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  <compounddef id="group__mfe__window" kind="group">
    <compoundname>mfe_window</compoundname>
    <title>Local (sliding window) MFE Prediction</title>
    <innerfile refid="mfe_2local_8h">local.h</innerfile>
    <innergroup refid="group__mfe__window__deprecated">Deprecated Interface for Local (Sliding Window) MFE Prediction</innergroup>
    <sectiondef kind="user-defined">
      <header>Basic local (sliding window) MFE prediction interface</header>
      <memberdef kind="function" id="group__mfe__window_1gacdbc049dcfc7a0e2eb37a327efab91e2" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>float</type>
        <definition>float vrna_mfe_window</definition>
        <argsstring>(vrna_fold_compound_t *fc, FILE *file)</argsstring>
        <name>vrna_mfe_window</name>
        <param>
          <type><ref refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" kindref="member">vrna_fold_compound_t</ref> *</type>
          <declname>fc</declname>
        </param>
        <param>
          <type>FILE *</type>
          <declname>file</declname>
        </param>
        <briefdescription>
<para>Local MFE prediction using a sliding window approach. </para>
        </briefdescription>
        <detaileddescription>
<para>Computes minimum free energy structures using a sliding window approach, where base pairs may not span outside the window. In contrast to <ref refid="group__mfe__global_1ga5577af664e5b9056b44fa5df29e9befb" kindref="member">vrna_mfe()</ref>, where a maximum base pair span may be set using the <ref refid="structvrna__md__s_1a659e5fcc6e8c9f1a68e7de6548eef3b0" kindref="member">vrna_md_t.max_bp_span</ref> attribute and one globally optimal structure is predicted, this function uses a sliding window to retrieve all locally optimal structures within each window. The size of the sliding window is set in the <ref refid="structvrna__md__s_1abea42f9229f8d8d6bcbedef316315bfc" kindref="member">vrna_md_t.window_size</ref> attribute, prior to the retrieval of the <ref refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" kindref="member">vrna_fold_compound_t</ref> using <ref refid="group__fold__compound_1gab89fe9844031711d42c70d1b9277c0d5" kindref="member">vrna_fold_compound()</ref> with option <ref refid="group__fold__compound_1ga2b2a8009ccdccc3eb1571556261aee8e" kindref="member">VRNA_OPTION_WINDOW</ref></para>
<para>The predicted structures are written on-the-fly, either to stdout, if a NULL pointer is passed as file parameter, or to the corresponding filehandle.</para>
<para><simplesect kind="see"><para><ref refid="group__fold__compound_1gab89fe9844031711d42c70d1b9277c0d5" kindref="member">vrna_fold_compound()</ref>, <ref refid="group__mfe__window_1ga90d3756f07aa78a47ffac187ead3c0aa" kindref="member">vrna_mfe_window_zscore()</ref>, <ref refid="group__mfe__global_1ga5577af664e5b9056b44fa5df29e9befb" kindref="member">vrna_mfe()</ref>, <ref refid="group__mfe__window_1ga4918cce52bf69c1913cda503b2ac75d8" kindref="member">vrna_Lfold()</ref>, <ref refid="group__mfe__window_1ga27fddda5fc63eb49c861e38845fc34b4" kindref="member">vrna_Lfoldz()</ref>, <ref refid="group__fold__compound_1ga2b2a8009ccdccc3eb1571556261aee8e" kindref="member">VRNA_OPTION_WINDOW</ref>, <ref refid="structvrna__md__s_1a659e5fcc6e8c9f1a68e7de6548eef3b0" kindref="member">vrna_md_t.max_bp_span</ref>, <ref refid="structvrna__md__s_1abea42f9229f8d8d6bcbedef316315bfc" kindref="member">vrna_md_t.window_size</ref></para>
</simplesect>
<parameterlist kind="param"><parameteritem>
<parameternamelist>
<parametername>fc</parametername>
</parameternamelist>
<parameterdescription>
<para>The <ref refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" kindref="member">vrna_fold_compound_t</ref> with preallocated memory for the DP matrices </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>file</parametername>
</parameternamelist>
<parameterdescription>
<para>The output file handle where predictions are written to (maybe NULL)</para>
</parameterdescription>
</parameteritem>
</parameterlist>
<xrefsect id="wrappers_1_wrappers000117"><xreftitle>SWIG Wrapper Notes</xreftitle><xrefdescription><para><parblock><para>This function is attached as overloaded method <computeroutput><ref refid="group__mfe__window" kindref="compound">Local (sliding window) MFE Prediction</ref></computeroutput> to objects of type <computeroutput><ref refid="group__fold__compound" kindref="compound">The Fold Compound</ref></computeroutput>. The parameter <computeroutput>FILE</computeroutput> has default value of <computeroutput>NULL</computeroutput> and can be omitted. See e.g.  <verbatim>embed:rst:inline :py:meth:`RNA.fold_compound.mfe_window()` in the :doc:`/api_python`</verbatim>. </para>
