$analysis_id, 'feature_id' => $feature_id); $result = tripal_core_chado_select('analysisfeature', $columns, $values); $analysisfeature_id = $result[0]->analysisfeature_id; } // get the property. return tripal_core_get_property('analysisfeature', $analysisfeature_id, $property, $cv_name); } /** * Insert a property for an analysis feature * * @param $analysis_id * The analysis ID for the analysis feature. This argument is optional but * if specified it must also be accompanied with a feature ID. * @param $feature_id * The feature ID for the analysis feature. This argument is optional but * if specified it must also be accompanied with an analysis ID. * @param $analysisfeature_id * The analysis feature ID for the analysis feature. This argument is * optional and can be used rather than specifying the $analysis_id and * $feature_id arguments. If all three arguments are specified (e.g. * an $analysis_id, $feature_id and $analysisfeature_id, then the * $analysisfeature_id is used and the other two arguments are ignored. * @param $property * The cvterm name of the property to insert * @param $value * The value of the property to insert * @param $update_if_present * A boolean indicated whether to update the record if it's already present * @param $cv_name * Optional. The name of the cv to which the property belongs. By * default this is the 'tripal' cv. * * @return * True of success, False otherwise * * @ingroup tripal_feature_api */ function tripal_feature_analysis_insert_property($analysis_id = NULL, $feature_id = NUll, $analysisfeature_id = NULL, $property, $value, $update_if_present = 0, $cv_name = 'tripal') { // check that the incoming arguments are correct if (($analysis_id and !$feature_id) or (!$analysis_id and $feature_id)) { watchdog('tripal_feature', 'tripal_feature_analysis_insert_property: Both an analysis ID and feature ID should be specified', array(), WATCHDOG_WARNING); } // get the analysisfeature_id if one is not provided if (!$analysisfeature_id) { $columns = array('analysisfeature_id'); $values = array('analysis_id' => $analysis_id, 'feature_id' => $feature_id); $result = tripal_core_chado_select('analysisfeature', $columns, $values); $analysisfeature_id = $result[0]->analysisfeature_id; } // insert the property. return tripal_core_insert_property('analysisfeature', $analysisfeature_id, $property, $cv_name, $value, $update_if_present); } /** * Update an analysis feature property using the property name. Use this * when a property only exists once for a given analysis feature. When more * than one value can exist for the same property use the * tripal_feature_analysis_update_property_by_id() function. * * @param $analysis_id * The analysis ID for the analysis feature. This argument is optional but * if specified it must also be accompanied with a feature ID. * @param $feature_id * The feature ID for the analysis feature. This argument is optional but * if specified it must also be accompanied with an analysis ID. * @param $analysisfeature_id * The analysis feature ID for the analysis feature. This argument is * optional and can be used rather than specifying the $analysis_id and * $feature_id arguments. If all three arguments are specified (e.g. * an $analysis_id, $feature_id and $analysisfeature_id, then the * $analysisfeature_id is used and the other two arguments are ignored. * @param $property * The cvterm name of the property to update * @param $value * The value of the property to update * @param $insert_if_missing * A boolean indicated whether to insert the record if it's absent * @param $cv_name * Optional. The name of the cv to which the property belongs. By * default this is the 'tripal' cv. * * Note: The property will be identified using the unique combination of the $analysis_id and $property * and then it will be updated with the supplied value * * @return * True of success, False otherwise * * @ingroup tripal_feature_api */ function tripal_feature_analysis_update_property($analysis_id = NULL, $feature_id = NUll, $analysisfeature_id = NULL, $property, $value, $insert_if_missing = 0, $cv_name = 'tripal') { // check that the incoming arguments are correct if (($analysis_id and !