<?xml version='1.0' encoding='UTF-8' standalone='no'?>
<doxygen xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:noNamespaceSchemaLocation="compound.xsd" version="1.15.0" xml:lang="en-US">
  <compounddef id="distance__measures_8dox" kind="file" language="C++">
    <compoundname>distance_measures.dox</compoundname>
    <briefdescription>
    </briefdescription>
    <detaileddescription>
    </detaileddescription>
    <programlisting>
<codeline lineno="1"><highlight class="normal"></highlight></codeline>
<codeline lineno="44"><highlight class="normal"><sp/><sp/><sp/>{<sp/><sp/><sp/>0,<sp/><sp/><sp/>2,<sp/><sp/><sp/>2,<sp/><sp/><sp/>2,<sp/><sp/><sp/>2,<sp/><sp/><sp/>1,<sp/><sp/><sp/>1},<sp/><sp/><sp/></highlight><highlight class="comment">/*<sp/>Null<sp/>replaced<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="45"><highlight class="normal"><sp/><sp/><sp/>{<sp/><sp/><sp/>2,<sp/><sp/><sp/>0,<sp/><sp/><sp/>2,<sp/><sp/><sp/>2,<sp/><sp/><sp/>2,<sp/>INF,<sp/>INF},<sp/><sp/><sp/></highlight><highlight class="comment">/*<sp/>H<sp/><sp/><sp/><sp/>replaced<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="46"><highlight class="normal"><sp/><sp/><sp/>{<sp/><sp/><sp/>2,<sp/><sp/><sp/>2,<sp/><sp/><sp/>0,<sp/><sp/><sp/>1,<sp/><sp/><sp/>2,<sp/>INF,<sp/>INF},<sp/><sp/><sp/></highlight><highlight class="comment">/*<sp/>B<sp/><sp/><sp/><sp/>replaced<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="47"><highlight class="normal"><sp/><sp/><sp/>{<sp/><sp/><sp/>2,<sp/><sp/><sp/>2,<sp/><sp/><sp/>1,<sp/><sp/><sp/>0,<sp/><sp/><sp/>2,<sp/>INF,<sp/>INF},<sp/><sp/><sp/></highlight><highlight class="comment">/*<sp/>I<sp/><sp/><sp/><sp/>replaced<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="48"><highlight class="normal"><sp/><sp/><sp/>{<sp/><sp/><sp/>2,<sp/><sp/><sp/>2,<sp/><sp/><sp/>2,<sp/><sp/><sp/>2,<sp/><sp/><sp/>0,<sp/>INF,<sp/>INF},<sp/><sp/><sp/></highlight><highlight class="comment">/*<sp/>M<sp/><sp/><sp/><sp/>replaced<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="49"><highlight class="normal"><sp/><sp/><sp/>{<sp/><sp/><sp/>1,<sp/>INF,<sp/>INF,<sp/>INF,<sp/>INF,<sp/><sp/><sp/>0,<sp/>INF},<sp/><sp/><sp/></highlight><highlight class="comment">/*<sp/>S<sp/><sp/><sp/><sp/>replaced<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="50"><highlight class="normal"><sp/><sp/><sp/>{<sp/><sp/><sp/>1,<sp/>INF,<sp/>INF,<sp/>INF,<sp/>INF,<sp/>INF,<sp/><sp/><sp/>0},<sp/><sp/><sp/></highlight><highlight class="comment">/*<sp/>E<sp/><sp/><sp/><sp/>replaced<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="51"><highlight class="normal"></highlight></codeline>
<codeline lineno="52"><highlight class="normal"></highlight></codeline>
<codeline lineno="53"><highlight class="normal"></highlight><highlight class="comment">/*<sp/>Null,<sp/><sp/><sp/>H,<sp/><sp/><sp/>B,<sp/><sp/><sp/>I,<sp/><sp/><sp/>M,<sp/><sp/><sp/>S,<sp/><sp/><sp/>E<sp/><sp/><sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="54"><highlight class="normal"><sp/><sp/><sp/>{<sp/><sp/><sp/>0,<sp/>100,<sp/><sp/><sp/>5,<sp/><sp/><sp/>5,<sp/><sp/>75,<sp/><sp/><sp/>5,<sp/><sp/><sp/>5},<sp/><sp/><sp/></highlight><highlight class="comment">/*<sp/>Null<sp/>replaced<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="55"><highlight class="normal"><sp/><sp/><sp/>{<sp/>100,<sp/><sp/><sp/>0,<sp/><sp/><sp/>8,<sp/><sp/><sp/>8,<sp/><sp/><sp/>8,<sp/>INF,<sp/>INF},<sp/><sp/><sp/></highlight><highlight class="comment">/*<sp/>H<sp/><sp/><sp/><sp/>replaced<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="56"><highlight