|  | @@ -29,7 +29,7 @@ require_once "includes/tripal_feature.form.inc";
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				|  |  |   *
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				|  |  |   * @ingroup tripal_feature
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				|  |  |   */
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				|  |  | -function tripal_feature_init() { 
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				|  |  | +function tripal_feature_init() {
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				|  |  |    drupal_add_css(drupal_get_path('module', 'tripal_feature') . '/theme/css/tripal_feature.css');
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				|  |  |    drupal_add_js(drupal_get_path('module', 'tripal_feature') . '/theme/js/tripal_feature.js');
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				|  |  |  }
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				|  | @@ -292,7 +292,7 @@ function tripal_feature_menu() {
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				|  |  |   */
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				|  |  |  function tripal_feature_theme($existing, $type, $theme, $path) {
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				|  |  |    $core_path = drupal_get_path('module', 'tripal_core');
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				|  |  | -  
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				|  |  | +
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				|  |  |    $items = array(
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				|  |  |      'node__chado_feature' => array(
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				|  |  |        'template' => 'node--chado-generic',
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				|  | @@ -377,12 +377,12 @@ function tripal_feature_theme($existing, $type, $theme, $path) {
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				|  |  |        'template' => 'tripal_organism_feature_counts',
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				|  |  |        'path' => "$path/theme/tripal_organism",
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				|  |  |      ),
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				|  |  | -    
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				|  |  | +
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				|  |  |      // themed forms
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				|  |  |      'tripal_feature_seq_extract_form' => array(
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				|  |  |         'arguments' => array('form'),
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				|  |  |      ),
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				|  |  | -    
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				|  |  | +
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				|  |  |      // themed teaser
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				|  |  |      'tripal_feature_teaser' => array(
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				|  |  |        'variables' => array('node' => NULL),
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				|  | @@ -390,7 +390,7 @@ function tripal_feature_theme($existing, $type, $theme, $path) {
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				|  |  |        'path' => "$path/theme/tripal_feature",
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				|  |  |      ),
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				|  |  |    );
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				|  |  | -  
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				|  |  | +
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				|  |  |    return $items;
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				|  |  |  }
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				|  |  |  /**
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				|  | @@ -401,37 +401,37 @@ function tripal_feature_theme($existing, $type, $theme, $path) {
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				|  |  |  function tripal_feature_block_info() {
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				|  |  |  
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				|  |  |    $blocks['references']['info'] = t('Tripal Feature References');
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				|  |  | -  $blocks['references']['cache'] = BLOCK_NO_CACHE;
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				|  |  | +  $blocks['references']['cache'] = 'BLOCK_NO_CACHE';
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				|  |  |  
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				|  |  |    $blocks['base']['info'] = t('Tripal Feature Details');
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				|  |  | -  $blocks['base']['cache'] = BLOCK_NO_CACHE;
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				|  |  | +  $blocks['base']['cache'] = 'BLOCK_NO_CACHE';
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				|  |  |  
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				|  |  |    $blocks['sequence']['info'] = t('Tripal Feature Sequence');
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				|  |  | -  $blocks['sequence']['cache'] = BLOCK_NO_CACHE;
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				|  |  | +  $blocks['sequence']['cache'] = 'BLOCK_NO_CACHE';
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				|  |  |  
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				|  |  |    $blocks['featureloc_sequences']['info'] = t('Tripal Feature Annotated Sequence');
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				|  |  | -  $blocks['featureloc_sequences']['cache'] = BLOCK_NO_CACHE;
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				|  |  | +  $blocks['featureloc_sequences']['cache'] = 'BLOCK_NO_CACHE';
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				|  |  |  
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				|  |  |    $blocks['synonyms']['info'] = t('Tripal Feature Synonyms');
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				|  |  | -  $blocks['synonyms']['cache'] = BLOCK_NO_CACHE;
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				|  |  | +  $blocks['synonyms']['cache'] = 'BLOCK_NO_CACHE';
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				|  |  |  
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				|  |  |    $blocks['properties']['info'] = t('Tripal Feature Properties');
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				|  |  | -  $blocks['properties']['cache'] = BLOCK_NO_CACHE;;
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				|  |  | +  $blocks['properties']['cache'] = 'BLOCK_NO_CACHE';;
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				|  |  |  
