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<codeline lineno="1"><highlight class="preprocessor">#ifndef<sp/>VIENNA_RNA_PACKAGE_SEQUENCES_MSA_H</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="2"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VIENNA_RNA_PACKAGE_SEQUENCES_MSA_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">#ifdef<sp/>VRNA_WARN_DEPRECATED</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="5"><highlight class="normal"></highlight><highlight class="preprocessor">#<sp/>if<sp/>defined(__clang__)</highlight><highlight class="normal"></highlight></codeline>
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<codeline lineno="8"><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>
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<codeline lineno="15"><highlight class="normal"></highlight></codeline>
<codeline lineno="21"><highlight class="normal"></highlight></codeline>
<codeline lineno="26"><highlight class="normal"></highlight></codeline>
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<codeline lineno="29"><highlight class="normal"></highlight></codeline>
<codeline lineno="30"><highlight class="normal"></highlight></codeline>
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<codeline lineno="35"><highlight class="normal"></highlight></codeline>
<codeline lineno="36"><highlight class="normal"></highlight></codeline>
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<codeline lineno="41"><highlight class="normal"></highlight></codeline>
<codeline lineno="42"><highlight class="normal"></highlight></codeline>
<codeline lineno="46" refid="group__aln__utils_1ga36affc310a5adedf1bdbf9669dd4bf85" refkind="member"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VRNA_ALN_DNA<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>2U</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="47"><highlight class="normal"></highlight></codeline>
<codeline lineno="48"><highlight class="normal"></highlight></codeline>
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<codeline lineno="53"><highlight class="normal"></highlight></codeline>
<codeline lineno="54"><highlight class="normal"></highlight></codeline>
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<codeline lineno="59"><highlight class="normal"></highlight></codeline>
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<codeline lineno="66"><highlight class="normal"></highlight></codeline>
<codeline lineno="67"><highlight class="normal"></highlight><highlight class="preprocessor">#ifndef<sp/>VRNA_DISABLE_BACKWARD_COMPATIBILITY</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="68"><highlight class="normal"></highlight></codeline>
<codeline lineno="69"><highlight class="normal"></highlight><highlight class="comment">/*<sp/>the<sp/>following<sp/>typedefs<sp/>are<sp/>for<sp/>backward<sp/>compatibility<sp/>only<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="70"><highlight class="normal"></highlight></codeline>
<codeline lineno="76" refid="group__aln__utils__deprecated_1ga7b61662a793ad0aa1ea38efc3a5baacc" refkind="member"><highlight class="normal"></highlight><highlight class="keyword">typedef</highlight><highlight class="normal"><sp/></highlight><highlight class="keyword">struct<sp/></highlight><highlight class="normal"><ref refid="structvrna__pinfo__s" kindref="compound">vrna_pinfo_s</ref><sp/><ref refid="group__aln__utils__deprecated_1ga7b61662a793ad0aa1ea38efc3a5baacc" kindref="member">pair_info</ref>;</highlight></codeline>
<codeline lineno="77"><highlight class="normal"></highlight></codeline>
<codeline lineno="78"><highlight class="normal"></highlight><highlight class="preprocessor">#endif</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="79"><highlight class="normal"></highlight></codeline>
<codeline lineno="80"><highlight class="normal"></highlight><highlight class="preprocessor">#include<sp/>&lt;<ref refid="fold__compound_8h" kindref="compound">ViennaRNA/fold_compound.h</ref>&gt;</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="81"><highlight class="normal"></highlight><highlight class="preprocessor">#include<sp/>&lt;<ref refid="model_8h" kindref="compound">ViennaRNA/model.h</ref>&gt;</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="82"><highlight class="normal"></highlight></codeline>
<codeline lineno="93" refid="structvrna__pinfo__s" refkind="compound"><highlight class="normal"></highlight><highlight class="keyword">struct<sp/></highlight><highlight class="normal"><ref refid="structvrna__pinfo__s" kindref="compound">vrna_pinfo_s</ref><sp/>{</highlight></codeline>
