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  <compounddef id="group__probing__data__strategy__zarringhalam" kind="group">
    <compoundname>probing_data_strategy_zarringhalam</compoundname>
    <title>Probing_data_strategy_zarringhalam</title>
    <sectiondef kind="func">
      <memberdef kind="function" id="group__probing__data__strategy__zarringhalam_1ga04d812410835c14b1544cab81bc6a1da" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>double *</type>
        <definition>double * vrna_probing_strategy_zarringhalam</definition>
        <argsstring>(vrna_fold_compound_t *fc, const double *data, size_t data_size, unsigned int target, void *options)</argsstring>
        <name>vrna_probing_strategy_zarringhalam</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_zarringhalam.h" line="47" column="1" declfile="ViennaRNA/probing/strategy_zarringhalam.h" declline="47" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="group__probing__data__strategy__zarringhalam_1ga9b527f6356bcc6ea2796a84791e948ef" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>void *</type>
        <definition>void * vrna_probing_strategy_zarringhalam_options</definition>
        <argsstring>(double beta, double default_probability, double max_value, 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_zarringhalam_options</name>
        <param>
          <type>double</type>
          <declname>beta</declname>
        </param>
        <param>
          <type>double</type>
          <declname>default_probability</declname>
        </param>
        <param>
          <type>double</type>
          <declname>max_value</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_zarringhalam.h" line="55" column="1" declfile="ViennaRNA/probing/strategy_zarringhalam.h" declline="55" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="group__probing__data__strategy__zarringhalam_1ga8b36e8f93a0eda149c2f846bd22bc430" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>void</type>
        <definition>void vrna_probing_strategy_zarringhalam_options_free</definition>
        <argsstring>(void *option)</argsstring>
        <name>vrna_probing_strategy_zarringhalam_options_free</name>
        <param>
          <type>void *</type>
          <declname>option</declname>
        </param>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/probing/strategy_zarringhalam.h" line="64" column="1" declfile="ViennaRNA/probing/strategy_zarringhalam.h" declline="64" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="group__probing__data__strategy__zarringhalam_1gaa68eaff93fd3c628ed25ca5fdfc5264b" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type><ref refid="group__probing__data_1gae981b94d5dabe6a32cbe74cd5dd7f925" kindref="member">vrna_probing_data_t</ref></type>
        <definition>vrna_probing_data_t vrna_probing_data_zarringhalam</definition>
        <argsstring>(const double *reactivities, unsigned int n, double beta, const char *pr_conversion, double pr_default)</argsstring>
        <name>vrna_probing_data_zarringhalam</name>
        <param>
          <type>const double *</type>
          <declname>reactivities</declname>
        </param>
        <param>
          <type>unsigned int</type>
          <declname>n</declname>
        </param>
        <param>
          <type>double</type>
          <declname>beta</declname>
        </param>
        <param>
          <type>const char *</type>
          <declname>pr_conversion</declname>
        </param>
        <param>
          <type>double</type>
          <declname>pr_default</declname>
        </param>
        <briefdescription>
<para>Prepare probing data according to Zarringhalam et al. 2012 method. </para>
        </briefdescription>
        <detaileddescription>
<para>Prepares a data structure to be used with <ref refid="group__probing__data_1gaea5dded27f3e993c69ff617ff0f09648" kindref="member">vrna_sc_probing()</ref> to directed RNA folding using the method of  <verbatim>embed:rst:inline  :cite:t:`zarringhalam:2012` </verbatim>.</para>
<para>This method first converts the observed probing data of nucleotide <formula id="55">$ i $</formula> into a probability <formula id="171">$ q_i $</formula> that position <formula id="55">$ i $</formula> is unpaired by means of a non-linear map. Then pseudo-energies of the form</para>
<para><formula id="172">\[ \Delta G_{\text{SHAPE}}(x,i) = \beta\ |x_i - q_i| \]</formula></para>
<para>are computed, where <formula id="173">$ x_i=0 $</formula> if position <formula id="55">$ i $</formula> is unpaired and <formula id="174">$ x_i=1 $</formula> if <formula id="55">$ i $</formula> is paired in a given secondary structure. The parameter <formula id="175">$ \beta $</formula> serves as scaling factor. The magnitude of discrepancy between prediction and experimental observation is represented by <formula id="176">$ |x_i - q_i| $</formula>.</para>
<para><simplesect kind="note"><para>For further details, we refer to  <verbatim>embed:rst:inline  :cite:t:`zarringhalam:2012` </verbatim></para>
</simplesect>