class="normal"><sp/><sp/><sp/>{<sp/><sp/><sp/>5,<sp/><sp/><sp/>8,<sp/><sp/><sp/>0,<sp/><sp/><sp/>3,<sp/><sp/><sp/>8,<sp/>INF,<sp/>INF},<sp/><sp/><sp/></highlight><highlight class="comment">/*<sp/>B<sp/><sp/><sp/><sp/>replaced<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="57"><highlight class="normal"><sp/><sp/><sp/>{<sp/><sp/><sp/>5,<sp/><sp/><sp/>8,<sp/><sp/><sp/>3,<sp/><sp/><sp/>0,<sp/><sp/><sp/>8,<sp/>INF,<sp/>INF},<sp/><sp/><sp/></highlight><highlight class="comment">/*<sp/>I<sp/><sp/><sp/><sp/>replaced<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="58"><highlight class="normal"><sp/><sp/><sp/>{<sp/><sp/>75,<sp/><sp/><sp/>8,<sp/><sp/><sp/>8,<sp/><sp/><sp/>8,<sp/><sp/><sp/>0,<sp/>INF,<sp/>INF},<sp/><sp/><sp/></highlight><highlight class="comment">/*<sp/>M<sp/><sp/><sp/><sp/>replaced<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="59"><highlight class="normal"><sp/><sp/><sp/>{<sp/><sp/><sp/>5,<sp/>INF,<sp/>INF,<sp/>INF,<sp/>INF,<sp/><sp/><sp/>0,<sp/>INF},<sp/><sp/><sp/></highlight><highlight class="comment">/*<sp/>S<sp/><sp/><sp/><sp/>replaced<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="60"><highlight class="normal"><sp/><sp/><sp/>{<sp/><sp/><sp/>5,<sp/>INF,<sp/>INF,<sp/>INF,<sp/>INF,<sp/>INF,<sp/><sp/><sp/>0},<sp/><sp/><sp/></highlight><highlight class="comment">/*<sp/>E<sp/><sp/><sp/><sp/>replaced<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="61"><highlight class="normal"></highlight><highlight class="keyword">@end</highlight><highlight class="normal">verbatim</highlight></codeline>
<codeline lineno="62"><highlight class="normal"></highlight></codeline>
<codeline lineno="63"><highlight class="normal">The<sp/>lower<sp/>matrix<sp/>uses<sp/>the<sp/>costs<sp/>given<sp/>in<sp/>@rstinline<sp/>:cite:t:`shapiro:1990`<sp/></highlight><highlight class="keyword">@end</highlight><highlight class="normal">rst.</highlight></codeline>
<codeline lineno="64"><highlight class="normal">All<sp/>distance<sp/>functions<sp/>use<sp/>the<sp/>following<sp/>global<sp/>variables:</highlight></codeline>
<codeline lineno="65"><highlight class="normal"></highlight></codeline>
<codeline lineno="66"><highlight class="normal">@verbatim</highlight></codeline>
<codeline lineno="67"><highlight class="normal"></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><ref refid="dist__vars_8h_1ab65d8ff14c6937612212526a60f59b3c" kindref="member">cost_matrix</ref>;</highlight></codeline>
<codeline lineno="68"><highlight class="normal"></highlight><highlight class="keyword">@end</highlight><highlight class="normal">verbatim</highlight></codeline>
<codeline lineno="69"><highlight class="normal">@copybrief<sp/><ref refid="dist__vars_8h_1ab65d8ff14c6937612212526a60f59b3c" kindref="member">cost_matrix</ref></highlight></codeline>
<codeline lineno="70"><highlight class="normal"></highlight></codeline>
<codeline lineno="71"><highlight class="normal">@verbatim</highlight></codeline>
<codeline lineno="72"><highlight class="normal"></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><ref refid="dist__vars_8h_1aa03194c513af6b860e7b33e370b82bdb" kindref="member">edit_backtrack</ref>;</highlight></codeline>
<codeline lineno="73"><highlight class="normal"></highlight><highlight class="keyword">@end</highlight><highlight class="normal">verbatim</highlight></codeline>
<codeline lineno="74"><highlight class="normal">@copybrief<sp/><ref refid="dist__vars_8h_1aa03194c513af6b860e7b33e370b82bdb" kindref="member">edit_backtrack</ref></highlight></codeline>
