/** * Edit Allele Frequencies * * Display the minor allele frequency edit fields. This function will * dynamically generate HTML based on the configuration preferences for * minor allele frequencies. It will only display frequencies that the * user has configured to be displayed. * * @author Sean Ephraim * @access public * @param object $variation * Database record for the variation * @param boolean $unlock * Editable fields or not * @return string HTML of input fields */ function edit_allele_frequencies($variation, $unlock) { // Which frequencies should be shown? $freqs = get_instance()->config->item('frequencies'); // Build a HTML string of allele frequency fields $html = ''; if (count($freqs) > 0) { // Begin collapsable accordion $html .= '<div class="accordion" id="accordion-variant-freqs">'; $html .= ' <div class="accordion-group">'; $html .= ' <div class="accordion-heading">'; $html .= ' <a class="accordion-toggle rowlink" data-toggle="collapse" data-parent="#accordion-variant-freqs" href="#edit-variant-freqs">'; $html .= ' <i class="icon-plus"></i> Variant Frequencies'; $html .= ' </a>'; $html .= ' </div>'; $html .= ' <div id="edit-variant-freqs" class="accordion-body collapse">'; $html .= ' <div class="accordion-inner">'; // EVS if (in_array('evs', $freqs)) { $html .= variant_form_input('evs_ea_ac', 'EVS European-American Alternate Allele Count', $variation->evs_ea_ac, $unlock); $html .= variant_form_input('evs_ea_an', 'EVS European-American Total Allele Count', $variation->evs_ea_an, $unlock); $html .= variant_form_input('evs_ea_af', 'EVS European-American Frequency', $variation->evs_ea_af, $unlock); $html .= variant_form_input('evs_aa_ac', 'EVS African-American Alternate Allele Count', $variation->evs_aa_ac, $unlock); $html .= variant_form_input('evs_aa_an', 'EVS African-American Total Allele Count', $variation->evs_aa_an, $unlock); $html .= variant_form_input('evs_aa_af', 'EVS African-American Frequency', $variation->evs_aa_af, $unlock); $html .= variant_form_input('evs_all_ac', 'EVS All Populations Alternate Allele Count', $variation->evs_all_ac, $unlock); $html .= variant_form_input('evs_all_an', 'EVS All Populations Total Allele Count', $variation->evs_all_an, $unlock); $html .= variant_form_input('evs_all_af', 'EVS All Populations Frequency', $variation->evs_all_af, $unlock); } // OtoSCOPE if (in_array('otoscope', $freqs)) { $html .= variant_form_input('otoscope_aj_ac', 'OtoSCOPE Ashkenazi Jewish Alternate Allele Count', $variation->otoscope_aj_ac, $unlock); $html .= variant_form_input('otoscope_aj_an', 'OtoSCOPE Ashkenazi Jewish Total Allele Count', $variation->otoscope_aj_an, $unlock); $html .= variant_form_input('otoscope_aj_af', 'OtoSCOPE Ashkenazi Jewish Allele Frequency', $variation->otoscope_aj_af, $unlock); $html .= variant_form_input('otoscope_co_ac', 'OtoSCOPE Colombian Allele Count', $variation->otoscope_co_ac, $unlock); $html .= variant_form_input('otoscope_co_an', 'OtoSCOPE Colombian Total Allele Count', $variation->otoscope_co_an, $unlock); $html .= variant_form_input('otoscope_co_af', 'OtoSCOPE Colombian Allele Frequency', $variation->otoscope_co_af, $unlock); $html .= variant_form_input('otoscope_us_ac', 'OtoSCOPE European-Americans Alternate Allele Count', $variation->otoscope_us_ac, $unlock); $html .= variant_form_input('otoscope_us_an', 'OtoSCOPE European-Americans Total Allele Count', $variation->otoscope_us_an, $unlock); $html .= variant_form_input('otoscope_us_af', 'OtoSCOPE European-Americans Allele Frequency', $variation->otoscope_us_af, $unlock); $html .= variant_form_input('otoscope_jp_ac', 'OtoSCOPE Japanese Alternate Allele Count', $variation->otoscope_jp_ac, $unlock); $html .= variant_form_input('otoscope_jp_an', 'OtoSCOPE Japanese Total Allele Count', $variation->otoscope_jp_an, $unlock); $html .= variant_form_input('otoscope_jp_af', 'OtoSCOPE Japanese Allele Frequency', $variation->otoscope_jp_af, $unlock); $html .= variant_form_input('otoscope_es_ac', 'OtoSCOPE Spanish Alternate Allele Count', $variation->otoscope_es_ac, $unlock); $html .