<simplesect kind="see"><para><ref refid="group__probing__data_1gae981b94d5dabe6a32cbe74cd5dd7f925" kindref="member">vrna_probing_data_t</ref>, <ref refid="group__probing__data_1ga8c8e987c91b357fd09913f356f5d25da" kindref="member">vrna_probing_data_free()</ref>, <ref refid="group__probing__data_1gaea5dded27f3e993c69ff617ff0f09648" kindref="member">vrna_sc_probing()</ref>, <ref refid="group__probing__data__strategy__zarringhalam_1ga166a5a5d9f6effde96fc1b79a17a003a" kindref="member">vrna_probing_data_zarringhalam_comparative()</ref>, <ref refid="group__probing__data__strategy__deigan_1gacf014a1ab73e49cde659fc441d59e38b" kindref="member">vrna_probing_data_deigan()</ref>, <ref refid="group__probing__data__strategy__deigan_1ga83a8ff8d6404614f9d17d37e6244349c" kindref="member">vrna_probing_data_deigan_comparative()</ref>, <ref refid="group__probing__data__strategy__eddy_1ga6238432ed277208b3034b917886e200b" kindref="member">vrna_probing_data_eddy()</ref>, <ref refid="group__probing__data__strategy__eddy_1gab4db5191cddaa5d34861affcab95353d" kindref="member">vrna_probing_data_eddy_comparative()</ref></para>
</simplesect>
<parameterlist kind="param"><parameteritem>
<parameternamelist>
<parametername>reactivities</parametername>
</parameternamelist>
<parameterdescription>
<para>1-based array of per-nucleotide probing data, e.g. SHAPE reactivities </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>n</parametername>
</parameternamelist>
<parameterdescription>
<para>The length of the <computeroutput>reactivities</computeroutput> list </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>beta</parametername>
</parameternamelist>
<parameterdescription>
<para>The scaling factor <formula id="175">$ \beta $</formula> of the conversion function </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>pr_conversion</parametername>
</parameternamelist>
<parameterdescription>
<para>A flag that specifies how to convert reactivities to probabilities </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>pr_default</parametername>
</parameternamelist>
<parameterdescription>
<para>The default probability for a nucleotide where reactivity data is missing for </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:`zarringhalam:2012` </verbatim> or <bold>NULL</bold> on any error. </para>
</simplesect>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/probing/strategy_zarringhalam.h" line="101" column="1" declfile="ViennaRNA/probing/strategy_zarringhalam.h" declline="101" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="group__probing__data__strategy__zarringhalam_1gaf74981831610fb85080d0976a3afe729" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type><ref refid="group__probing__data_1gae981b94d5dabe6a32cbe74cd5dd7f925" kindref="member">vrna_probing_data_t</ref></type>
        <definition>vrna_probing_data_t vrna_probing_data_zarringhalam_trans</definition>
        <argsstring>(const double *reactivities, unsigned int n, double beta, double pr_default, 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_zarringhalam_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>beta</declname>
        </param>
        <param>
          <type>double</type>
          <declname>pr_default</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_zarringhalam.h" line="109" column="1" declfile="ViennaRNA/probing/strategy_zarringhalam.h" declline="109" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="group__probing__data__strategy__zarringhalam_1ga166a5a5d9f6effde96fc1b79a17a003a" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type><ref refid="group__probing__data_1gae981b94d5dabe6a32cbe74cd5dd7f925" kindref="member">vrna_probing_data_t</ref></type>
        <definition>vrna_probing_data_t vrna_probing_data_zarringhalam_comparative</definition>
        <argsstring>(const double **reactivities, unsigned int *n, unsigned int n_seq, double *betas, const char **pr_conversions, double *pr_defaults, unsigned int multi_params)</argsstring>
        <name>vrna_probing_data_zarringhalam_comparative</name>
        <param>
          <type>const double **</type>
          <declname>reactivities</declname>
        </param>
        <param>
          <type>unsigned int *</type>
          <declname>n</declname>
        </param>
        <param>
          <type>unsigned int</type>
          <declname>n_seq</declname>
        </param>
        <param>
          <type>double *</type>
          <declname>betas</declname>
        </param>
        <param>
          <type>const char **</type>
          <declname>pr_conversions</declname>
        </param>
        <param>
          <type>double *</type>
          <declname>pr_defaults</declname>
        </param>
        <param>
          <type>unsigned int</type>
          <declname>multi_params</declname>
        </param>
        <briefdescription>
<para>Prepare probing data according to Zarringhalam et al. 2012 method for comparative structure predictions. </para>
        </briefdescription>
        <detaileddescription>