$feature_id) or (!$analysis_id and $feature_id)) { watchdog('tripal_feature', 'tripal_feature_analysis_update_property: Both an analysis ID and feature ID should be specified', array(), WATCHDOG_WARNING); } // get the analysisfeature_id if one is not provided if (!$analysisfeature_id) { $columns = array('analysisfeature_id'); $values = array('analysis_id' => $analysis_id, 'feature_id' => $feature_id); $result = tripal_core_chado_select('analysisfeature', $columns, $values); $analysisfeature_id = $result[0]->analysisfeature_id; } // update the property. return tripal_core_update_property('analysisfeature', $analysisfeature_id, $property, $cv_name, $value, $insert_if_missing); } /** * Update a property for an analysis feature using the analysisfeatureprop_id. * * @param $analysisfeatureprop_id * The analysis feature property ID for the analysis feature. * @param $property * The cvterm name of the property * @param $value * The value of the property * @param $cv_name * Optional. The name of the cv to which the property belongs. By * default this is the 'tripal' cv. * * * @return * True of success, False otherwise * * @ingroup tripal_feature_api */ function tripal_feature_analysis_update_property_by_id($analysisfeatureprop_id, $property, $value, $cv_name = 'tripal') { // update the property. return tripal_core_update_property_by_id('analysisfeature', $analysisfeatureprop_id, $property, $cv_name, $value); } /** * Delete an analysis feature property using the property name. Use this * when a property only exists once for a given analysis feature. When more * than one value can exist for the same property use the * tripal_feature_analysis_delete_property_by_id() function. * * @param $analysis_id * The analysis ID for the analysis feature. This argument is optional but * if specified it must also be accompanied with a feature ID. * @param $feature_id * The feature ID for the analysis feature. This argument is optional but * if specified it must also be accompanied with an analysis ID. * @param $analysisfeature_id * The analysis feature ID for the analysis feature. This argument is * optional and can be used rather than specifying the $analysis_id and * $feature_id arguments. If all three arguments are specified (e.g. * an $analysis_id, $feature_id and $analysisfeature_id, then the * $analysisfeature_id is used and the other two arguments are ignored. * @param $property * The cvterm name of the property to delete * @param $cv_name * Optional. The name of the cv to which the property belongs. By * default this is the 'tripal' cv. * * Note: The property will be identified using the unique combination of the $analysis_id and $property * and then it will be deleted * * @return * True of success, False otherwise * * @ingroup tripal_feature_api */ function tripal_feature_analysis_delete_property($analysis_id = NULL, $feature_id = NUll, $analysisfeature_id = NULL, $property, $cv_name = 'tripal') { // check that the incoming arguments are correct if (($analysis_id and !$feature_id) or (!$analysis_id and $feature_id)) { watchdog('tripal_feature', 'tripal_feature_analysis_delete_property: Both an analysis ID and feature ID should be specified', array(), WATCHDOG_WARNING); } // get the analysisfeature_id if one is not provided if (!$analysisfeature_id) { $columns = array('analysisfeature_id'); $values = array('analysis_id' => $analysis_id, 'feature_id' => $feature_id); $result = tripal_core_chado_select('analysisfeature', $columns, $values); $analysisfeature_id = $result[0]->analysisfeature_id; } // get the property. return tripal_core_delete_property('analysisfeature', $analysisfeature_id, $property, $cv_name); } /** * Delete a property using the analysisfeatureprop_id * * @param $analysisfeatureprop_id * The analysis feature property ID for the analysis feature. * * @return * True of success, False otherwise * * @ingroup tripal_feature_api */ function tripal_feature_analysis_delete_property_by_id($analysisfeatureprop_id) { // get the property. return tripal_core_delete_property_by_id('analysisfeature', $analysisfeatureprop_id); } /** * Retrieve