<codeline lineno="130"><highlight class="normal"></highlight></codeline>
<codeline lineno="131"><highlight class="normal"></highlight><highlight class="keywordtype">void</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="132"><highlight class="normal">free_pu_contrib(<ref refid="structpu__contrib" kindref="compound">pu_contrib</ref><sp/>*pu);</highlight></codeline>
<codeline lineno="133"><highlight class="normal"></highlight></codeline>
<codeline lineno="137"><highlight class="normal"></highlight></codeline>
<codeline lineno="138"><highlight class="normal"></highlight><highlight class="preprocessor">#endif</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="139"><highlight class="normal"></highlight></codeline>
<codeline lineno="140"><highlight class="normal"></highlight><highlight class="preprocessor">#endif</highlight></codeline>
    </programlisting>
    <location file="ViennaRNA/part_func_up.h"/>
  </compounddef>
</doxygen>