</parblock></para>
</xrefdescription></xrefsect></para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/mfe/local.h" line="120" column="1" declfile="ViennaRNA/mfe/local.h" declline="120" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="group__mfe__window_1ga3ade396421340b0f2f989c7936fda3d9" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>float</type>
        <definition>float vrna_mfe_window_cb</definition>
        <argsstring>(vrna_fold_compound_t *fc, vrna_mfe_window_f cb, void *data)</argsstring>
        <name>vrna_mfe_window_cb</name>
        <param>
          <type><ref refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" kindref="member">vrna_fold_compound_t</ref> *</type>
          <declname>fc</declname>
        </param>
        <param>
          <type><ref refid="group__mfe__window_1gaa97863c328b909d7da26d618e0c83fb9" kindref="member">vrna_mfe_window_f</ref></type>
          <declname>cb</declname>
        </param>
        <param>
          <type>void *</type>
          <declname>data</declname>
        </param>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
<para><xrefsect id="wrappers_1_wrappers000118"><xreftitle>SWIG Wrapper Notes</xreftitle><xrefdescription><para><parblock><para>This function is attached as overloaded method <computeroutput>mfe_window_cb()</computeroutput> to objects of type <computeroutput><ref refid="group__fold__compound" kindref="compound">The Fold Compound</ref></computeroutput>. The parameter <computeroutput>data</computeroutput> has default value of <computeroutput>NULL</computeroutput> and can be omitted. See e.g.  <verbatim>embed:rst:inline :py:meth:`RNA.fold_compound.mfe_window_cb()` in the :doc:`/api_python`</verbatim>. </para>
</parblock></para>
</xrefdescription></xrefsect></para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/mfe/local.h" line="125" column="1" declfile="ViennaRNA/mfe/local.h" declline="125" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="group__mfe__window_1ga90d3756f07aa78a47ffac187ead3c0aa" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>float</type>
        <definition>float vrna_mfe_window_zscore</definition>
        <argsstring>(vrna_fold_compound_t *fc, double min_z, FILE *file)</argsstring>
        <name>vrna_mfe_window_zscore</name>
        <param>
          <type><ref refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" kindref="member">vrna_fold_compound_t</ref> *</type>
          <declname>fc</declname>
        </param>
        <param>
          <type>double</type>
          <declname>min_z</declname>
        </param>
        <param>
          <type>FILE *</type>
          <declname>file</declname>
        </param>
        <briefdescription>
<para>Local MFE prediction using a sliding window approach (with z-score cut-off). </para>
        </briefdescription>
        <detaileddescription>
<para>Computes minimum free energy structures using a sliding window approach, where base pairs may not span outside the window. This function is the z-score version of <ref refid="group__mfe__window_1gacdbc049dcfc7a0e2eb37a327efab91e2" kindref="member">vrna_mfe_window()</ref>, i.e. only predictions above a certain z-score cut-off value are printed. As for <ref refid="group__mfe__window_1gacdbc049dcfc7a0e2eb37a327efab91e2" kindref="member">vrna_mfe_window()</ref>, the size of the sliding window is set in the <ref refid="structvrna__md__s_1abea42f9229f8d8d6bcbedef316315bfc" kindref="member">vrna_md_t.window_size</ref> attribute, prior to the retrieval of the <ref refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" kindref="member">vrna_fold_compound_t</ref> using <ref refid="group__fold__compound_1gab89fe9844031711d42c70d1b9277c0d5" kindref="member">vrna_fold_compound()</ref> with option <ref refid="group__fold__compound_1ga2b2a8009ccdccc3eb1571556261aee8e" kindref="member">VRNA_OPTION_WINDOW</ref>.</para>
<para>The predicted structures are written on-the-fly, either to stdout, if a NULL pointer is passed as file parameter, or to the corresponding filehandle.</para>
