<?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="dist__vars_8h" kind="file" language="C++">
    <compoundname>dist_vars.h</compoundname>
    <includedby refid="stringdist_8h" local="no">ViennaRNA/stringdist.h</includedby>
    <includedby refid="treedist_8h" local="no">ViennaRNA/treedist.h</includedby>
    <invincdepgraph>
      <node id="1">
        <label>ViennaRNA/dist_vars.h</label>
        <link refid="dist__vars_8h"/>
        <childnode refid="2" relation="include">
        </childnode>
        <childnode refid="3" relation="include">
        </childnode>
      </node>
      <node id="2">
        <label>ViennaRNA/stringdist.h</label>
        <link refid="stringdist_8h"/>
      </node>
      <node id="3">
        <label>ViennaRNA/treedist.h</label>
        <link refid="treedist_8h"/>
      </node>
    </invincdepgraph>
    <innerclass refid="structPostorder__list" prot="public">Postorder_list</innerclass>
    <innerclass refid="structTree" prot="public">Tree</innerclass>
    <innerclass refid="structswString" prot="public">swString</innerclass>
    <sectiondef kind="var">
      <memberdef kind="variable" id="dist__vars_8h_1aa03194c513af6b860e7b33e370b82bdb" prot="public" static="no" extern="yes" mutable="no">
        <type>int</type>
        <definition>int edit_backtrack</definition>
        <argsstring></argsstring>
        <name>edit_backtrack</name>
        <briefdescription>
<para>Produce an alignment of the two structures being compared by tracing the editing path giving the minimum distance. </para>
        </briefdescription>
        <detaileddescription>
<para>set to 1 if you want backtracking </para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/dist_vars.h" line="17" column="14" declfile="ViennaRNA/dist_vars.h" declline="17" declcolumn="14"/>
      </memberdef>
      <memberdef kind="variable" id="dist__vars_8h_1ac1605fe3448ad0a0b809c4fb8f6a854a" prot="public" static="no" extern="yes" mutable="no">
        <type>char *</type>
        <definition>char* aligned_line[4]</definition>
        <argsstring>[4]</argsstring>
        <name>aligned_line</name>
        <briefdescription>
<para>Contains the two aligned structures after a call to one of the distance functions with <ref refid="dist__vars_8h_1aa03194c513af6b860e7b33e370b82bdb" kindref="member">edit_backtrack</ref> set to 1. </para>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/dist_vars.h" line="23" column="13" declfile="ViennaRNA/dist_vars.h" declline="23" declcolumn="13"/>
      </memberdef>
      <memberdef kind="variable" id="dist__vars_8h_1ab65d8ff14c6937612212526a60f59b3c" prot="public" static="no" extern="yes" mutable="no">
        <type>int</type>
        <definition>int cost_matrix</definition>
        <argsstring></argsstring>
        <name>cost_matrix</name>
        <briefdescription>
<para>Specify the cost matrix to be used for distance calculations. </para>
        </briefdescription>
        <detaileddescription>
<para>if 0, use the default cost matrix (upper matrix in example), otherwise use Shapiro&apos;s costs (lower matrix). </para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/dist_vars.h" line="31" column="13" declfile="ViennaRNA/dist_vars.h" declline="31" declcolumn="13"/>
      </memberdef>
    </sectiondef>
    <briefdescription>
<para>Global variables for Distance-Package. </para>
    </briefdescription>
    <detaileddescription>
    </detaileddescription>
    <programlisting>
<codeline lineno="1"><highlight class="preprocessor">#ifndef<sp/>VIENNA_RNA_PACKAGE_DIST_VARS_H</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="2"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VIENNA_RNA_PACKAGE_DIST_VARS_H</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="3"><highlight class="normal"></highlight></codeline>
<codeline lineno="8"><highlight class="normal"></highlight></codeline>
<codeline lineno="9"><highlight class="normal"></highlight><highlight class="preprocessor">#ifndef<sp/>VRNA_DISABLE_BACKWARD_COMPATIBILITY</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="10"><highlight class="normal"></highlight></codeline>
<codeline lineno="17"><highlight class="normal"></highlight><highlight class="keyword">extern</highlight><highlight class="normal"><sp/></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="18"><highlight class="normal"></highlight></codeline>
<codeline lineno="23"><highlight class="normal"></highlight><highlight class="keyword">extern</highlight><highlight class="normal"><sp/></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="24"><highlight class="normal"></highlight></codeline>
<codeline lineno="31"><highlight class="normal"></highlight><highlight class="keyword">extern</highlight><highlight class="normal"><sp/></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="32"><highlight class="normal"></highlight></codeline>
<codeline lineno="33"><highlight class="normal"></highlight><highlight class="comment">/*<sp/><sp/>Global<sp/>type<sp/>defs<sp/>for<sp/>Distance-Package<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="34"><highlight class="normal"></highlight></codeline>
<codeline lineno="38" refid="structPostorder__list" refkind="compound"><highlight class="normal"></highlight><highlight class="keyword">typedef</highlight><highlight class="normal"><sp/></highlight><highlight class="keyword">struct<sp/></highlight><highlight class="normal">{</highlight></codeline>
<codeline lineno="39"><highlight class="normal"><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/>type;</highlight></codeline>
<codeline lineno="40"><highlight class="normal"><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/>weight;</highlight></codeline>
<codeline lineno="41"><highlight class="normal"><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/>father;</highlight></codeline>
<codeline lineno="42"><highlight class="normal"><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/>sons;</highlight></codeline>
<codeline lineno="43"><highlight class="normal"><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/>leftmostleaf;</highlight></codeline>
<codeline lineno="44"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>}<sp/><ref refid="structPostorder__list" kindref="compound">Postorder_list</ref>;</highlight></codeline>
<codeline lineno="45"><highlight class="normal"></highlight></codeline>
<codeline lineno="49" refid="structTree" refkind="compound"><highlight class="normal"></highlight><highlight class="keyword">typedef</highlight><highlight class="normal"><sp/></highlight><highlight class="keyword">struct<sp/></highlight><highlight class="normal">{</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/><ref refid="structPostorder__list" kindref="compound">Postorder_list</ref><sp/>*postorder_list;</highlight></codeline>
<codeline lineno="51"><highlight class="normal"><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/>*keyroots;</highlight></codeline>
<codeline lineno="52"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>}<sp/><ref refid="structTree" kindref="compound">Tree</ref>;</highlight></codeline>
<codeline lineno="53"><highlight class="normal"></highlight></codeline>
<codeline lineno="57" refid="structswString" refkind="compound"><highlight class="normal"></highlight><highlight class="keyword">typedef</highlight><highlight class="normal"><sp/></highlight><highlight class="keyword">struct<sp/></highlight><highlight class="normal">{</highlight></codeline>
<codeline lineno="58"><highlight class="normal"><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/>type;</highlight></codeline>
<codeline lineno="59"><highlight class="normal"><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/>sign;</highlight></codeline>
<codeline lineno="60"><highlight class="normal"><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/>weight;</highlight></codeline>
<codeline lineno="61"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>}<sp/><ref refid="structswString" kindref="compound">swString</ref>;</highlight></codeline>
<codeline lineno="62"><highlight class="normal"></highlight><highlight class="preprocessor">#endif</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="63"><highlight class="normal"></highlight></codeline>
<codeline lineno="64"><highlight class="normal"></highlight><highlight class="preprocessor">#endif</highlight></codeline>
    </programlisting>
    <location file="ViennaRNA/dist_vars.h"/>
  </compounddef>
</doxygen>