properties of a given type for a given feature * * @param $feature_id * The feature_id of the properties you would like to retrieve * @param $property * The cvterm name of the properties to retrieve * @param $cv_name * Optional. The name of the cv to which the property belongs. By * default this is the 'tripal' cv. * * @return * A feature chado variable with the specified properties expanded * * @ingroup tripal_feature_api */ function tripal_feature_get_property($feature_id, $property, $cv_name='tripal') { return tripal_core_get_property('feature', $feature_id, $property, $cv_name); } /** * Insert a given property * * @param $feature_id * The feature_id of the property to insert * @param $property * The cvterm name of the property to insert * @param $value * The value of the property to insert * @param $update_if_present * A boolean indicated whether to update the record if it's already present * @param $cv_name * Optional. The name of the cv to which the property belongs. By * default this is the 'tripal' cv. * * @return * True of success, False otherwise * * @ingroup tripal_feature_api */ function tripal_feature_insert_property($feature_id, $property, $value, $update_if_present = 0, $cv_name = 'tripal') { return tripal_core_insert_property('feature', $feature_id, $property, $cv_name, $value, $update_if_present); } /** * Update a feature property using the property name. Only use this * if the property is unique and only exist once for the feature. * * @param $feature_id * The feature_id of the property to update * @param $property * The cvterm name of the property to update * @param $value * The value of the property to update * @param $insert_if_missing * A boolean indicated whether to insert the record if it's absent * @param $cv_name * Optional. The name of the cv to which the property belongs. By * default this is the 'tripal' cv. * * Note: The property will be identified using the unique combination of the $feature_id and $property * and then it will be updated with the supplied value * * @return * True of success, False otherwise * * @ingroup tripal_feature_api */ function tripal_feature_update_property($feature_id, $property, $value, $insert_if_missing = 0, $cv_name = 'tripal') { return tripal_core_update_property('feature', $feature_id, $property, $cv_name, $value, $insert_if_missing); } /** * Update a given feature property using the featureprop_id * * @param $featureprop_id * The featureprop_id of the property to update * @param $property * The cvterm name of the property * @param $value * The value of the property * @param $cv_name * Optional. The name of the cv to which the property belongs. By * default this is the 'tripal' cv. * * @return * True of success, False otherwise * * @ingroup tripal_feature_api */ function tripal_feature_update_property_by_id($featureprop_id, $property, $value, $cv_name = 'tripal') { return tripal_core_update_property_by_id('feature', $featureprop_id, $property, $cv_name, $value); } /** * Delete a given feature property using the property name. Only use this * if the property is unique and only exists once for the feature. * * @param $feature_id * The feature_id of the property to delete * @param $property * The cvterm name of the property to delete * @param $cv_name * Optional. The name of the cv to which the property belongs. By * default this is the 'tripal' cv. * * Note: The property will be identified using the unique combination of the $feature_id and $property * and then it will be deleted * * @return * True of success, False otherwise * * @ingroup tripal_feature_api */ function tripal_feature_delete_property($feature_id, $property, $cv_name='tripal') { return tripal_core_delete_property('feature', $feature_id, $property, $cv_name); } /** * Delete a given feature property using the featureprop_id * * @param $featureprop_id * The feature_id of the property to delete * * @return * True of success, False otherwise * * @ingroup tripal_feature_api */ function tripal_feature_delete_property_by_id($featureprop_id) { return tripal_core_delete_property_by_id('feature', $featureprop_id); } /** * Performs a reverse