= variant_form_input('otoscope_es_an', 'OtoSCOPE Spanish Total Allele Count', $variation->otoscope_es_an, $unlock); $html .= variant_form_input('otoscope_es_af', 'OtoSCOPE Spanish Allele Frequency', $variation->otoscope_es_af, $unlock); $html .= variant_form_input('otoscope_tr_ac', 'OtoSCOPE Turkish Alternate Allele Count', $variation->otoscope_tr_ac, $unlock); $html .= variant_form_input('otoscope_tr_an', 'OtoSCOPE Turkish Total Allele Count', $variation->otoscope_tr_an, $unlock); $html .= variant_form_input('otoscope_tr_af', 'OtoSCOPE Turkish Allele Frequency', $variation->otoscope_tr_af, $unlock); $html .= variant_form_input('otoscope_all_ac', 'OtoSCOPE All Populations Alternate Allele Count', $variation->otoscope_all_ac, $unlock); $html .= variant_form_input('otoscope_all_an', 'OtoSCOPE All Populations Total Allele Count', $variation->otoscope_all_an, $unlock); $html .= variant_form_input('otoscope_all_af', 'OtoSCOPE All Populations Allele Frequency', $variation->otoscope_all_af, $unlock); } // 1000 Genomes if (in_array('1000genomes', $freqs)) { $html .= variant_form_input('tg_afr_ac', '1000 Genomes African Alternate Allele Count', $variation->tg_afr_ac, $unlock); $html .= variant_form_input('tg_afr_an', '1000 Genomes African Total Allele Count', $variation->tg_afr_an, $unlock); $html .= variant_form_input('tg_afr_af', '1000 Genomes African Allele Frequency', $variation->tg_afr_af, $unlock); $html .= variant_form_input('tg_eur_ac', '1000 Genomes European Alternate Allele Count', $variation->tg_eur_ac, $unlock); $html .= variant_form_input('tg_eur_an', '1000 Genomes European Total Allele Count', $variation->tg_eur_an, $unlock); $html .= variant_form_input('tg_eur_af', '1000 Genomes European Allele Frequency', $variation->tg_eur_af, $unlock); $html .= variant_form_input('tg_amr_ac', '1000 Genomes American Alternate Allele Count', $variation->tg_amr_ac, $unlock); $html .= variant_form_input('tg_amr_an', '1000 Genomes American Total Allele Count', $variation->tg_amr_an, $unlock); $html .= variant_form_input('tg_amr_af', '1000 Genomes American Allele Frequency', $variation->tg_amr_af, $unlock); $html .= variant_form_input('tg_asn_ac', '1000 Genomes Asian Alternate Allele Count', $variation->tg_asn_ac, $unlock); $html .= variant_form_input('tg_asn_an', '1000 Genomes Asian Total Allele Count', $variation->tg_asn_an, $unlock); $html .= variant_form_input('tg_asn_af', '1000 Genomes Asian Allele Frequency', $variation->tg_asn_af, $unlock); $html .= variant_form_input('tg_all_ac', '1000 Genomes All Populations Alternate Allele Count', $variation->tg_all_ac, $unlock); $html .= variant_form_input('tg_all_an', '1000 Genomes All Populations Total Allele Count', $variation->tg_all_an, $unlock); $html .= variant_form_input('tg_all_af', '1000 Genomes All Populations Allele Frequency', $variation->tg_all_af, $unlock); } // End collapsable accordion $html .= ' </div>'; $html .= ' </div>'; $html .= ' </div>'; $html .= '</div>'; } // End if return $html; }
echo variant_form_input('lrt_pred', 'LRT Prediction', $variation->lrt_pred, $unlock); ?> <?php echo variant_form_input('mutationtaster_score', 'MutationTaster Score', $variation->mutationtaster_score, $unlock); ?> <?php echo variant_form_input('mutationtaster_pred', 'MutationTaster Prediction', $variation->mutationtaster_pred, $unlock); ?> <?php echo variant_form_input('gerp_nr', 'GERP++ Neutral Rate', $variation->gerp_nr, $unlock); ?> <?php echo variant_form_input('gerp_rs', 'GERP++ Rejected Substitutions (RS) Score', $variation->gerp_rs, $unlock); ?> <?php echo variant_form_input('gerp_pred', 'GERP++ Prediction', $variation->gerp_pred, $unlock); ?> </div> </div> </div> </div> <?php echo edit_allele_frequencies($variation, $unlock); ?> <label for="comments"> Comments <span class="edit-icon-wrapper"><i class="icon-pencil"></i></span> </label> <textarea id="comments" name="comments" class="input-block-level <?php echo highlight_if_changed($variation->id, 'comments'); ?> " rows="3"><?php