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  <compounddef id="ProfileAln_8h" kind="file" language="C++">
    <compoundname>ProfileAln.h</compoundname>
    <sectiondef kind="func">
      <memberdef kind="function" id="ProfileAln_8h_1ad39b2710140d80c59ec6b416c20bf4e3" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>float</type>
        <definition>float profile_aln</definition>
        <argsstring>(const float *T1, const char *seq1, const float *T2, const char *seq2)</argsstring>
        <name>profile_aln</name>
        <param>
          <type>const float *</type>
          <declname>T1</declname>
        </param>
        <param>
          <type>const char *</type>
          <declname>seq1</declname>
        </param>
        <param>
          <type>const float *</type>
          <declname>T2</declname>
        </param>
        <param>
          <type>const char *</type>
          <declname>seq2</declname>
        </param>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/ProfileAln.h" line="4" column="7" declfile="ViennaRNA/ProfileAln.h" declline="4" declcolumn="7"/>
      </memberdef>
      <memberdef kind="function" id="ProfileAln_8h_1abbf75dbd44fe03e514297855b9e4c1e3" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>int</type>
        <definition>int set_paln_params</definition>
        <argsstring>(double gap_open, double gap_ext, double seqweight, int free_ends)</argsstring>
        <name>set_paln_params</name>
        <param>
          <type>double</type>
          <declname>gap_open</declname>
        </param>
        <param>
          <type>double</type>
          <declname>gap_ext</declname>
        </param>
        <param>
          <type>double</type>
          <declname>seqweight</declname>
        </param>
        <param>
          <type>int</type>
          <declname>free_ends</declname>
        </param>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/ProfileAln.h" line="10" column="5" declfile="ViennaRNA/ProfileAln.h" declline="10" declcolumn="5"/>
      </memberdef>
    </sectiondef>
    <briefdescription>
    </briefdescription>
    <detaileddescription>
    </detaileddescription>
    <programlisting>
<codeline lineno="1"><highlight class="preprocessor">#ifndef<sp/>VIENNA_RNA_PACKAGE_PROFILEALN_H</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="2"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VIENNA_RNA_PACKAGE_PROFILEALN_H</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="3"><highlight class="normal"></highlight></codeline>
<codeline lineno="4"><highlight class="normal"></highlight><highlight class="keywordtype">float</highlight><highlight class="normal"><sp/>profile_aln(</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="5"><highlight class="normal"><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/>*seq1,</highlight></codeline>
<codeline lineno="6"><highlight class="normal"><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="7"><highlight class="normal"><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/>*seq2);</highlight></codeline>
<codeline lineno="8"><highlight class="normal"></highlight></codeline>
<codeline lineno="9"><highlight class="normal"></highlight></codeline>
<codeline lineno="10"><highlight class="normal"></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>set_paln_params(</highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/><sp/>gap_open,</highlight></codeline>
<codeline lineno="11"><highlight class="normal"><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/>gap_ext,</highlight></codeline>
<codeline lineno="12"><highlight class="normal"><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/>seqweight,</highlight></codeline>
<codeline lineno="13"><highlight class="normal"><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/>free_ends);</highlight></codeline>
<codeline lineno="14"><highlight class="normal"></highlight></codeline>
<codeline lineno="15"><highlight class="normal"></highlight></codeline>
<codeline lineno="16"><highlight class="normal"></highlight><highlight class="preprocessor">#endif</highlight></codeline>
    </programlisting>
    <location file="ViennaRNA/ProfileAln.h"/>
  </compounddef>
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