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  <compounddef id="group__probing__data__strategy__eddy" kind="group">
    <compoundname>probing_data_strategy_eddy</compoundname>
    <title>Probing_data_strategy_eddy</title>
    <sectiondef kind="func">
      <memberdef kind="function" id="group__probing__data__strategy__eddy_1ga152544fec8fec7e774eacd1f3fdb425e" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>double *</type>
        <definition>double * vrna_probing_strategy_eddy</definition>
        <argsstring>(vrna_fold_compound_t *fc, const double *data, size_t data_size, unsigned int target, void *options)</argsstring>
        <name>vrna_probing_strategy_eddy</name>
        <param>
          <type><ref refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" kindref="member">vrna_fold_compound_t</ref> *</type>
          <declname>fc</declname>
        </param>
        <param>
          <type>const double *</type>
          <declname>data</declname>
        </param>
        <param>
          <type>size_t</type>
          <declname>data_size</declname>
        </param>
        <param>
          <type>unsigned int</type>
          <declname>target</declname>
        </param>
        <param>
          <type>void *</type>
          <declname>options</declname>
        </param>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/probing/strategy_eddy.h" line="42" column="1" declfile="ViennaRNA/probing/strategy_eddy.h" declline="42" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="group__probing__data__strategy__eddy_1gab1a9c04454a66ea557124e3f41b4c8cc" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>void *</type>
        <definition>void * vrna_probing_strategy_eddy_options</definition>
        <argsstring>(double temperature, unsigned char options, const double *prior_unpaired, size_t prior_unpaired_size, const double *prior_paired, size_t prior_paired_size, vrna_math_fun_dbl_f cb_preprocess, vrna_math_fun_dbl_opt_t cb_preprocess_opt, vrna_math_fun_dbl_opt_free_f cb_preprocess_opt_free)</argsstring>
        <name>vrna_probing_strategy_eddy_options</name>
        <param>
          <type>double</type>
          <declname>temperature</declname>
        </param>
        <param>
          <type>unsigned char</type>
          <declname>options</declname>
        </param>
        <param>
          <type>const double *</type>
          <declname>prior_unpaired</declname>
        </param>
        <param>
          <type>size_t</type>
          <declname>prior_unpaired_size</declname>
        </param>
        <param>
          <type>const double *</type>
          <declname>prior_paired</declname>
        </param>
        <param>
          <type>size_t</type>
          <declname>prior_paired_size</declname>
        </param>
        <param>
          <type><ref refid="group__math__scalar_1ga868f4010e57fb868ce11804b77f04c2f" kindref="member">vrna_math_fun_dbl_f</ref></type>
          <declname>cb_preprocess</declname>
        </param>
        <param>
          <type><ref refid="group__math__scalar_1ga486680b7d43688e2bcbec959a547ffee" kindref="member">vrna_math_fun_dbl_opt_t</ref></type>
          <declname>cb_preprocess_opt</declname>
        </param>
        <param>
          <type><ref refid="group__math__scalar_1ga8a609e60df9775ae99eb5c29f9bfb7a8" kindref="member">vrna_math_fun_dbl_opt_free_f</ref></type>
          <declname>cb_preprocess_opt_free</declname>
        </param>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/probing/strategy_eddy.h" line="50" column="1" declfile="ViennaRNA/probing/strategy_eddy.h" declline="50" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="group__probing__data__strategy__eddy_1ga02da675fe96c8c2243932502aaf2ce88" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>void</type>
        <definition>void vrna_probing_strategy_eddy_options_free</definition>
        <argsstring>(void *options)</argsstring>
        <name>vrna_probing_strategy_eddy_options_free</name>