compliment of a nucleotide sequence * * @param $sequence * The nucelotide sequence * * @return * an upper-case reverse complemented sequence * * @ingroup tripal_feature_api */ function tripal_feature_reverse_complement($sequence) { $seq = strtoupper($sequence); $seq = strrev($seq); $seq = str_replace("A", "t", $seq); $seq = str_replace("T", "a", $seq); $seq = str_replace("G", "c", $seq); $seq = str_replace("C", "g", $seq); $seq = str_replace("Y", "r", $seq); $seq = str_replace("R", "y", $seq); $seq = str_replace("W", "w", $seq); $seq = str_replace("S", "s", $seq); $seq = str_replace("K", "m", $seq); $seq = str_replace("M", "k", $seq); $seq = str_replace("D", "h", $seq); $seq = str_replace("V", "b", $seq); $seq = str_replace("H", "d", $seq); $seq = str_replace("B", "v", $seq); return strtoupper($seq); } /** * Retrieves the sequence for a feature. * * @param $feature_id * The feature_id of the feature for which the sequence will be retrieved * @param $feature_name * The feature name. This will appear on the FASTA definition line * @param $num_bases_per_line * Indicate the number of bases to use per line. A new line will be added * after the specified number of bases on each line. * @param $derive_from_parent * Set to '1' if the sequence should be obtained from the parent to which * this feature is aligned. * @param $aggregate * Set to '1' if the sequence should only contain sub features, excluding * intra sub feature sequence. For example, set this option to obtain just * the coding sequence of an mRNA. * @param $output_format * The type of format. Valid formats include 'fasta_html', 'fasta_txt' and * 'raw'. The format 'fasta_txt' outputs line * breaks as
tags and the entire return value is in a tag * with a fixed-width font definition. 'fasta_txt' outputs line breaks with * windows format carriage returns (e.g. \r\n) with no other formatting. The * raw format is simply the sequence with now FASTA formatting and no * line breaks. * @param $upstream * An integer specifing the number of upstream bases to include in the output * @param $downstream * An integer specifying the number of downstream bases to include in the * output. * * @return * The DNA/protein sequence formated as requested. * * @ingroup tripal_feature_api */ function tripal_feature_get_formatted_sequence($feature_id, $feature_name, $num_bases_per_line, $derive_from_parent, $aggregate, $output_format, $upstream, $downstream, $sub_features = array()) { // to speed things up we need to make sure we have a persistent connection $connection = tripal_db_persistent_chado(); if (!$upstream) { $upstream = 0; } if (!$downstream) { $downstream = 0; } // prepare statements we'll need to use later if (!tripal_core_is_sql_prepared('sequence_by_parent')) { // prepare the queries we're going to use later during the render phase // This SQL statement uses conditionals in the select clause to handle // cases cases where the alignment is in the reverse direction and when // the upstream and downstream extensions go beyond the lenght of the // parent sequence. $psql ='PREPARE sequence_by_parent (int, int, int) AS SELECT srcname, srcfeature_id, strand, srctypename, typename, fmin, fmax, upstream, downstream, adjfmin, adjfmax, substring(residues from (adjfmin + 1) for (upstream + (fmax - fmin) + downstream)) as residues FROM ( SELECT OF.name srcname, FL.srcfeature_id, FL.strand, OCVT.name as srctypename, SCVT.name as typename, FL.fmin, FL.fmax, CASE WHEN FL.strand >= 0 THEN CASE WHEN FL.fmin - $1 <= 0 THEN 0 ELSE FL.fmin - $1 END WHEN FL.strand < 0 THEN CASE WHEN FL.fmin - $2 <= 0 THEN 0 ELSE FL.fmin - $2 END END as adjfmin, CASE WHEN FL.strand >= 0 THEN CASE WHEN FL.fmax + $2 > OF.seqlen THEN OF.seqlen ELSE FL.fmax + $2 END WHEN FL.strand < 0 THEN CASE WHEN FL.fmax + $1 > OF.seqlen THEN OF.seqlen ELSE FL.fmax + $1 END END as adjfmax, CASE WHEN FL.strand >= 0 THEN CASE WHEN FL.fmin - $1 <= 0 THEN FL.fmin ELSE $1 END ELSE CASE WHEN FL.fmax + $1 > OF.seqlen THEN OF.seqlen - FL.fmax ELSE $1 END END as upstream, CASE WHEN FL.strand >= 0 THEN CASE WHEN FL.fmax + $2 > OF.seqlen THEN OF.seqlen - FL.fmax ELSE $2 END ELSE CASE WHEN FL.fmin - $2 <= 0 THEN FL.fmin ELSE $2 END END as downstream, OF.residues FROM featureloc FL INNER JOIN feature SF on FL.feature_id = SF.feature_id INNER JOIN cvterm SCVT on SF.type_id = SCVT.cvterm_id INNER JOIN feature OF on FL.srcfeature_id = OF.feature_id INNER JOIN cvterm OCVT on OF.type_id = OCVT.cvterm_id WHERE SF.feature_id = $3) as tbl1 '; $status = tripal_core_chado_prepare('sequence_by_parent', $psql, array('int', 'int', 'int')); if (!