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				|  |  |    $blocks['terms']['info'] = t('Tripal Annotated Terms');
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				|  |  | -  $blocks['terms']['cache'] = BLOCK_NO_CACHE;;
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				|  |  | +  $blocks['terms']['cache'] = 'BLOCK_NO_CACHE';;
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				|  |  |  
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				|  |  |    $blocks['alignments']['info'] = t('Tripal Feature Alignments');
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				|  |  | -  $blocks['alignments']['cache'] = BLOCK_NO_CACHE;
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				|  |  | +  $blocks['alignments']['cache'] = 'BLOCK_NO_CACHE';
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				|  |  |  
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				|  |  |    $blocks['relationships']['info'] = t('Tripal Feature Relationships');
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				|  |  | -  $blocks['relationships']['cache'] = BLOCK_NO_CACHE;
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				|  |  | +  $blocks['relationships']['cache'] = 'BLOCK_NO_CACHE';
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				|  |  |  
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				|  |  |    $blocks['org_feature_counts']['info'] = t('Tripal Organism Feature Counts');
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				|  |  | -  $blocks['org_feature_counts']['cache'] = BLOCK_NO_CACHE;
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				|  |  | +  $blocks['org_feature_counts']['cache'] = 'BLOCK_NO_CACHE';
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				|  |  |  
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				|  |  |    $blocks['org_feature_browser']['info'] = t('Tripal Organism Feature Browser');
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				|  |  | -  $blocks['org_feature_browser']['cache'] = BLOCK_NO_CACHE;
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				|  |  | +  $blocks['org_feature_browser']['cache'] = 'BLOCK_NO_CACHE';
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				|  |  |  
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				|  |  |    return $blocks;
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				|  |  |  }
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				|  | @@ -513,19 +513,19 @@ function tripal_feature_block_view($delta = '') {
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				|  |  |   * @ingroup tripal_feature
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				|  |  |   */
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				|  |  |  function chado_feature_insert($node) {
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				|  |  | -  
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				|  |  | +
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				|  |  |    $node->uniquename   = trim($node->uniquename);
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				|  |  |    $node->fname        = trim($node->fname);
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				|  |  |    $node->feature_type = trim($node->feature_type);
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				|  |  |    $node->residues     = trim($node->residues);
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				|  |  | -  
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				|  |  | +
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				|  |  |    // remove spaces, newlines from residues
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				|  |  |    $residues = preg_replace("/[\n\r\s]/", "", $node->residues);
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				|  |  |    $obsolete = 'FALSE';
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				|  |  |    if ($node->is_obsolete) {
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				|  |  |      $obsolete = 'TRUE';
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				|  |  |    }
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				|  |  | -  
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				|  |  | +
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				|  |  |    $feature_id = '';
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				|  |  |  
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				|  |  |    // if there is an feature_id in the $node object then this must be a sync so
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				|  | @@ -550,7 +550,7 @@ function chado_feature_insert($node) {
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				|  |  |        return;
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				|  |  |      }
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				|  |  |      $feature_id = $feature->feature_id;
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				|  |  | -    
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				|  |  | +
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				|  |  |      // add the genbank accession and synonyms
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				|  |  |      chado_feature_add_synonyms($node->synonyms, $node->feature_id);
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				|  |  |    }
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				|  | @@ -576,12 +576,12 @@ function chado_feature_insert($node) {
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				|  |  |   * @ingroup tripal_feature
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				|  |  |   */
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				|  |  |  function chado_feature_update($node) {
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				|  |  | -  
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				|  |  | +
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				|  |  |    $node->uniquename   = trim($node->uniquename);
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				|  |  |    $node->fname        = trim($node->fname);
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				|  |  |    $node->feature_type = trim($node->feature_type);
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				|  |  |    $node->residues     = trim($node->residues);
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				|  |  | -  
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				|  |  | +
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				|  |  |    if ($node->revision) {
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				|  |  |      // there is no way to handle revisions in Chado but leave
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				|  |  |      // this here just to make not we've addressed it.