<codeline lineno="94" refid="structvrna__pinfo__s_1ab91db0a87ef8402dc151795ba5a64c6f" refkind="member"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">unsigned</highlight><highlight class="normal"><sp/><sp/><ref refid="structvrna__pinfo__s_1ab91db0a87ef8402dc151795ba5a64c6f" kindref="member">i</ref>;<sp/><sp/><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="95" refid="structvrna__pinfo__s_1a4142e38d6ba127acccdf680300a88e1f" refkind="member"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">unsigned</highlight><highlight class="normal"><sp/><sp/><ref refid="structvrna__pinfo__s_1a4142e38d6ba127acccdf680300a88e1f" kindref="member">j</ref>;<sp/><sp/><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="96" refid="structvrna__pinfo__s_1a71990eae41fa100db8b557e4512ec281" refkind="member"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">float</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><ref refid="structvrna__pinfo__s_1a71990eae41fa100db8b557e4512ec281" kindref="member">p</ref>;<sp/><sp/><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="97" refid="structvrna__pinfo__s_1a5ab2a63f3da8e12c6d54d8e9dd9e3e73" refkind="member"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">float</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><ref refid="structvrna__pinfo__s_1a5ab2a63f3da8e12c6d54d8e9dd9e3e73" kindref="member">ent</ref>;<sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="98" refid="structvrna__pinfo__s_1aa5feac5559b36dcd7cb38111c45d444d" refkind="member"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">short</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><ref refid="structvrna__pinfo__s_1aa5feac5559b36dcd7cb38111c45d444d" kindref="member">bp</ref>[8];<sp/><sp/></highlight></codeline>
<codeline lineno="99" refid="structvrna__pinfo__s_1a0720ae74ce53802a759ee9f98e9c8c43" refkind="member"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><ref refid="structvrna__pinfo__s_1a0720ae74ce53802a759ee9f98e9c8c43" kindref="member">comp</ref>;<sp/><sp/><sp/></highlight></codeline>
<codeline lineno="100"><highlight class="normal">};</highlight></codeline>
<codeline lineno="101"><highlight class="normal"></highlight></codeline>
<codeline lineno="102"><highlight class="normal"></highlight></codeline>
<codeline lineno="109"><highlight class="normal"></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="110" refid="group__aln__utils_1gade5a1f2d16e7fd9a57b37d8514f08e8e" refkind="member"><highlight class="normal"><ref refid="group__aln__utils_1gade5a1f2d16e7fd9a57b37d8514f08e8e" kindref="member">vrna_aln_mpi</ref>(</highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>**alignment);</highlight></codeline>
<codeline lineno="111"><highlight class="normal"></highlight></codeline>
<codeline lineno="112"><highlight class="normal"></highlight></codeline>
<codeline lineno="126"><highlight class="normal"><ref refid="group__aln__utils_1ga6660dfca23debee7306e0cd53341263f" kindref="member">vrna_pinfo_t</ref><sp/>*</highlight></codeline>
<codeline lineno="127" refid="group__aln__utils_1gaac78a02d9939e68d570ff296547ff519" refkind="member"><highlight class="normal"><ref refid="group__aln__utils_1gaac78a02d9939e68d570ff296547ff519" kindref="member">vrna_aln_pinfo</ref>(<ref refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" kindref="member">vrna_fold_compound_t</ref><sp/>*fc,</highlight></codeline>
<codeline lineno="128"><highlight class="normal"><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*structure,</highlight></codeline>
<codeline lineno="129"><highlight class="normal"><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/><sp/><sp/><sp/>threshold);</highlight></codeline>
<codeline lineno="130"><highlight class="normal"></highlight></codeline>
<codeline lineno="131"><highlight class="normal"></highlight></codeline>
<codeline lineno="132"><highlight class="normal"></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>*</highlight></codeline>
<codeline lineno="133" refid="group__aln__utils_1ga697bf6f44356918cceeff4ed8ee885e1" refkind="member"><highlight class="normal"><ref refid="group__aln__utils_1ga697bf6f44356918cceeff4ed8ee885e1" kindref="member">vrna_aln_pscore</ref>(</highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/><sp/>**alignment,</highlight></codeline>
<codeline lineno="134"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><ref refid="group__model__details_1ga1f8a10e12a0a1915f2a4eff0b28ea17c" kindref="member">vrna_md_t</ref><sp/><sp/><sp/>*md);</highlight></codeline>
<codeline lineno="135"><highlight class="normal"></highlight></codeline>
<codeline lineno="136"><highlight class="normal"></highlight></codeline>
<codeline lineno="137"><highlight class="normal"></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="138"><highlight class="normal">vrna_pscore(<ref refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" kindref="member">vrna_fold_compound_t</ref><sp/><sp/>*fc,</highlight></codeline>
<codeline lineno="139"><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>i,</highlight></codeline>