$status) { watchdog('tripal_views_handler_field_sequence', "init: not able to prepare SQL statement '%name'", array('%name' => 'sequence_by_parent'), 'WATCHDOG ERROR'); } // this query is meant to get all of the sub features of any given // feature (arg #1) and order them as they appear on the reference // feature (arg #2). $psql ='PREPARE sub_features (int, int) AS SELECT SF.feature_id, CVT.name as type_name, SF.type_id FROM feature_relationship FR INNER JOIN feature SF on SF.feature_id = FR.subject_id INNER JOIN cvterm CVT on CVT.cvterm_id = SF.type_id INNER JOIN featureloc FL on FL.feature_id = FR.subject_id INNER JOIN feature PF on PF.feature_id = FL.srcfeature_id WHERE FR.object_id = $1 and PF.feature_id = $2 ORDER BY FL.fmin ASC'; $status = tripal_core_chado_prepare('sub_features', $psql, array('int', 'int')); if (!$status) { watchdog('tripal_views_handler_field_sequence', "init: not able to prepare SQL statement '%name'", array('%name' => 'ssub_features'), 'WATCHDOG ERROR'); } $psql ='PREPARE count_sub_features (int, int) AS SELECT count(*) as num_children FROM feature_relationship FR INNER JOIN feature SF on SF.feature_id = FR.subject_id INNER JOIN cvterm CVT on CVT.cvterm_id = SF.type_id INNER JOIN featureloc FL on FL.feature_id = FR.subject_id INNER JOIN feature PF on PF.feature_id = FL.srcfeature_id WHERE FR.object_id = $1 and PF.feature_id = $2'; $status = tripal_core_chado_prepare('count_sub_features', $psql, array('int', 'int')); if (!$status) { watchdog('tripal_views_handler_field_sequence', "init: not able to prepare SQL statement '%name'", array('%name' => 'count_sub_features'), 'WATCHDOG ERROR'); } } // if we need to get the sequence from the parent then do so now. if ($derive_from_parent) { // execute the query to get the sequence from the parent $sql = "EXECUTE sequence_by_parent (%d, %d, %d)"; $parents = chado_query($sql, $upstream, $downstream, $feature_id); while ($parent = db_fetch_object($parents)) { $seq = ''; // initialize the sequence for each parent // if we are to aggregate then we will ignore the feature returned // by the query above and rebuild it using the sub features if ($aggregate) { // now get the sub features that are located on the parent. $sql = "EXECUTE sub_features (%d, %d)"; $children = chado_query($sql, $feature_id, $parent->srcfeature_id); $sql = "EXECUTE count_sub_features (%d, %d)"; $num_children = db_fetch_object(chado_query($sql, $feature_id, $parent->srcfeature_id)); // iterate through the sub features and concat their sequences. They // should already be in order. $types = array(); $i = 0; while ($child = db_fetch_object($children)) { // if the callee has specified that only certain sub features should be // included then continue of this child is not one of those allowed // subfeatures if (count($sub_features) > 0 and !in_array($child->type_name, $sub_features)) { continue; } // keep up with the types if (!in_array($child->type_name, $types)) { $types[] = $child->type_name; } $sql = "EXECUTE sequence_by_parent (%d, %d, %d)"; // if the first sub feature we need to include the upstream bases if ($i == 0 and $parent->strand >= 0) { // forward direction // -------------------------- ref // ....----> ----> // up 1 2 $q = chado_query($sql, $upstream, 0, $child->feature_id); } elseif ($i == 0 and $parent->strand < 0) { // reverse direction // -------------------------- ref // ....