        <param>
          <type>void *</type>
          <declname>options</declname>
        </param>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/probing/strategy_eddy.h" line="62" column="1" declfile="ViennaRNA/probing/strategy_eddy.h" declline="62" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="group__probing__data__strategy__eddy_1ga6238432ed277208b3034b917886e200b" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>struct vrna_probing_data_s *</type>
        <definition>struct vrna_probing_data_s * vrna_probing_data_eddy</definition>
        <argsstring>(const double *reactivities, unsigned int n, double temperature, unsigned char options, const double *unpaired_data, unsigned int unpaired_len, const double *paired_data, unsigned int paired_len)</argsstring>
        <name>vrna_probing_data_eddy</name>
        <param>
          <type>const double *</type>
          <declname>reactivities</declname>
        </param>
        <param>
          <type>unsigned int</type>
          <declname>n</declname>
        </param>
        <param>
          <type>double</type>
          <declname>temperature</declname>
        </param>
        <param>
          <type>unsigned char</type>
          <declname>options</declname>
        </param>
        <param>
          <type>const double *</type>
          <declname>unpaired_data</declname>
        </param>
        <param>
          <type>unsigned int</type>
          <declname>unpaired_len</declname>
        </param>
        <param>
          <type>const double *</type>
          <declname>paired_data</declname>
        </param>
        <param>
          <type>unsigned int</type>
          <declname>paired_len</declname>
        </param>
        <briefdescription>
<para>Add probing data as soft constraints (Eddy/RNAprob-2 method). </para>
        </briefdescription>
        <detaileddescription>
<para>This approach of probing data directed RNA folding uses the probability framework proposed by  <verbatim>embed:rst:inline  :cite:t:`eddy:2014` </verbatim>:</para>
<para><formula id="182">\[ \Delta G_{\text{data}}(i) = - RT\ln(\mathbb{P}(\text{data}(i)\mid x_i\pi_i)) \]</formula></para>
<para>to convert probing data to pseudo energies for given nucleotide <formula id="178">$ x_i $</formula> and class probability <formula id="179">$ \pi_i $</formula> at position <formula id="55">$ i $</formula>. The conditional probability is taken from a prior-distribution of probing data for the respective classes.</para>
<para>Here, the method distinguishes exactly two different classes of structural context, (i) unpaired and (ii) paired positions, following the lines of the RNAprob-2 method of  <verbatim>embed:rst:inline  :cite:t:`deng:2016` </verbatim>. The reactivity distribution is computed using Gaussian kernel density estimation (KDE) with bandwidth <formula id="114">$ h $</formula> computed using Scott factor</para>
<para><formula id="180">\[ h = n^{-\frac{1}{5}} \]</formula></para>
<para>where <formula id="113">$ n $</formula> is the number of data points of the prior distribution.</para>
<para><simplesect kind="note"><para>For further details, we refer to  <verbatim>embed:rst:inline  :cite:t:`eddy:2014` </verbatim> and  <verbatim>embed:rst:inline  :cite:t:`deng:2016` </verbatim>.</para>
</simplesect>
<simplesect kind="see"><para><ref refid="group__probing__data_1gae981b94d5dabe6a32cbe74cd5dd7f925" kindref="member">vrna_probing_data_t</ref>, <ref refid="group__probing__data_1ga8c8e987c91b357fd09913f356f5d25da" kindref="member">vrna_probing_data_free()</ref>, <ref refid="group__probing__data_1gaea5dded27f3e993c69ff617ff0f09648" kindref="member">vrna_sc_probing()</ref>, <ref refid="group__probing__data__strategy__eddy_1gab4db5191cddaa5d34861affcab95353d" kindref="member">vrna_probing_data_eddy_comparative()</ref>, <ref refid="group__probing__data__strategy__deigan_1gacf014a1ab73e49cde659fc441d59e38b" kindref="member">vrna_probing_data_deigan()</ref>, <ref