<codeline lineno="140"><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>j);</highlight></codeline>
<codeline lineno="141"><highlight class="normal"></highlight></codeline>
<codeline lineno="142"><highlight class="normal"></highlight></codeline>
<codeline lineno="143"><highlight class="normal"></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="144"><highlight class="normal">vrna_pscore_freq(<ref refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" kindref="member">vrna_fold_compound_t</ref><sp/>*fc,</highlight></codeline>
<codeline lineno="145"><highlight class="normal"><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">unsigned</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/>*frequencies,</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/></highlight><highlight class="keywordtype">unsigned</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><ref refid="group__struct__utils__deprecated_1ga6341cbb704924824e0236c1dce791032" kindref="member">pairs</ref>);</highlight></codeline>
<codeline lineno="147"><highlight class="normal"></highlight></codeline>
<codeline lineno="161"><highlight class="normal"></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>**</highlight></codeline>
<codeline lineno="162" refid="group__aln__utils_1gaab40cf1f120da37ffe2e80ae9d91815f" refkind="member"><highlight class="normal"><ref refid="group__aln__utils_1gaab40cf1f120da37ffe2e80ae9d91815f" kindref="member">vrna_aln_slice</ref>(</highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/><sp/><sp/>**alignment,</highlight></codeline>
<codeline lineno="163"><highlight class="normal"><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/>i,</highlight></codeline>
<codeline lineno="164"><highlight class="normal"><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/>j);</highlight></codeline>
<codeline lineno="165"><highlight class="normal"></highlight></codeline>
<codeline lineno="166"><highlight class="normal"></highlight></codeline>
<codeline lineno="172"><highlight class="normal"></highlight><highlight class="keywordtype">void</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="173" refid="group__aln__utils_1gac00dc80b8a324f151f92f11ab6850ecf" refkind="member"><highlight class="normal"><ref refid="group__aln__utils_1gac00dc80b8a324f151f92f11ab6850ecf" kindref="member">vrna_aln_free</ref>(</highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>**alignment);</highlight></codeline>
<codeline lineno="174"><highlight class="normal"></highlight></codeline>
<codeline lineno="175"><highlight class="normal"></highlight></codeline>
<codeline lineno="184"><highlight class="normal"></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>**</highlight></codeline>
<codeline lineno="185" refid="group__aln__utils_1gae78fb593225fc9c82e5a28c7c76e0e40" refkind="member"><highlight class="normal"><ref refid="group__aln__utils_1gae78fb593225fc9c82e5a28c7c76e0e40" kindref="member">vrna_aln_uppercase</ref>(</highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>**alignment);</highlight></codeline>
<codeline lineno="186"><highlight class="normal"></highlight></codeline>
<codeline lineno="187"><highlight class="normal"></highlight></codeline>
<codeline lineno="196"><highlight class="normal"></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>**</highlight></codeline>
<codeline lineno="197" refid="group__aln__utils_1gab64cc5d5d6672a1213f6442bd766a726" refkind="member"><highlight class="normal"><ref refid="group__aln__utils_1gab64cc5d5d6672a1213f6442bd766a726" kindref="member">vrna_aln_toRNA</ref>(</highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>**alignment);</highlight></codeline>
<codeline lineno="198"><highlight class="normal"></highlight></codeline>
<codeline lineno="199"><highlight class="normal"></highlight></codeline>
<codeline lineno="213"><highlight class="normal"></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>**</highlight></codeline>
<codeline lineno="214" refid="group__aln__utils_1ga31d79a1b1eb8bc5673303efc18461091" refkind="member"><highlight class="normal"><ref refid="group__aln__utils_1ga31d79a1b1eb8bc5673303efc18461091" kindref="member">vrna_aln_copy</ref>(</highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/><sp/><sp/><sp/>**alignment,</highlight></codeline>
<codeline lineno="215"><highlight class="normal"><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/><sp/>options);</highlight></codeline>
<codeline lineno="216"><highlight class="normal"></highlight></codeline>
<codeline lineno="217"><highlight class="normal"></highlight></codeline>
<codeline lineno="232"><highlight class="normal"></highlight><highlight class="keywordtype">float</highlight><highlight class="normal"><sp/>*</highlight></codeline>