<para><simplesect kind="see"><para><ref refid="group__fold__compound_1gab89fe9844031711d42c70d1b9277c0d5" kindref="member">vrna_fold_compound()</ref>, <ref refid="group__mfe__window_1ga90d3756f07aa78a47ffac187ead3c0aa" kindref="member">vrna_mfe_window_zscore()</ref>, <ref refid="group__mfe__global_1ga5577af664e5b9056b44fa5df29e9befb" kindref="member">vrna_mfe()</ref>, <ref refid="group__mfe__window_1ga4918cce52bf69c1913cda503b2ac75d8" kindref="member">vrna_Lfold()</ref>, <ref refid="group__mfe__window_1ga27fddda5fc63eb49c861e38845fc34b4" kindref="member">vrna_Lfoldz()</ref>, <ref refid="group__fold__compound_1ga2b2a8009ccdccc3eb1571556261aee8e" kindref="member">VRNA_OPTION_WINDOW</ref>, <ref refid="structvrna__md__s_1a659e5fcc6e8c9f1a68e7de6548eef3b0" kindref="member">vrna_md_t.max_bp_span</ref>, <ref refid="structvrna__md__s_1abea42f9229f8d8d6bcbedef316315bfc" kindref="member">vrna_md_t.window_size</ref></para>
</simplesect>
<parameterlist kind="param"><parameteritem>
<parameternamelist>
<parametername>fc</parametername>
</parameternamelist>
<parameterdescription>
<para>The <ref refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" kindref="member">vrna_fold_compound_t</ref> with preallocated memory for the DP matrices </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>min_z</parametername>
</parameternamelist>
<parameterdescription>
<para>The minimal z-score for a predicted structure to appear in the output </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>file</parametername>
</parameternamelist>
<parameterdescription>
<para>The output file handle where predictions are written to (maybe NULL)</para>
</parameterdescription>
</parameteritem>
</parameterlist>
<xrefsect id="wrappers_1_wrappers000119"><xreftitle>SWIG Wrapper Notes</xreftitle><xrefdescription><para><parblock><para>This function is attached as overloaded method <computeroutput>mfe_window_zscore()</computeroutput> to objects of type <computeroutput><ref refid="group__fold__compound" kindref="compound">The Fold Compound</ref></computeroutput>. The parameter <computeroutput>FILE</computeroutput> has default value of <computeroutput>NULL</computeroutput> and can be omitted. See e.g.  <verbatim>embed:rst:inline :py:meth:`RNA.fold_compound.mfe_window_zscore()` in the :doc:`/api_python`</verbatim>. </para>
</parblock></para>
</xrefdescription></xrefsect></para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/mfe/local.h" line="157" column="1" declfile="ViennaRNA/mfe/local.h" declline="157" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="group__mfe__window_1ga5df4a67ce381ed329c289370b0c8adcb" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>float</type>
        <definition>float vrna_mfe_window_zscore_cb</definition>
        <argsstring>(vrna_fold_compound_t *fc, double min_z, vrna_mfe_window_zscore_f cb, void *data)</argsstring>
        <name>vrna_mfe_window_zscore_cb</name>
        <param>
          <type><ref refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" kindref="member">vrna_fold_compound_t</ref> *</type>
          <declname>fc</declname>
        </param>
        <param>
          <type>double</type>
          <declname>min_z</declname>
        </param>
        <param>
          <type>vrna_mfe_window_zscore_f</type>
          <declname>cb</declname>
        </param>
        <param>
          <type>void *</type>
          <declname>data</declname>
        </param>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
<para><xrefsect id="wrappers_1_wrappers000120"><xreftitle>SWIG Wrapper Notes</xreftitle><xrefdescription><para><parblock><para>This function is attached as overloaded method <computeroutput>mfe_window_zscore_cb()</computeroutput> to objects of type <computeroutput><ref refid="group__fold__compound" kindref="compound">The Fold Compound</ref></computeroutput>. The parameter <computeroutput>data</computeroutput> has default value of <computeroutput>NULL</computeroutput> and can be omitted. See e.g.  <verbatim>embed:rst:inline :py:meth:`RNA.fold_compound.mfe_window_zscore()` in the :doc:`/api_python`</verbatim>. </para>
</parblock></para>
</xrefdescription></xrefsect></para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/mfe/local.h" line="163" column="1" declfile="ViennaRNA/mfe/local.h" declline="163" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="group__mfe__window_1ga17ac221d685bb1e74e2acdbfb02ec86d" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>int</type>
        <definition>int vrna_backtrack_window</definition>
        <argsstring>(vrna_fold_compound_t *fc, const char *Lfold_filename, long file_pos, char **structure, double mfe)</argsstring>
        <name>vrna_backtrack_window</name>
        <param>
          <type><ref refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" kindref="member">vrna_fold_compound_t</ref> *</type>
          <declname>fc</declname>
        </param>
        <param>
          <type>const char *</type>
          <declname>Lfold_filename</declname>
        </param>
        <param>
          <type>long</type>