refid="group__probing__data__strategy__deigan_1ga83a8ff8d6404614f9d17d37e6244349c" kindref="member">vrna_probing_data_deigan_comparative()</ref>, <ref refid="group__probing__data__strategy__zarringhalam_1gaa68eaff93fd3c628ed25ca5fdfc5264b" kindref="member">vrna_probing_data_zarringhalam()</ref>, <ref refid="group__probing__data__strategy__zarringhalam_1ga166a5a5d9f6effde96fc1b79a17a003a" kindref="member">vrna_probing_data_zarringhalam_comparative()</ref>, <ref refid="group__probing__data__strategy__eddy_1ga80aa1a69a2ccaa8135936d4e303eb478" kindref="member">VRNA_PROBING_STRATEGY_EDDY_NO_TEMPERATURE_RESCALING</ref>, <ref refid="group__probing__data__strategy__eddy_1gadef68d6c0aa61f11b7b1b757b52d9e15" kindref="member">VRNA_PROBING_STRATEGY_EDDY_OPTIONS_DEFAULT</ref></para>
</simplesect>
<parameterlist kind="param"><parameteritem>
<parameternamelist>
<parametername>reactivities</parametername>
</parameternamelist>
<parameterdescription>
<para>A 1-based vector of probing data, e.g. normalized SHAPE reactivities </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>n</parametername>
</parameternamelist>
<parameterdescription>
<para>Length of <computeroutput>reactivities</computeroutput> </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>temperature</parametername>
</parameternamelist>
<parameterdescription>
<para>The thermodynamic temperature <formula id="181">$ T $</formula> </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>options</parametername>
</parameternamelist>
<parameterdescription>
<para>Options bit flags to change the behavior of the strategy </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>unpaired_data</parametername>
</parameternamelist>
<parameterdescription>
<para>Pointer to an array of probing data for unpaired nucleotides </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>unpaired_len</parametername>
</parameternamelist>
<parameterdescription>
<para>Length of <computeroutput>unpaired_data</computeroutput> </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>paired_data</parametername>
</parameternamelist>
<parameterdescription>
<para>Pointer to an array of probing data for paired nucleotides </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>paired_len</parametername>
</parameternamelist>
<parameterdescription>
<para>Length of <computeroutput>paired_data</computeroutput> </para>
</parameterdescription>
</parameteritem>
</parameterlist>
<simplesect kind="return"><para>A pointer to a data structure containing the probing data and any preparations necessary to use it in <ref refid="group__probing__data_1gaea5dded27f3e993c69ff617ff0f09648" kindref="member">vrna_sc_probing()</ref> according to the method of  <verbatim>embed:rst:inline  :cite:t:`eddy:2014` </verbatim> or <bold>NULL</bold> on any error. </para>
</simplesect>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/probing/strategy_eddy.h" line="110" column="1" declfile="ViennaRNA/probing/strategy_eddy.h" declline="110" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="group__probing__data__strategy__eddy_1gaf681d773eea028999caff3fe9676c833" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>struct vrna_probing_data_s *</type>
        <definition>struct vrna_probing_data_s * vrna_probing_data_eddy_trans</definition>
        <argsstring>(const double *reactivities, unsigned int n, double temperature, unsigned char options, const double *unpaired_data, unsigned int unpaired_len, const double *paired_data, unsigned int paired_len, vrna_math_fun_dbl_f cb_preprocess, vrna_math_fun_dbl_opt_t cb_preprocess_opt, vrna_math_fun_dbl_opt_free_f cb_preprocess_opt_free)</argsstring>
        <name>vrna_probing_data_eddy_trans</name>
        <param>
          <type>const double *</type>
          <declname>reactivities</declname>
        </param>
        <param>
          <type>unsigned int</type>
          <declname>n</declname>
        </param>
        <param>
          <type>double</type>
          <declname>temperature</declname>
        </param>
        <param>