<codeline lineno="233" refid="group__aln__utils_1gab6f16a2ea93f3bfd4d089cc8d448bb16" refkind="member"><highlight class="normal"><ref refid="group__aln__utils_1gab6f16a2ea93f3bfd4d089cc8d448bb16" kindref="member">vrna_aln_conservation_struct</ref>(</highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/>**alignment,</highlight></codeline>
<codeline lineno="234"><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/></highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*structure,</highlight></codeline>
<codeline lineno="235"><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/></highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/><ref refid="group__model__details_1ga1f8a10e12a0a1915f2a4eff0b28ea17c" kindref="member">vrna_md_t</ref><sp/><sp/>*md);</highlight></codeline>
<codeline lineno="236"><highlight class="normal"></highlight></codeline>
<codeline lineno="237"><highlight class="normal"></highlight></codeline>
<codeline lineno="255"><highlight class="normal"></highlight><highlight class="keywordtype">float</highlight><highlight class="normal"><sp/>*</highlight></codeline>
<codeline lineno="256" refid="group__aln__utils_1gaa12b481a7e7b965ef2eb1bcc4399e759" refkind="member"><highlight class="normal"><ref refid="group__aln__utils_1gaa12b481a7e7b965ef2eb1bcc4399e759" kindref="member">vrna_aln_conservation_col</ref>(</highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/>**alignment,</highlight></codeline>
<codeline lineno="257"><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/></highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/><ref refid="group__model__details_1ga1f8a10e12a0a1915f2a4eff0b28ea17c" kindref="member">vrna_md_t</ref><sp/>*md_p,</highlight></codeline>
<codeline lineno="258"><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/></highlight><highlight class="keywordtype">unsigned</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/>options);</highlight></codeline>
<codeline lineno="259"><highlight class="normal"></highlight></codeline>
<codeline lineno="260"><highlight class="normal"></highlight></codeline>
<codeline lineno="268"><highlight class="normal"></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>*</highlight></codeline>
<codeline lineno="269" refid="group__aln__utils_1gac6a33fa856d66dcb6f5d40ce0b61d7c7" refkind="member"><highlight class="normal"><ref refid="group__aln__utils_1gac6a33fa856d66dcb6f5d40ce0b61d7c7" kindref="member">vrna_aln_consensus_sequence</ref>(</highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/>**alignment,</highlight></codeline>
<codeline lineno="270"><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/></highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/><ref refid="group__model__details_1ga1f8a10e12a0a1915f2a4eff0b28ea17c" kindref="member">vrna_md_t</ref><sp/>*md_p);</highlight></codeline>
<codeline lineno="271"><highlight class="normal"></highlight></codeline>
<codeline lineno="283"><highlight class="normal"></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>*</highlight></codeline>
<codeline lineno="284" refid="group__aln__utils_1gacd02c66d9e6f8dd5318f4fca0dc76cba" refkind="member"><highlight class="normal"><ref refid="group__aln__utils_1gacd02c66d9e6f8dd5318f4fca0dc76cba" kindref="member">vrna_aln_consensus_mis</ref>(</highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/>**alignment,</highlight></codeline>
<codeline lineno="285"><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/></highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/><ref refid="group__model__details_1ga1f8a10e12a0a1915f2a4eff0b28ea17c" kindref="member">vrna_md_t</ref><sp/><sp/>*md_p);</highlight></codeline>
<codeline lineno="286"><highlight class="normal"></highlight></codeline>
<codeline lineno="287"><highlight class="normal"></highlight></codeline>
<codeline lineno="288"><highlight class="normal"></highlight><highlight class="preprocessor">#ifndef<sp/>VRNA_DISABLE_BACKWARD_COMPATIBILITY</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="289"><highlight class="normal"></highlight></codeline>
<codeline lineno="290"><highlight class="normal"></highlight><highlight class="preprocessor">#include<sp/>&lt;stdio.h&gt;</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="294"><highlight class="normal">DEPRECATED(</highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>read_clustal(FILE<sp/><sp/>*clust,</highlight></codeline>
<codeline lineno="295"><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/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/><sp/>*AlignedSeqs[],</highlight></codeline>
<codeline lineno="296"><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/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/><sp/>*names[]),</highlight></codeline>