<codeline lineno="75"><highlight class="normal"></highlight></codeline>
<codeline lineno="76"><highlight class="normal">@verbatim</highlight></codeline>
<codeline lineno="77"><highlight class="normal"></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>*<ref refid="dist__vars_8h_1ac1605fe3448ad0a0b809c4fb8f6a854a" kindref="member">aligned_line</ref>[4];</highlight></codeline>
<codeline lineno="78"><highlight class="normal"></highlight><highlight class="keyword">@end</highlight><highlight class="normal">verbatim</highlight></codeline>
<codeline lineno="79"><highlight class="normal">@copybrief<sp/><ref refid="dist__vars_8h_1ac1605fe3448ad0a0b809c4fb8f6a854a" kindref="member">aligned_line</ref></highlight></codeline>
<codeline lineno="80"><highlight class="normal"></highlight></codeline>
<codeline lineno="81"><highlight class="normal">@see<sp/>utils.h,<sp/>dist_vars.h<sp/>and<sp/>stringdist.h<sp/></highlight><highlight class="keywordflow">for</highlight><highlight class="normal"><sp/>more<sp/>details</highlight></codeline>
<codeline lineno="82"><highlight class="normal"></highlight></codeline>
<codeline lineno="83"><highlight class="normal">@section<sp/><sp/>sec_tree_edit_distance<sp/><sp/>Functions<sp/></highlight><highlight class="keywordflow">for</highlight><highlight class="normal"><sp/><ref refid="structTree" kindref="compound">Tree</ref><sp/>Edit<sp/>Distances</highlight></codeline>
<codeline lineno="84"><highlight class="normal"></highlight></codeline>
<codeline lineno="85"><highlight class="normal">@verbatim</highlight></codeline>
<codeline lineno="86"><highlight class="normal"><ref refid="structTree" kindref="compound">Tree</ref><sp/><sp/><sp/>*<ref refid="treedist_8h_1a0991c4fa794283a70c1bef0d626d5721" kindref="member">make_tree</ref><sp/>(</highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>*struc)</highlight></codeline>
<codeline lineno="87"><highlight class="normal"></highlight><highlight class="keyword">@end</highlight><highlight class="normal">verbatim</highlight></codeline>
<codeline lineno="88"><highlight class="normal">@copybrief<sp/><ref refid="treedist_8h_1a0991c4fa794283a70c1bef0d626d5721" kindref="member">make_tree</ref>()</highlight></codeline>
<codeline lineno="89"><highlight class="normal"></highlight></codeline>
<codeline lineno="90"><highlight class="normal">@verbatim</highlight></codeline>
<codeline lineno="91"><highlight class="normal"></highlight><highlight class="keywordtype">float</highlight><highlight class="normal"><sp/><sp/><sp/><ref refid="treedist_8h_1a3b21f1925f7071f46d93431a835217bb" kindref="member">tree_edit_distance</ref><sp/>(<ref refid="structTree" kindref="compound">Tree</ref><sp/>*T1,</highlight></codeline>
<codeline lineno="92"><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/><ref refid="structTree" kindref="compound">Tree</ref><sp/>*T2)<sp/></highlight></codeline>
<codeline lineno="93"><highlight class="normal"></highlight><highlight class="keyword">@end</highlight><highlight class="normal">verbatim</highlight></codeline>
<codeline lineno="94"><highlight class="normal">@copybrief<sp/><ref refid="treedist_8h_1a3b21f1925f7071f46d93431a835217bb" kindref="member">tree_edit_distance</ref>()</highlight></codeline>
<codeline lineno="95"><highlight class="normal"></highlight></codeline>
<codeline lineno="96"><highlight class="normal">@verbatim</highlight></codeline>