          <declname>file_pos</declname>
        </param>
        <param>
          <type>char **</type>
          <declname>structure</declname>
        </param>
        <param>
          <type>double</type>
          <declname>mfe</declname>
        </param>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/mfe/local.h" line="172" column="1" declfile="ViennaRNA/mfe/local.h" declline="172" declcolumn="1"/>
      </memberdef>
    </sectiondef>
    <sectiondef kind="user-defined">
      <header>Simplified local MFE prediction using sequence(s) or multiple sequence alignment(s)</header>
      <memberdef kind="function" id="group__mfe__window_1ga4918cce52bf69c1913cda503b2ac75d8" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>float</type>
        <definition>float vrna_Lfold</definition>
        <argsstring>(const char *string, int window_size, FILE *file)</argsstring>
        <name>vrna_Lfold</name>
        <param>
          <type>const char *</type>
          <declname>string</declname>
        </param>
        <param>
          <type>int</type>
          <declname>window_size</declname>
        </param>
        <param>
          <type>FILE *</type>
          <declname>file</declname>
        </param>
        <briefdescription>
<para>Local MFE prediction using a sliding window approach (simplified interface). </para>
        </briefdescription>
        <detaileddescription>
<para>This simplified interface to <ref refid="group__mfe__window_1gacdbc049dcfc7a0e2eb37a327efab91e2" kindref="member">vrna_mfe_window()</ref> computes the MFE and locally optimal secondary structure using default options. Structures are predicted using a sliding window approach, where base pairs may not span outside the window. Memory required for dynamic programming (DP) matrices will be allocated and free&apos;d on-the-fly. Hence, after return of this function, the recursively filled matrices are not available any more for any post-processing.</para>
<para><simplesect kind="note"><para>In case you want to use the filled DP matrices for any subsequent post-processing step, or you require other conditions than specified by the default model details, use <ref refid="group__mfe__window_1gacdbc049dcfc7a0e2eb37a327efab91e2" kindref="member">vrna_mfe_window()</ref>, and the data structure <ref refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" kindref="member">vrna_fold_compound_t</ref> instead.</para>
</simplesect>
<simplesect kind="see"><para><ref refid="group__mfe__window_1gacdbc049dcfc7a0e2eb37a327efab91e2" kindref="member">vrna_mfe_window()</ref>, <ref refid="group__mfe__window_1ga27fddda5fc63eb49c861e38845fc34b4" kindref="member">vrna_Lfoldz()</ref>, <ref refid="group__mfe__window_1ga90d3756f07aa78a47ffac187ead3c0aa" kindref="member">vrna_mfe_window_zscore()</ref></para>
</simplesect>
<parameterlist kind="param"><parameteritem>
<parameternamelist>
<parametername>string</parametername>
</parameternamelist>
<parameterdescription>
<para>The nucleic acid sequence </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>window_size</parametername>
</parameternamelist>
<parameterdescription>
<para>The window size for locally optimal structures </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>file</parametername>
</parameternamelist>
<parameterdescription>
<para>The output file handle where predictions are written to (if NULL, output is written to stdout)</para>
</parameterdescription>
</parameteritem>
</parameterlist>
<xrefsect id="wrappers_1_wrappers000121"><xreftitle>SWIG Wrapper Notes</xreftitle><xrefdescription><para><parblock><para>This function is available as overloaded function <computeroutput><ref refid="group__mfe__window__deprecated_1gafdd1e11b5c7ad443b9f86b818e67bab4" kindref="member">Lfold()</ref></computeroutput> in the global namespace. The parameter <computeroutput>file</computeroutput> defaults to <computeroutput>NULL</computeroutput> and may be omitted. See e.g.  <verbatim>embed:rst:inline :py:func:`RNA.Lfold()` in the :doc:`/api_python`</verbatim>. </para>
</parblock></para>
</xrefdescription></xrefsect></para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/mfe/local.h" line="208" column="1" declfile="ViennaRNA/mfe/local.h" declline="208" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="group__mfe__window_1ga84dcc36fd88063e1692c2e1e68a5f689" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>float</type>
        <definition>float vrna_Lfold_cb</definition>
        <argsstring>(const char *string, int window_size, vrna_mfe_window_f cb, void *data)</argsstring>
        <name>vrna_Lfold_cb</name>
        <param>