          <type>unsigned char</type>
          <declname>options</declname>
        </param>
        <param>
          <type>const double *</type>
          <declname>unpaired_data</declname>
        </param>
        <param>
          <type>unsigned int</type>
          <declname>unpaired_len</declname>
        </param>
        <param>
          <type>const double *</type>
          <declname>paired_data</declname>
        </param>
        <param>
          <type>unsigned int</type>
          <declname>paired_len</declname>
        </param>
        <param>
          <type><ref refid="group__math__scalar_1ga868f4010e57fb868ce11804b77f04c2f" kindref="member">vrna_math_fun_dbl_f</ref></type>
          <declname>cb_preprocess</declname>
        </param>
        <param>
          <type><ref refid="group__math__scalar_1ga486680b7d43688e2bcbec959a547ffee" kindref="member">vrna_math_fun_dbl_opt_t</ref></type>
          <declname>cb_preprocess_opt</declname>
        </param>
        <param>
          <type><ref refid="group__math__scalar_1ga8a609e60df9775ae99eb5c29f9bfb7a8" kindref="member">vrna_math_fun_dbl_opt_free_f</ref></type>
          <declname>cb_preprocess_opt_free</declname>
        </param>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/probing/strategy_eddy.h" line="121" column="1" declfile="ViennaRNA/probing/strategy_eddy.h" declline="121" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="group__probing__data__strategy__eddy_1gab4db5191cddaa5d34861affcab95353d" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>struct vrna_probing_data_s *</type>
        <definition>struct vrna_probing_data_s * vrna_probing_data_eddy_comparative</definition>
        <argsstring>(const double **reactivities, const unsigned int *n, unsigned int n_seq, double temperature, unsigned char options, const double **unpaired_datas, const unsigned int *unpaired_lens, const double **paired_datas, const unsigned int *paired_lens, unsigned int multi_params)</argsstring>
        <name>vrna_probing_data_eddy_comparative</name>
        <param>
          <type>const double **</type>
          <declname>reactivities</declname>
        </param>
        <param>
          <type>const unsigned int *</type>
          <declname>n</declname>
        </param>
        <param>
          <type>unsigned int</type>
          <declname>n_seq</declname>
        </param>
        <param>
          <type>double</type>
          <declname>temperature</declname>
        </param>
        <param>
          <type>unsigned char</type>
          <declname>options</declname>
        </param>
        <param>
          <type>const double **</type>
          <declname>unpaired_datas</declname>
        </param>
        <param>
          <type>const unsigned int *</type>
          <declname>unpaired_lens</declname>
        </param>
        <param>
          <type>const double **</type>
          <declname>paired_datas</declname>
        </param>
        <param>
          <type>const unsigned int *</type>
          <declname>paired_lens</declname>
        </param>
        <param>
          <type>unsigned int</type>
          <declname>multi_params</declname>
        </param>
        <briefdescription>
<para>Add probing data as soft constraints (Eddy/RNAprob-2 method) for comparative structure predictions. </para>
        </briefdescription>
        <detaileddescription>
<para>Similar to <ref refid="group__probing__data__strategy__eddy_1ga6238432ed277208b3034b917886e200b" kindref="member">vrna_probing_data_eddy()</ref>, this function prepares a data structure for probing data directed RNA folding. It uses the probability framework proposed by  <verbatim>embed:rst:inline  :cite:t:`eddy:2014` </verbatim>:</para>
<para><formula id="182">\[ \Delta G_{\text{data}}(i) = - RT\ln(\mathbb{P}(\text{data}(i)\mid x_i\pi_i)) \]</formula></para>