<codeline lineno="97"><highlight class="normal"></highlight><highlight class="keywordtype">void</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><ref refid="treedist_8h_1acbc1cb9bce582ea945e4a467c76a57aa" kindref="member">free_tree</ref>(<ref refid="structTree" kindref="compound">Tree</ref><sp/>*t)</highlight></codeline>
<codeline lineno="98"><highlight class="normal"></highlight><highlight class="keyword">@end</highlight><highlight class="normal">verbatim</highlight></codeline>
<codeline lineno="99"><highlight class="normal">@copybrief<sp/><ref refid="treedist_8h_1acbc1cb9bce582ea945e4a467c76a57aa" kindref="member">free_tree</ref>()</highlight></codeline>
<codeline lineno="100"><highlight class="normal"></highlight></codeline>
<codeline lineno="101"><highlight class="normal">@see<sp/>dist_vars.h<sp/>and<sp/>treedist.h<sp/></highlight><highlight class="keywordflow">for</highlight><highlight class="normal"><sp/>prototypes<sp/>and<sp/>more<sp/>detailed<sp/>descriptions</highlight></codeline>
<codeline lineno="102"><highlight class="normal"></highlight></codeline>
<codeline lineno="103"><highlight class="normal">@section<sp/><sp/>sec_string_alignment<sp/><sp/>Functions<sp/></highlight><highlight class="keywordflow">for</highlight><highlight class="normal"><sp/>String<sp/>Alignment</highlight></codeline>
<codeline lineno="104"><highlight class="normal"></highlight></codeline>
<codeline lineno="105"><highlight class="normal">@verbatim</highlight></codeline>
<codeline lineno="106"><highlight class="normal"><ref refid="structswString" kindref="compound">swString</ref><sp/>*<ref refid="stringdist_8h_1a3d651eb191423401b816d0f0639d42c2" kindref="member">Make_swString</ref><sp/>(</highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>*</highlight><highlight class="keywordtype">string</highlight><highlight class="normal">)</highlight></codeline>
<codeline lineno="107"><highlight class="normal"></highlight><highlight class="keyword">@end</highlight><highlight class="normal">verbatim</highlight></codeline>
<codeline lineno="108"><highlight class="normal">@copybrief<sp/><ref refid="stringdist_8h_1a3d651eb191423401b816d0f0639d42c2" kindref="member">Make_swString</ref>()</highlight></codeline>
<codeline lineno="109"><highlight class="normal"></highlight></codeline>
<codeline lineno="110"><highlight class="normal">@verbatim</highlight></codeline>
<codeline lineno="111"><highlight class="normal"></highlight><highlight class="keywordtype">float</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><ref refid="stringdist_8h_1a89e3c335ef17780576d7c0e713830db9" kindref="member">string_edit_distance</ref><sp/>(<ref refid="structswString" kindref="compound">swString</ref><sp/>*T1,</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/><ref refid="structswString" kindref="compound">swString</ref><sp/>*T2)</highlight></codeline>
<codeline lineno="113"><highlight class="normal"></highlight><highlight class="keyword">@end</highlight><highlight class="normal">verbatim</highlight></codeline>
<codeline lineno="114"><highlight class="normal">@copybrief<sp/><ref refid="stringdist_8h_1a89e3c335ef17780576d7c0e713830db9" kindref="member">string_edit_distance</ref>()</highlight></codeline>
<codeline lineno="115"><highlight class="normal"></highlight></codeline>
<codeline lineno="116"><highlight class="normal">@see<sp/>dist_vars.h<sp/>and<sp/>stringdist.h<sp/></highlight><highlight class="keywordflow">for</highlight><highlight class="normal"><sp/>prototypes<sp/>and<sp/>more<sp/>detailed<sp/>descriptions</highlight></codeline>