          <type>const char *</type>
          <declname>string</declname>
        </param>
        <param>
          <type>int</type>
          <declname>window_size</declname>
        </param>
        <param>
          <type><ref refid="group__mfe__window_1gaa97863c328b909d7da26d618e0c83fb9" kindref="member">vrna_mfe_window_f</ref></type>
          <declname>cb</declname>
        </param>
        <param>
          <type>void *</type>
          <declname>data</declname>
        </param>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
<para><xrefsect id="wrappers_1_wrappers000122"><xreftitle>SWIG Wrapper Notes</xreftitle><xrefdescription><para><parblock><para>This function is available as overloaded function <computeroutput>Lfold_cb()</computeroutput> in the global namespace. The parameter <computeroutput>data</computeroutput> defaults to <computeroutput>NULL</computeroutput> and may be omitted. See e.g.  <verbatim>embed:rst:inline :py:func:`RNA.Lfold_cb()` in the :doc:`/api_python`</verbatim>. </para>
</parblock></para>
</xrefdescription></xrefsect></para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/mfe/local.h" line="214" column="1" declfile="ViennaRNA/mfe/local.h" declline="214" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="group__mfe__window_1ga27fddda5fc63eb49c861e38845fc34b4" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>float</type>
        <definition>float vrna_Lfoldz</definition>
        <argsstring>(const char *string, int window_size, double min_z, FILE *file)</argsstring>
        <name>vrna_Lfoldz</name>
        <param>
          <type>const char *</type>
          <declname>string</declname>
        </param>
        <param>
          <type>int</type>
          <declname>window_size</declname>
        </param>
        <param>
          <type>double</type>
          <declname>min_z</declname>
        </param>
        <param>
          <type>FILE *</type>
          <declname>file</declname>
        </param>
        <briefdescription>
<para>Local MFE prediction using a sliding window approach with z-score cut-off (simplified interface). </para>
        </briefdescription>
        <detaileddescription>
<para>This simplified interface to <ref refid="group__mfe__window_1ga90d3756f07aa78a47ffac187ead3c0aa" kindref="member">vrna_mfe_window_zscore()</ref> computes the MFE and locally optimal secondary structure using default options. Structures are predicted using a sliding window approach, where base pairs may not span outside the window. Memory required for dynamic programming (DP) matrices will be allocated and free&apos;d on-the-fly. Hence, after return of this function, the recursively filled matrices are not available any more for any post-processing. This function is the z-score version of <ref refid="group__mfe__window_1ga4918cce52bf69c1913cda503b2ac75d8" kindref="member">vrna_Lfold()</ref>, i.e. only predictions above a certain z-score cut-off value are printed.</para>
<para><simplesect kind="note"><para>In case you want to use the filled DP matrices for any subsequent post-processing step, or you require other conditions than specified by the default model details, use <ref refid="group__mfe__window_1gacdbc049dcfc7a0e2eb37a327efab91e2" kindref="member">vrna_mfe_window()</ref>, and the data structure <ref refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" kindref="member">vrna_fold_compound_t</ref> instead.</para>
</simplesect>
<simplesect kind="see"><para><ref refid="group__mfe__window_1ga90d3756f07aa78a47ffac187ead3c0aa" kindref="member">vrna_mfe_window_zscore()</ref>, <ref refid="group__mfe__window_1ga4918cce52bf69c1913cda503b2ac75d8" kindref="member">vrna_Lfold()</ref>, <ref refid="group__mfe__window_1gacdbc049dcfc7a0e2eb37a327efab91e2" kindref="member">vrna_mfe_window()</ref></para>
</simplesect>
<parameterlist kind="param"><parameteritem>
<parameternamelist>
<parametername>string</parametername>
</parameternamelist>
<parameterdescription>
<para>The nucleic acid sequence </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>window_size</parametername>
</parameternamelist>
<parameterdescription>
<para>The window size for locally optimal structures </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>min_z</parametername>
</parameternamelist>
<parameterdescription>
<para>The minimal z-score for a predicted structure to appear in the output </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>file</parametername>
</parameternamelist>
<parameterdescription>
<para>The output file handle where predictions are written to (if NULL, output is written to stdout) </para>
</parameterdescription>