<para>to convert probing data to pseudo energies for given nucleotide <formula id="178">$ x_i $</formula> and class probability <formula id="179">$ \pi_i $</formula> at position <formula id="55">$ i $</formula>. The conditional probability is taken from a prior-distribution of probing data for the respective classes.</para>
<para>This functions purpose is to allow for adding multiple probing data as required for comparative structure predictions over multiple sequence alignments (MSA) with <computeroutput>n_seq</computeroutput> sequences. For that purpose, <computeroutput>reactivities</computeroutput> can be provided for any of the sequences in the MSA. Individual probing data is always expected to be specified in sequence coordinates, i.e. without considering gaps in the MSA. Therefore, each set of <computeroutput>reactivities</computeroutput> may have a different length as specified the parameter <computeroutput>n</computeroutput>. In addition, each set of probing data may undergo the conversion using different prior distributions for unpaired and paired nucleotides. Whether or not multiple sets of conversion priors are provided must be specified using the <computeroutput>multi_params</computeroutput> flag parameter. Use <ref refid="group__probing__data__strategy_1ga06223ef2a11bb23461916bd269081949" kindref="member">VRNA_PROBING_METHOD_MULTI_PARAMS_1</ref> to indicate that <computeroutput>unpaired_datas</computeroutput> points to an array of unpaired probing data for each sequence. Similarly, <ref refid="group__probing__data__strategy_1ga3f95e63f8c11768a4c146b8471296a27" kindref="member">VRNA_PROBING_METHOD_MULTI_PARAMS_2</ref> indicates that <computeroutput>paired_datas</computeroutput> is pointing to an array paired probing data for each sequence. Bitwise-OR of the two values renders both parameters to be sequence specific.</para>
<para><simplesect kind="note"><para>For further details, we refer to  <verbatim>embed:rst:inline  :cite:t:`eddy:2014` </verbatim> and  <verbatim>embed:rst:inline  :cite:t:`deng:2016` </verbatim>.</para>
</simplesect>
<simplesect kind="see"><para><ref refid="group__probing__data_1gae981b94d5dabe6a32cbe74cd5dd7f925" kindref="member">vrna_probing_data_t</ref>, <ref refid="group__probing__data_1ga8c8e987c91b357fd09913f356f5d25da" kindref="member">vrna_probing_data_free()</ref>, <ref refid="group__probing__data_1gaea5dded27f3e993c69ff617ff0f09648" kindref="member">vrna_sc_probing()</ref>, <ref refid="group__probing__data__strategy__eddy_1ga6238432ed277208b3034b917886e200b" kindref="member">vrna_probing_data_eddy()</ref>, <ref refid="group__probing__data__strategy__deigan_1gacf014a1ab73e49cde659fc441d59e38b" kindref="member">vrna_probing_data_deigan()</ref>, <ref refid="group__probing__data__strategy__deigan_1ga83a8ff8d6404614f9d17d37e6244349c" kindref="member">vrna_probing_data_deigan_comparative()</ref>, <ref refid="group__probing__data__strategy__zarringhalam_1gaa68eaff93fd3c628ed25ca5fdfc5264b" kindref="member">vrna_probing_data_zarringhalam()</ref>, <ref refid="group__probing__data__strategy__zarringhalam_1ga166a5a5d9f6effde96fc1b79a17a003a" kindref="member">vrna_probing_data_zarringhalam_comparative()</ref>, <ref refid="group__probing__data__strategy_1gaf5db9deaaa290d8147aaa047fc5116ee" kindref="member">VRNA_PROBING_METHOD_MULTI_PARAMS_0</ref>, <ref refid="group__probing__data__strategy_1ga06223ef2a11bb23461916bd269081949" kindref="member">VRNA_PROBING_METHOD_MULTI_PARAMS_1</ref>, <ref refid="group__probing__data__strategy_1ga3f95e63f8c11768a4c146b8471296a27" kindref="member">VRNA_PROBING_METHOD_MULTI_PARAMS_2</ref>, <ref refid="group__probing__data__strategy_1ga79617a4098fe287edcee01ca0992e3f9" kindref="member">VRNA_PROBING_METHOD_MULTI_PARAMS_DEFAULT</ref></para>
</simplesect>
<parameterlist kind="param"><parameteritem>
<parameternamelist>
<parametername>reactivities</parametername>
</parameternamelist>
<parameterdescription>
<para>0-based array of 1-based arrays of per-nucleotide probing data, e.g. SHAPE reactivities </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>n</parametername>
</parameternamelist>