<para>Similar to <ref refid="group__probing__data__strategy__zarringhalam_1gaa68eaff93fd3c628ed25ca5fdfc5264b" kindref="member">vrna_probing_data_zarringhalam()</ref>, this function prepares a data structure to be used with <ref refid="group__probing__data_1gaea5dded27f3e993c69ff617ff0f09648" kindref="member">vrna_sc_probing()</ref> to guide RNA folding using the method of  <verbatim>embed:rst:inline  :cite:t:`zarringhalam:2012` </verbatim>.</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 parameters <formula id="183">$ beta $</formula>. Additionally, the probing data to probability conversions strategy and default values for missing data can be specified in a sequence-based manner. Whether or not multiple conversion parameters are provided must be specified using the <computeroutput>multi_params</computeroutput> flag parameter. Use <ref refid="group__probing__data__strategy_1ga06223ef2a11bb23461916bd269081949" kindref="member">VRNA_PROBING_METHOD_MULTI_PARAMS_1</ref> to indicate that <computeroutput>betas</computeroutput> points to an array of <formula id="183">$ beta $</formula> values for each sequence. <ref refid="group__probing__data__strategy_1ga3f95e63f8c11768a4c146b8471296a27" kindref="member">VRNA_PROBING_METHOD_MULTI_PARAMS_2</ref> indicates that <computeroutput>pr_conversions</computeroutput> is pointing to an array of probing data to probability conversion strategies, and <ref refid="group__probing__data__strategy_1gad76a1f9cfbfc795980bbe9c87ec92c5c" kindref="member">VRNA_PROBING_METHOD_MULTI_PARAMS_3</ref> indicates multiple default probabilities for missing data. Bitwise-OR of the three values renders all of them to be sequence specific.</para>
<para><simplesect kind="note"><para>For further details, we refer to  <verbatim>embed:rst:inline  :cite:t:`zarringhalam:2012` </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__zarringhalam_1ga166a5a5d9f6effde96fc1b79a17a003a" kindref="member">vrna_probing_data_zarringhalam_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__eddy_1ga6238432ed277208b3034b917886e200b" kindref="member">vrna_probing_data_eddy()</ref>, <ref refid="group__probing__data__strategy__eddy_1gab4db5191cddaa5d34861affcab95353d" kindref="member">vrna_probing_data_eddy_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_1gad76a1f9cfbfc795980bbe9c87ec92c5c" kindref="member">VRNA_PROBING_METHOD_MULTI_PARAMS_3</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>betas</parametername>
</parameternamelist>
<parameterdescription>
<para>0-based array with scaling factors <formula id="175">$ \beta $</formula> of the conversion function or the address of a scaling factor to be applied for all data </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>pr_conversions</parametername>
</parameternamelist>
<parameterdescription>
<para>0-based array of flags that specifies how to convert reactivities to probabilities or the address of a conversion strategy to be applied for all data </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>pr_defaults</parametername>
</parameternamelist>
<parameterdescription>
<para>0-based array of default probabilities for a nucleotide where reactivity data is missing for or the address of a single default probability to be applied for all data </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>multi_params</parametername>
</parameternamelist>
<parameterdescription>
<para>A flag indicating what is passed through parameters <computeroutput>betas</computeroutput>, <computeroutput>pr_conversions</computeroutput>, and <computeroutput>pr_defaults</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:`zarringhalam:2012` </verbatim> or <bold>NULL</bold> on any error. </para>
</simplesect>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/probing/strategy_zarringhalam.h" line="162" column="1" declfile="ViennaRNA/probing/strategy_zarringhalam.h" declline="162" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="group__probing__data__strategy__zarringhalam_1gafed242cd606d1273f7362840f13fb116" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type><ref refid="group__probing__data_1gae981b94d5dabe6a32cbe74cd5dd7f925" kindref="member">vrna_probing_data_t</ref></type>
        <definition>vrna_probing_data_t vrna_probing_data_zarringhalam_trans_comparative</definition>
        <argsstring>(const double **reactivities, unsigned int *n, unsigned int n_seq, double *betas, double *pr_defaults, 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_zarringhalam_trans_comparative</name>
        <param>
          <type>const double **</type>
          <declname>reactivities</declname>
        </param>
        <param>
          <type>unsigned int *</type>
          <declname>n</declname>
        </param>
        <param>
          <type>unsigned int</type>
          <declname>n_seq</declname>
        </param>
        <param>
          <type>double *</type>
          <declname>betas</declname>
        </param>
        <param>
          <type>double *</type>
          <declname>pr_defaults</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>
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<para><simplesect kind="see"><para><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__zarringhalam_1ga00d6900fbbe3551e9337d1994d7a5437" kindref="member">VRNA_PROBING_METHOD_ZARRINGHALAM2012_DEFAULT_beta</ref>, <ref refid="group__probing__data__strategy__zarringhalam_1ga73a94e419762f42dc05007fb6f7fe101" kindref="member">VRNA_PROBING_METHOD_ZARRINGHALAM2012_DEFAULT_probability</ref> </para>
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