<---- <---- // down 1 2 $q = chado_query($sql, 0, $downstream, $child->feature_id); } // if the last sub feature we need to include the downstream bases elseif ($i == $num_children->num_children - 1 and $parent->strand >= 0) { // forward direction // -------------------------- ref // ----> ---->.... // 1 2 down $q = chado_query($sql, 0, $downstream, $child->feature_id); } elseif ($i == $num_children->num_children - 1 and $parent->strand < 0) { // reverse direction // -------------------------- ref // <---- <----.... // 1 2 up $q = chado_query($sql, $upstream, 0, $child->feature_id); } // for internal sub features we don't want upstream or downstream bases else { $sql = "EXECUTE sequence_by_parent (%d, %d, %d)"; $q = chado_query($sql, 0, 0, $child->feature_id); } while ($subseq = db_fetch_object($q)) { // concatenate the sequences of all the sub features if ($subseq->srcfeature_id == $parent->srcfeature_id) { $seq .= $subseq->residues; } } $i++; } } // if this isn't an aggregate then use the parent residues else { $seq = $parent->residues; } // get the reverse compliment if feature is on the reverse strand $dir = 'forward'; if ($parent->strand < 0) { $seq = tripal_feature_reverse_complement($seq); $dir = 'reverse'; } // now format for display if ($output_format == 'fasta_html') { $seq = wordwrap($seq, $num_bases_per_line, "
", TRUE); } elseif ($output_format == 'fasta_txt') { $seq = wordwrap($seq, $num_bases_per_line, "\n", TRUE); } $residues .= ">$feature_name ($parent->typename) $parent->srcname:" . ($parent->adjfmin + 1) . ".." . $parent->adjfmax ." ($dir). "; if (count($types) > 0) { $residues .= "Excludes all bases but those of type(s): " . implode(', ', $types) . ". " ; } if ($parent->upstream > 0) { $residues .= "Includes " . $parent->upstream . " bases upstream. "; } if ($parent->downstream > 0) { $residues .= "Includes " . $parent->downstream . " bases downstream. "; } if (!$seq) { if ($output_format == 'fasta_html') { $residues .= "No sequence available.
"; } else { $residues .= "No sequence available.\n"; } } else { if ($output_format == 'fasta_html') { $residues .= "
"; } $residues .= "\n" . $seq . "\n"; if ($output_format == 'fasta_html') { $residues .= "
"; } } } } // if we are not getting the sequence from the parent sequence then // use what comes through from the feature record else { $sql = "SELECT * FROM feature F WHERE feature_id = %d"; $values = db_fetch_object(chado_query($sql, $feature_id)); $residues = $values->residues; if ($output_format == 'fasta_html') { $residues = wordwrap($residues, $num_bases_per_line, "
", TRUE); } elseif ($output_format == 'fasta_txt') { $residues = wordwrap($residues, $num_bases_per_line, "\n", TRUE); } $residues = ">$feature_name\n$residues\n"; } // format the residues for display if ($residues and $num_bases_per_line) { if ($output_format == 'fasta_html') { $residues = '' . $residues . ''; } } return $residues; } /** * This function defines the custom tables that will be created * in the chado schema. * * @ingroup tripal_feature */ function tripal_feature_get_custom_tables($table = NULL) { if (!$table or strcmp($table, 'tripal_gff_temp')==0) { $schema['tripal_gff_temp'] = array( 'table' => 'tripal_gff_temp', 'fields' => array( 'feature_id' => array( 'type' => 'int', 'not null' => TRUE, ), 'organism_id' => array( 'type' => 'int', 'not null' => TRUE, ), 'uniquename' => array( 'type' => 'text', 'not null' => TRUE, ), 'type_name' => array( 'type' => 'varchar', 'length' => '1024', 'not null' => TRUE, ), ), 'indexes' => array( 'tripal_gff_temp_idx0' => array('feature_id'), 'tripal_gff_temp_idx0' => array('organism_id'), 'tripal_gff_temp_idx1' => array('uniquename'), ), 'unique keys' => array( 'tripal_gff_temp_uq0' => array('feature_id'), 'tripal_gff_temp_uq1' => array('uniquename', 'organism_id', 'type_name'), ), ); } return $schema; } /** * Using the tripal_core_expand_chado_vars function to retrieve a set * of relationships can be very slow, especialy if there are many relationships * This function is intended to help speed up the retrieval of relationships * by only retrieving the base information for the relationship and returning * an array with * * @param $feature * The feature object * @return * An array with two objects * * @ingroup tripal_feature_api */ function tripal_feature_get_feature_relationships($feature) { // expand the feature object to include the feature relationships. $options = array( 'return_array' => 1, 'order_by' => array('rank' => 'ASC'), ); $feature = tripal_core_expand_chado_vars($feature, 'table', 'feature_relationship', $options); // get the subject relationships $srelationships = $feature->feature_relationship->subject_id; $orelationships = $feature->feature_relationship->object_id; // get alignment as child. The $feature->featureloc element // is already populated from the alignment preprocess function $feature = tripal_core_expand_chado_vars($feature, 'table', 'featureloc'); $cfeaturelocs = $feature->featureloc->feature_id; if (!