<parameterdescription>
<para>0-based array of lengths of the <computeroutput>reactivities</computeroutput> lists </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>n_seq</parametername>
</parameternamelist>
<parameterdescription>
<para>The number of sequences in the MSA </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>temperature</parametername>
</parameternamelist>
<parameterdescription>
<para>The thermodynamic temperature <formula id="181">$ T $</formula> </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>options</parametername>
</parameternamelist>
<parameterdescription>
<para>Options bit flags to change the behavior of the strategy </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>unpaired_datas</parametername>
</parameternamelist>
<parameterdescription>
<para>0-based array of 0-based arrays with probing data for unpaired nucleotides or address of a single array of such data </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>unpaired_lens</parametername>
</parameternamelist>
<parameterdescription>
<para>0-based array of lengths for each probing data array in <computeroutput>unpaired_datas</computeroutput> </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>paired_datas</parametername>
</parameternamelist>
<parameterdescription>
<para>0-based array of 0-based arrays with probing data for paired nucleotides or address of a single array of such data </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>paired_lens</parametername>
</parameternamelist>
<parameterdescription>
<para>0-based array of lengths for each probing data array in <computeroutput>paired_data</computeroutput> </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>multi_params</parametername>
</parameternamelist>
<parameterdescription>
<para>A flag indicating what is passed through parameters <computeroutput>unpaired_datas</computeroutput> and <computeroutput>paired_datas</computeroutput> </para>
</parameterdescription>
</parameteritem>
</parameterlist>
<simplesect kind="return"><para>A pointer to a data structure containing the probing data and any preparations necessary to use it in <ref refid="group__probing__data_1gaea5dded27f3e993c69ff617ff0f09648" kindref="member">vrna_sc_probing()</ref> according to the method of  <verbatim>embed:rst:inline  :cite:t:`eddy:2014` </verbatim> or <bold>NULL</bold> on any error. </para>
</simplesect>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/probing/strategy_eddy.h" line="186" column="1" declfile="ViennaRNA/probing/strategy_eddy.h" declline="186" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="group__probing__data__strategy__eddy_1ga42c41ca0cdf4fe17d6cfe063f03bda19" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>struct vrna_probing_data_s *</type>
        <definition>struct vrna_probing_data_s * vrna_probing_data_eddy_trans_comparative</definition>
        <argsstring>(const double **reactivities, const unsigned int *n, unsigned int n_seq, double temperature, unsigned char options, const double **unpaired_datas, const unsigned int *unpaired_lens, const double **paired_datas, const unsigned int *paired_lens, unsigned int multi_params, vrna_math_fun_dbl_f *cb_preprocess, vrna_math_fun_dbl_opt_t *cb_preprocess_opt, vrna_math_fun_dbl_opt_free_f *cb_preprocess_opt_free)</argsstring>
        <name>vrna_probing_data_eddy_trans_comparative</name>
        <param>
          <type>const double **</type>
          <declname>reactivities</declname>
        </param>
        <param>
          <type>const unsigned int *</type>
          <declname>n</declname>
        </param>
        <param>
          <type>unsigned int</type>
          <declname>n_seq</declname>
        </param>
        <param>
          <type>double</type>
          <declname>temperature</declname>
        </param>
        <param>
          <type>unsigned char</type>
          <declname>options</declname>
        </param>
        <param>
          <type>const double **</type>
          <declname>unpaired_datas</declname>