</parameteritem>
</parameterlist>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/mfe/local.h" line="246" column="1" declfile="ViennaRNA/mfe/local.h" declline="246" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="group__mfe__window_1gae982184f119219b616f3e5a8b3f558ec" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>float</type>
        <definition>float vrna_Lfoldz_cb</definition>
        <argsstring>(const char *string, int window_size, double min_z, vrna_mfe_window_zscore_f cb, void *data)</argsstring>
        <name>vrna_Lfoldz_cb</name>
        <param>
          <type>const char *</type>
          <declname>string</declname>
        </param>
        <param>
          <type>int</type>
          <declname>window_size</declname>
        </param>
        <param>
          <type>double</type>
          <declname>min_z</declname>
        </param>
        <param>
          <type>vrna_mfe_window_zscore_f</type>
          <declname>cb</declname>
        </param>
        <param>
          <type>void *</type>
          <declname>data</declname>
        </param>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
<para><xrefsect id="wrappers_1_wrappers000124"><xreftitle>SWIG Wrapper Notes</xreftitle><xrefdescription><para><parblock><para>This function is available as overloaded function <computeroutput>Lfoldz_cb()</computeroutput> in the global namespace. The parameter <computeroutput>data</computeroutput> defaults to <computeroutput>NULL</computeroutput> and may be omitted. See e.g.  <verbatim>embed:rst:inline :py:func:`RNA.Lfoldz_cb()` in the :doc:`/api_python`</verbatim>. </para>
</parblock></para>
</xrefdescription></xrefsect></para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/mfe/local.h" line="253" column="1" declfile="ViennaRNA/mfe/local.h" declline="253" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="group__mfe__window_1gaa43d3de352753529a4578cb02cd8bc52" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>float</type>
        <definition>float vrna_aliLfold</definition>
        <argsstring>(const char **alignment, int maxdist, FILE *fp)</argsstring>
        <name>vrna_aliLfold</name>
        <param>
          <type>const char **</type>
          <declname>alignment</declname>
        </param>
        <param>
          <type>int</type>
          <declname>maxdist</declname>
        </param>
        <param>
          <type>FILE *</type>
          <declname>fp</declname>
        </param>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
<para><xrefsect id="wrappers_1_wrappers000125"><xreftitle>SWIG Wrapper Notes</xreftitle><xrefdescription><para><parblock><para>This function is available as overloaded function <computeroutput>aliLfold()</computeroutput> in the global namespace. The parameter <computeroutput>fp</computeroutput> defaults to <computeroutput>NULL</computeroutput> and may be omitted. See e.g.  <verbatim>embed:rst:inline :py:func:`RNA.aliLfold()` in the :doc:`/api_python`</verbatim>. </para>
</parblock></para>
</xrefdescription></xrefsect></para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/mfe/local.h" line="263" column="1" declfile="ViennaRNA/mfe/local.h" declline="263" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="group__mfe__window_1gae9b2e312c316961d4a067f9b789cc9d7" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>float</type>
        <definition>float vrna_aliLfold_cb</definition>
        <argsstring>(const char **alignment, int maxdist, vrna_mfe_window_f cb, void *data)</argsstring>
        <name>vrna_aliLfold_cb</name>
        <param>
          <type>const char **</type>
          <declname>alignment</declname>
        </param>
        <param>
          <type>int</type>
          <declname>maxdist</declname>
        </param>
        <param>
          <type><ref refid="group__mfe__window_1gaa97863c328b909d7da26d618e0c83fb9" kindref="member">vrna_mfe_window_f</ref></type>
          <declname>cb</declname>
        </param>
        <param>
          <type>void *</type>
          <declname>data</declname>
        </param>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
<para><xrefsect id="wrappers_1_wrappers000126"><xreftitle>SWIG Wrapper Notes</xreftitle><xrefdescription><para><parblock><para>This function is available as overloaded function <computeroutput>aliLfold_cb()</computeroutput> in the global namespace. The parameter <computeroutput>data</computeroutput> defaults to <computeroutput>NULL</computeroutput> and may be omitted. See e.g.  <verbatim>embed:rst:inline :py:func:`RNA.aliLfold_cb()` in the :doc:`/api_python`</verbatim>. </para>
</parblock></para>