$cfeaturelocs) { $cfeaturelocs = array(); } elseif (!is_array($cfeaturelocs)) { $cfeaturelocs = array($cfeaturelocs); } // prepare the SQL statement to get the featureloc for the // feature in the relationships. $connection = tripal_db_persistent_chado(); $psql = " PREPARE sel_featureloc_preprocess_relationships (int, int) AS SELECT FL.featureloc_id, F.name as srcfeature_name, FL.srcfeature_id, FL.feature_id, FL.fmin, FL.fmax, FL.strand, FL.phase FROM featureloc FL INNER JOIN feature F ON F.feature_id = FL.srcfeature_id WHERE FL.feature_id = $1 and FL.srcfeature_id = $2 "; tripal_core_chado_prepare('sel_featureloc_preprocess_relationships', $psql, array('int', 'int')); // combine both object and subject relationshisp into a single array $relationships = array(); $relationships['object'] = array(); $relationships['subject'] = array(); // iterate through the object relationships if ($orelationships) { foreach ($orelationships as $relationship) { $rel = new stdClass(); // get locations where the child feature and this feature overlap with the // same landmark feature. $rel->child_featurelocs = array(); foreach ($cfeaturelocs as $featureloc) { $res = chado_query("EXECUTE sel_featureloc_preprocess_relationships (%d, %d)", $relationship->subject_id->feature_id, $featureloc->srcfeature_id->feature_id); while ($loc = db_fetch_object($res)) { // add in the node id of the src feature if it exists and save this location $loc->nid = $featureloc->srcfeature_id->nid; $rel->child_featurelocs[] = $loc; } } $rel->record = $relationship; // get the relationship and child types $rel_type = t(preg_replace('/_/', " ", $relationship->type_id->name)); $child_type = $relationship->subject_id->type_id->name; // get the node id of the subject $sql = "SELECT nid FROM {chado_feature} WHERE feature_id = %d"; $n = db_fetch_object(db_query($sql, $relationship->subject_id->feature_id)); if ($n) { $rel->record->nid = $n->nid; } if (!array_key_exists($rel_type, $relationships['object'])) { $relationships['object'][$rel_type] = array(); } if (!array_key_exists($child_type, $relationships['object'][$rel_type])) { $relationships['object'][$rel_type][$child_type] = array(); } $relationships['object'][$rel_type][$child_type][] = $rel; } } // now add in the subject relationships if ($srelationships) { foreach ($srelationships as $relationship) { $rel = new stdClass(); // get locations where this feature overlaps with the parent $rel->parent_featurelocs = array(); foreach ($cfeaturelocs as $featureloc) { $res = chado_query("EXECUTE sel_featureloc_preprocess_relationships (%d, %d)", $relationship->object_id->feature_id, $featureloc->srcfeature_id->feature_id); while ($loc = db_fetch_object($res)) { // add in the node id of the src feature if it exists and save this location $loc->nid = $featureloc->srcfeature_id->nid; $rel->parent_featurelocs[] = $loc; } } $rel->record = $relationship; $rel_type = t(preg_replace('/_/', " ", $relationship->type_id->name)); $parent_type = $relationship->object_id->type_id->name; // get the node id of the subject $sql = "SELECT nid FROM {chado_feature} WHERE feature_id = %d"; $n = db_fetch_object(db_query($sql, $relationship->object_id->feature_id)); if ($n) { $rel->record->nid = $n->nid; } if (!array_key_exists($rel_type, $relationships['subject'])) { $relationships['subject'][$rel_type] = array(); } if (!array_key_exists($child_type, $relationships['subject'][$rel_type])) { $relationships['subject'][$rel_type][$parent_type] = array(); } $relationships['subject'][$rel_type][$parent_type][] = $rel; } } return $relationships; }