<codeline lineno="297"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;Use<sp/>vrna_file_msa_read()<sp/>and<sp/>vrna_file_msa_read_record()<sp/>instead&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="298"><highlight class="normal"></highlight></codeline>
<codeline lineno="299"><highlight class="normal"></highlight></codeline>
<codeline lineno="303"><highlight class="normal">DEPRECATED(</highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>*consensus(</highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>*AS[]),</highlight></codeline>
<codeline lineno="304"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;Use<sp/>vrna_aln_consensus_sequence()<sp/>instead!&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="305"><highlight class="normal"></highlight></codeline>
<codeline lineno="306"><highlight class="normal"></highlight></codeline>
<codeline lineno="310"><highlight class="normal">DEPRECATED(</highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>*consens_mis(</highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>*AS[]),</highlight></codeline>
<codeline lineno="311"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;Use<sp/>vrna_aln_consensus_mis()<sp/>instead!&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="312"><highlight class="normal"></highlight></codeline>
<codeline lineno="313"><highlight class="normal"></highlight></codeline>
<codeline lineno="317"><highlight class="normal">DEPRECATED(</highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>*get_ungapped_sequence(</highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>*seq),</highlight></codeline>
<codeline lineno="318"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;Use<sp/>vrna_seq_ungapped()<sp/>instead!&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="319"><highlight class="normal"></highlight></codeline>
<codeline lineno="320"><highlight class="normal"></highlight></codeline>
<codeline lineno="332"><highlight class="normal">DEPRECATED(</highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><ref refid="group__aln__utils__deprecated_1gaa2d600be90844094ec145ea14a314d2f" kindref="member">get_mpi</ref>(</highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>*Alseq[],</highlight></codeline>
<codeline lineno="333"><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/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/>n_seq,</highlight></codeline>
<codeline lineno="334"><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/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/>length,</highlight></codeline>
<codeline lineno="335"><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/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/>*mini),</highlight></codeline>
<codeline lineno="336" refid="group__aln__utils__deprecated_1gaa2d600be90844094ec145ea14a314d2f" refkind="member"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;Use<sp/>vrna_aln_mpi()<sp/>instead&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="337"><highlight class="normal"></highlight></codeline>
<codeline lineno="338"><highlight class="normal"></highlight><highlight class="comment">/*</highlight></codeline>
<codeline lineno="339"><highlight class="comment"><sp/>#############################################################</highlight></codeline>
<codeline lineno="340"><highlight class="comment"><sp/>#<sp/>some<sp/>helper<sp/>functions<sp/>that<sp/>might<sp/>be<sp/>useful<sp/>in<sp/>the<sp/>library<sp/>#</highlight></codeline>
<codeline lineno="341"><highlight class="comment"><sp/>#############################################################</highlight></codeline>
<codeline lineno="342"><highlight class="comment"><sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="343"><highlight class="normal"></highlight></codeline>
<codeline lineno="359"><highlight class="normal">DEPRECATED(</highlight><highlight class="keywordtype">void</highlight><highlight class="normal"><sp/><ref refid="group__aln__utils__deprecated_1gaa3e40277c837d6f7603afe319884c786" kindref="member">encode_ali_sequence</ref>(</highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/>*sequence,</highlight></codeline>
<codeline lineno="360"><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">short</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*S,</highlight></codeline>
<codeline lineno="361"><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">short</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*s5,</highlight></codeline>
<codeline lineno="362"><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">short</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*s3,</highlight></codeline>
<codeline lineno="363"><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">char</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*ss,</highlight></codeline>
<codeline lineno="364"><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">short</highlight><highlight class="normal"><sp/><sp/>*as,</highlight></codeline>