        </param>
        <param>
          <type>const unsigned int *</type>
          <declname>unpaired_lens</declname>
        </param>
        <param>
          <type>const double **</type>
          <declname>paired_datas</declname>
        </param>
        <param>
          <type>const unsigned int *</type>
          <declname>paired_lens</declname>
        </param>
        <param>
          <type>unsigned int</type>
          <declname>multi_params</declname>
        </param>
        <param>
          <type><ref refid="group__math__scalar_1ga868f4010e57fb868ce11804b77f04c2f" kindref="member">vrna_math_fun_dbl_f</ref> *</type>
          <declname>cb_preprocess</declname>
        </param>
        <param>
          <type><ref refid="group__math__scalar_1ga486680b7d43688e2bcbec959a547ffee" kindref="member">vrna_math_fun_dbl_opt_t</ref> *</type>
          <declname>cb_preprocess_opt</declname>
        </param>
        <param>
          <type><ref refid="group__math__scalar_1ga8a609e60df9775ae99eb5c29f9bfb7a8" kindref="member">vrna_math_fun_dbl_opt_free_f</ref> *</type>
          <declname>cb_preprocess_opt_free</declname>
        </param>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/probing/strategy_eddy.h" line="199" column="1" declfile="ViennaRNA/probing/strategy_eddy.h" declline="199" declcolumn="1"/>
      </memberdef>
    </sectiondef>
    <sectiondef kind="define">
      <memberdef kind="define" id="group__probing__data__strategy__eddy_1gadef68d6c0aa61f11b7b1b757b52d9e15" prot="public" static="no">
        <name>VRNA_PROBING_STRATEGY_EDDY_OPTIONS_DEFAULT</name>
        <initializer>0</initializer>
        <briefdescription>
<para>Default options for the  <verbatim>embed:rst:inline  :cite:t:`eddy:2014` </verbatim>: probing data conversion strategy. </para>
        </briefdescription>
        <detaileddescription>
<para><simplesect kind="see"><para>vrna_probing_strategy_eddy_options(), <ref refid="group__probing__data__strategy__eddy_1ga6238432ed277208b3034b917886e200b" kindref="member">vrna_probing_data_eddy()</ref>, vrna_probing_data_eddy_trans(), <ref refid="group__probing__data__strategy__eddy_1gab4db5191cddaa5d34861affcab95353d" kindref="member">vrna_probing_data_eddy_comparative()</ref>, vrna_probing_data_eddy_trans_comparative() </para>
</simplesect>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/probing/strategy_eddy.h" line="26" column="9" bodyfile="ViennaRNA/probing/strategy_eddy.h" bodystart="26" bodyend="-1"/>
      </memberdef>
      <memberdef kind="define" id="group__probing__data__strategy__eddy_1ga80aa1a69a2ccaa8135936d4e303eb478" prot="public" static="no">
        <name>VRNA_PROBING_STRATEGY_EDDY_NO_TEMPERATURE_RESCALING</name>
        <initializer>(1 &lt;&lt; 5)</initializer>
        <briefdescription>
<para>Prevent temperature dependent energy rescaling in  <verbatim>embed:rst:inline  :cite:t:`eddy:2014` </verbatim> strategy. </para>
        </briefdescription>
        <detaileddescription>
<para>This option flag forces the probing data conversion strategy to always use the same thermodynamic temperature <formula id="181">$ T $</formula>, no matter what temperature the predictions are made for.</para>
<para><simplesect kind="see"><para>vrna_probing_strategy_eddy_options(), <ref refid="group__probing__data__strategy__eddy_1ga6238432ed277208b3034b917886e200b" kindref="member">vrna_probing_data_eddy()</ref>, vrna_probing_data_eddy_trans(), <ref refid="group__probing__data__strategy__eddy_1gab4db5191cddaa5d34861affcab95353d" kindref="member">vrna_probing_data_eddy_comparative()</ref>, vrna_probing_data_eddy_trans_comparative() </para>
</simplesect>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/probing/strategy_eddy.h" line="38" column="9" bodyfile="ViennaRNA/probing/strategy_eddy.h" bodystart="38" bodyend="-1"/>
      </memberdef>
    </sectiondef>
    <briefdescription>
    </briefdescription>
    <detaileddescription>
    </detaileddescription>
  </compounddef>
</doxygen>