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				|  | @@ -697,7 +697,7 @@ function chado_feature_add_synonyms($synonyms, $feature_id) {
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				|  |  |    foreach ($syn_array as $syn) {
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				|  |  |      // skip this item if it's empty
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				|  |  |      if (!$syn) {
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				|  |  | -      break; 
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				|  |  | +      break;
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				|  |  |      }
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				|  |  |  
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				|  |  |      // check to see if we have this accession number already in the database
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				|  | @@ -747,7 +747,7 @@ function chado_feature_load($nodes) {
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				|  |  |    foreach ($nodes as $nid => $node) {
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				|  |  |      // find the feature and add in the details
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				|  |  |      $feature_id = chado_get_id_for_node('feature', $nid);
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				|  |  | -  
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				|  |  | +
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				|  |  |      // build the feature variable
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				|  |  |      $values = array('feature_id' => $feature_id);
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				|  |  |      $feature = tripal_core_generate_chado_var('feature', $values);
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				|  | @@ -1455,7 +1455,7 @@ function tripal_feature_node_update($node) {
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				|  |  |  function tripal_feature_preprocess_tripal_feature_sequence(&$variables) {
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				|  |  |    // we want to provide a new variable that contains the matched features.
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				|  |  |    $feature = $variables['node']->feature;
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				|  |  | -  
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				|  |  | +
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				|  |  |    // get the featureloc src features
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				|  |  |    $options = array(
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				|  |  |      'return_array' => 1,
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				|  | @@ -1467,11 +1467,11 @@ function tripal_feature_preprocess_tripal_feature_sequence(&$variables) {
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				|  |  |    );
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				|  |  |  
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				|  |  |    $feature = tripal_core_expand_chado_vars($feature, 'table', 'featureloc', $options);
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				|  |  | -  
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				|  |  | +
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				|  |  |    // because there are two foriegn keys in the featureloc table with the feature table
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				|  |  |    // we have to access the records for each by specifying the field name after the table name:
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				|  |  |    $ffeaturelocs = $feature->featureloc->feature_id;
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				|  |  | -  
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				|  |  | +
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				|  |  |    // now extract the sequences
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				|  |  |    $featureloc_sequences = tripal_feature_load_featureloc_sequences($feature->feature_id, $ffeaturelocs);
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				|  |  |    $feature->featureloc_sequences = $featureloc_sequences;
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				|  | @@ -1568,7 +1568,7 @@ function tripal_feature_preprocess_tripal_feature_alignments(&$variables) {
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				|  |  |      }
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				|  |  |      $alignment = new stdClass();
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				|  |  |      $alignment->record = $featureloc;
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				|  |  | -    $alignment->name = $featureloc->srcfeature_id->name;    
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				|  |  | +    $alignment->name = $featureloc->srcfeature_id->name;
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				|  |  |      $alignment->type = $featureloc->srcfeature_id->type_id->name;
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				|  |  |      $alignment->fmin = $featureloc->fmin;
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				|  |  |      $alignment->is_fmin_partial = $featureloc->is_fmin_partial;
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				|  | @@ -1911,7 +1911,7 @@ function tripal_feature_match_features_page($id) {
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				|  |  |  
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				|  |  |  /**
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				|  |  |   * Implementation of hook_form_alter()
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				|  |  | - * 
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				|  |  | + *
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				|  |  |   * @param $form
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				|  |  |   * @param $form_state
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				|  |  |   * @param $form_id
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