<codeline lineno="117"><highlight class="normal"></highlight></codeline>
<codeline lineno="118"><highlight class="normal">@section<sp/>sec_compare_base_pair_probs<sp/><sp/>Functions<sp/></highlight><highlight class="keywordflow">for</highlight><highlight class="normal"><sp/>Comparison<sp/>of<sp/>Base<sp/>Pair<sp/>Probabilities</highlight></codeline>
<codeline lineno="119"><highlight class="normal"></highlight></codeline>
<codeline lineno="120"><highlight class="normal">For<sp/>comparison<sp/>of<sp/>base<sp/>pair<sp/>probability<sp/>matrices,<sp/>the<sp/>matrices<sp/>are<sp/>first</highlight></codeline>
<codeline lineno="121"><highlight class="normal">condensed<sp/>into<sp/>probability<sp/>profiles<sp/>which<sp/>are<sp/>the<sp/>compared<sp/>by<sp/>alignment.</highlight></codeline>
<codeline lineno="122"><highlight class="normal"></highlight></codeline>
<codeline lineno="123"><highlight class="normal">@verbatim</highlight></codeline>
<codeline lineno="124"><highlight class="normal"></highlight><highlight class="keywordtype">float</highlight><highlight class="normal"><sp/>*<ref refid="profiledist_8h_1a512ae37eed5828cc1cd3fcb9ce2326a2" kindref="member">Make_bp_profile_bppm</ref><sp/>(<sp/></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/>*bppm,</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/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>length)</highlight></codeline>
<codeline lineno="126"><highlight class="normal"></highlight><highlight class="keyword">@end</highlight><highlight class="normal">verbatim</highlight></codeline>
<codeline lineno="127"><highlight class="normal">@copybrief<sp/><ref refid="profiledist_8h_1a512ae37eed5828cc1cd3fcb9ce2326a2" kindref="member">Make_bp_profile_bppm</ref>()</highlight></codeline>
<codeline lineno="128"><highlight class="normal"></highlight></codeline>
<codeline lineno="129"><highlight class="normal">@verbatim</highlight></codeline>
<codeline lineno="130"><highlight class="normal"></highlight><highlight class="keywordtype">float</highlight><highlight class="normal"><sp/><ref refid="profiledist_8h_1abe75e90e00a1e5dd8862944ed53dad5d" kindref="member">profile_edit_distance</ref><sp/>(<sp/></highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">float</highlight><highlight class="normal"><sp/>*T1,</highlight></codeline>
<codeline lineno="131"><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/></highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">float</highlight><highlight class="normal"><sp/>*T2)</highlight></codeline>
<codeline lineno="132"><highlight class="normal"></highlight><highlight class="keyword">@end</highlight><highlight class="normal">verbatim</highlight></codeline>
<codeline lineno="133"><highlight class="normal">@copybrief<sp/><ref refid="profiledist_8h_1abe75e90e00a1e5dd8862944ed53dad5d" kindref="member">profile_edit_distance</ref>()</highlight></codeline>
<codeline lineno="134"><highlight class="normal"></highlight></codeline>
<codeline lineno="135"><highlight class="normal">@see<sp/>ProfileDist.h<sp/></highlight><highlight class="keywordflow">for</highlight><highlight class="normal"><sp/>prototypes<sp/>and<sp/>more<sp/>details<sp/>of<sp/>the<sp/>above<sp/>functions</highlight></codeline>
<codeline lineno="136"><highlight class="normal"></highlight></codeline>
<codeline lineno="137"><highlight class="normal">*/</highlight></codeline>
    </programlisting>
    <location file="doc/doxygen/refman.include/distance_measures.dox"/>
  </compounddef>
</doxygen>