</xrefdescription></xrefsect></para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/mfe/local.h" line="269" column="1" declfile="ViennaRNA/mfe/local.h" declline="269" declcolumn="1"/>
      </memberdef>
    </sectiondef>
    <sectiondef kind="typedef">
      <memberdef kind="typedef" id="group__mfe__window_1gaa97863c328b909d7da26d618e0c83fb9" prot="public" static="no">
        <type>void(*</type>
        <definition>typedef void(* vrna_mfe_window_f) (unsigned int start, unsigned int end, const char *structure, float en, void *data)</definition>
        <argsstring>)(unsigned int start, unsigned int end, const char *structure, float en, void *data)</argsstring>
        <name>vrna_mfe_window_f</name>
        <briefdescription>
<para>The default callback for sliding window MFE structure predictions. </para>
        </briefdescription>
        <detaileddescription>
<para><xrefsect id="callbacks_1_callbacks000019"><xreftitle>Notes on Callback Functions</xreftitle><xrefdescription><para><parblock><para>This function will be called for each hit in a sliding window MFE prediction. </para>
</parblock></para>
</xrefdescription></xrefsect></para>
<para><simplesect kind="see"><para><ref refid="group__mfe__window_1gacdbc049dcfc7a0e2eb37a327efab91e2" kindref="member">vrna_mfe_window()</ref></para>
</simplesect>
<parameterlist kind="param"><parameteritem>
<parameternamelist>
<parametername>start</parametername>
</parameternamelist>
<parameterdescription>
<para>provides the first position of the hit (1-based, relative to entire sequence/alignment) </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>end</parametername>
</parameternamelist>
<parameterdescription>
<para>provides the last position of the hit (1-based, relative to the entire sequence/alignment) </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>structure</parametername>
</parameternamelist>
<parameterdescription>
<para>provides the (sub)structure in dot-bracket notation </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>en</parametername>
</parameternamelist>
<parameterdescription>
<para>is the free energy of the structure hit in kcal/mol </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>data</parametername>
</parameternamelist>
<parameterdescription>
<para>is some arbitrary data pointer passed through by the function executing the callback </para>
</parameterdescription>
</parameteritem>
</parameterlist>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/mfe/local.h" line="58" column="9" bodyfile="ViennaRNA/mfe/local.h" bodystart="58" bodyend="-1"/>
      </memberdef>
      <memberdef kind="typedef" id="group__mfe__window_1ga215bef80ed74d36daba71ea4fb7d4388" prot="public" static="no">
        <type>void</type>
        <definition>typedef void vrna_mfe_window_callback(int start, int end, const char *structure, float en, void *data)</definition>
        <argsstring>(int start, int end, const char *structure, float en, void *data)</argsstring>
        <name>vrna_mfe_window_callback</name>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/mfe/local.h" line="69" column="10" bodyfile="ViennaRNA/mfe/local.h" bodystart="69" bodyend="-1"/>
      </memberdef>
      <memberdef kind="typedef" id="group__mfe__window_1gad41cef447889684ac02787d6e7ddf670" prot="public" static="no">
        <type>void(*</type>
        <definition>typedef void(* vrna_mfe_window_zscore_f) (unsigned int start, unsigned int end, const char *structure, float en, float zscore, void *data)</definition>
        <argsstring>)(unsigned int start, unsigned int end, const char *structure, float en, float zscore, void *data)</argsstring>
        <name>vrna_mfe_window_zscore_f</name>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/mfe/local.h" line="73" column="9" bodyfile="ViennaRNA/mfe/local.h" bodystart="73" bodyend="-1"/>
      </memberdef>
      <memberdef kind="typedef" id="group__mfe__window_1ga67e8a2d04140c9220e2b134ed3a08b4e" prot="public" static="no">
        <type>void</type>
        <definition>typedef void vrna_mfe_window_zscore_callback(int start, int end, const char *structure, float en, float zscore, void *data)</definition>
        <argsstring>(int start, int end, const char *structure, float en, float zscore, void *data)</argsstring>
        <name>vrna_mfe_window_zscore_callback</name>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/mfe/local.h" line="86" column="10" bodyfile="ViennaRNA/mfe/local.h" bodystart="86" bodyend="-1"/>
      </memberdef>
    </sectiondef>
    <briefdescription>
    </briefdescription>
    <detaileddescription>
    </detaileddescription>
  </compounddef>
</doxygen>