<codeline lineno="365"><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">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><ref refid="group__model__details_1gaf9202a1a09f5828dc731e2d9a10fa111" kindref="member">circ</ref>),</highlight></codeline>
<codeline lineno="366" refid="group__aln__utils__deprecated_1gaa3e40277c837d6f7603afe319884c786" 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="367"><highlight class="normal"></highlight></codeline>
<codeline lineno="368"><highlight class="normal"></highlight></codeline>
<codeline lineno="385"><highlight class="normal">DEPRECATED(</highlight><highlight class="keywordtype">void</highlight><highlight class="normal"><sp/><sp/><ref refid="group__aln__utils__deprecated_1ga8a560930f7f2582cc3967723a86cfdfa" kindref="member">alloc_sequence_arrays</ref>(</highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/>**sequences,</highlight></codeline>
<codeline lineno="386"><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/></highlight><highlight class="keywordtype">short</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>***S,</highlight></codeline>
<codeline lineno="387"><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/></highlight><highlight class="keywordtype">short</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>***S5,</highlight></codeline>
<codeline lineno="388"><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/></highlight><highlight class="keywordtype">short</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>***S3,</highlight></codeline>
<codeline lineno="389"><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/></highlight><highlight class="keywordtype">unsigned</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">short</highlight><highlight class="normal"><sp/>***a2s,</highlight></codeline>
<codeline lineno="390"><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/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>***Ss,</highlight></codeline>
<codeline lineno="391"><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/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><ref refid="group__model__details_1gaf9202a1a09f5828dc731e2d9a10fa111" kindref="member">circ</ref>),</highlight></codeline>
<codeline lineno="392" refid="group__aln__utils__deprecated_1ga8a560930f7f2582cc3967723a86cfdfa" 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="393"><highlight class="normal"></highlight></codeline>
<codeline lineno="394"><highlight class="normal"></highlight></codeline>
<codeline lineno="410"><highlight class="normal">DEPRECATED(</highlight><highlight class="keywordtype">void</highlight><highlight class="normal"><sp/><sp/><ref refid="group__aln__utils__deprecated_1ga298a420a8c879202e2617b3f724fde38" kindref="member">free_sequence_arrays</ref>(</highlight><highlight class="keywordtype">unsigned</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/>n_seq,</highlight></codeline>
<codeline lineno="411"><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">short</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>***S,</highlight></codeline>
<codeline lineno="412"><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">short</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>***S5,</highlight></codeline>
<codeline lineno="413"><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">short</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>***S3,</highlight></codeline>
<codeline lineno="414"><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">unsigned</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">short</highlight><highlight class="normal"><sp/><sp/>***a2s,</highlight></codeline>
<codeline lineno="415"><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">char</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>***Ss),</highlight></codeline>
<codeline lineno="416" refid="group__aln__utils__deprecated_1ga298a420a8c879202e2617b3f724fde38" refkind="member"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;This<sp/>fucntion<sp/>is<sp/>obsolete&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="417"><highlight class="normal"></highlight></codeline>
<codeline lineno="418"><highlight class="normal"></highlight><highlight class="preprocessor">#endif</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="419"><highlight class="normal"></highlight></codeline>
<codeline lineno="423"><highlight class="normal"></highlight></codeline>
<codeline lineno="424"><highlight class="normal"></highlight></codeline>
<codeline lineno="425"><highlight class="normal"></highlight><highlight class="preprocessor">#endif</highlight></codeline>
    </programlisting>
    <location file="ViennaRNA/sequences/alignments.h"/>
  </compounddef>
</doxygen>
