tripal/tripal_feature/tripal_feature.module

<?php

/**
 * @defgroup tripal_feature Feature
 * @{
 * Provides functions for managing chado features including creating details pages for each feature
 * @}
 * @ingroup tripal_modules
 */
 
require_once "tripal_feature.admin.inc";
require_once "syncFeatures.php";
require_once "indexFeatures.php";
require_once "fasta_loader.php";
require_once "gff_loader.php";

require_once "tripal_feature.api.inc";

require_once "tripal_feature-secondary_tables.inc";
require_once "tripal_feature-properties.inc";
require_once "tripal_feature-relationships.inc";
require_once "tripal_feature-db_references.inc";


/**
 *
 * @ingroup tripal_feature
 */
function tripal_feature_init(){

   // add the jGCharts JS and CSS
   drupal_add_js (drupal_get_path('theme', 'tripal').'/js/tripal_feature.js'); 
   drupal_add_js (drupal_get_path('theme', 'tripal').'/js/jgcharts/jgcharts.js'); 

   drupal_add_css(drupal_get_path('theme', 'tripal').
                                  '/css/tripal_feature.css');
}

/**
 * Implements hook_views_api()
 *
 * Purpose: Essentially this hook tells drupal that there is views support for
 *  for this module which then includes tripal_db.views.inc where all the
 *  views integration code is
 *
 * @ingroup tripal_feature
 */ 
function tripal_feature_views_api() {
   return array(
      'api' => 2.0,
   );
}

/**
 * Display help and module information
 *
 * @param 
 *   path which path of the site we're displaying help
 * @param 
 *   arg array that holds the current path as would be returned from arg() function
 *
 * @return 
 *   help text for the path
 *
 * @ingroup tripal_feature
 */
function tripal_feature_help($path, $arg) {
   $output = '';
   switch ($path) {
      case "admin/help#tripal_feature":
         $output='<p>'.t("Displays links to nodes created on this date").'</p>';
         break;
   }
   return $output;
}

/**
 *  Provide information to drupal about the node types that we're creating
 *  in this module
 *
 * @ingroup tripal_feature
 */
function tripal_feature_node_info() {
   $nodes = array();

   $nodes['chado_feature'] = array(
      'name' => t('Feature'),
      'module' => 'chado_feature',
      'description' => t('A feature from the chado database'),
      'has_title' => FALSE,
      'title_label' => t('Feature'),
      'has_body' => FALSE,
      'body_label' => t('Feature Description'),
      'locked' => TRUE
   );
   return $nodes;
}

/**
 *  Set the permission types that the chado module uses.  Essentially we
 *  want permissionis that protect creation, editing and deleting of chado
 *  data objects
 *
 * @ingroup tripal_feature
 */
function tripal_feature_perm(){
   return array(
      'access chado_feature content',
      'create chado_feature content',
      'delete chado_feature content',
      'edit chado_feature content',
      'manage chado_feature aggregator',
   );
}

/**
 *  Set the permission types that the module uses.
 *
 * @ingroup tripal_feature
 */
function chado_feature_access($op, $node, $account) {
   if ($op == 'create') {
      return user_access('create chado_feature content', $account);
   }

   if ($op == 'update') {
      if (user_access('edit chado_feature content', $account)) {
         return TRUE;
      }
   }
   if ($op == 'delete') {
      if (user_access('delete chado_feature content', $account)) {
         return TRUE;
      }
   }
   if ($op == 'view') {
      if (user_access('access chado_feature content', $account)) {
         return TRUE;
      }
   }
   return FALSE;
}
/**
 *  Menu items are automatically added for the new node types created
 *  by this module to the 'Create Content' Navigation menu item.  This function
 *  adds more menu items needed for this module.
 *
 * @ingroup tripal_feature
 */
function tripal_feature_menu() {
   $items = array();

   // the administative settings menu
   $items['admin/tripal/tripal_feature'] = array(
     'title' => 'Features',
     'description' => 'Basic Description of Tripal Organism Module Functionality',
     'page callback' => 'tripal_feature_module_description_page',
     'access arguments' => array('administer site configuration'),
     'type' => MENU_NORMAL_ITEM,
   );
   $items['admin/tripal/tripal_feature/configuration'] = array(
     'title' => 'Feature Configuration',
     'description' => 'Settings for Chado Features',
     'page callback' => 'drupal_get_form',
     'page arguments' => array('tripal_feature_admin'),
     'access arguments' => array('administer site configuration'),
     'type' => MENU_NORMAL_ITEM,
   );
   $items['admin/tripal/tripal_feature/fasta_loader'] = array(
     'title' => 'Import a multi-FASTA file',
     'description' => 'Load sequences from a multi-FASTA file into Chado',
     'page callback' => 'drupal_get_form',
     'page arguments' => array('tripal_feature_fasta_load_form'),
     'access arguments' => array('administer site configuration'),
     'type' => MENU_NORMAL_ITEM,
   );
   $items['admin/tripal/tripal_feature/gff3_load'] = array(
     'title' => 'Import a GFF3 file',
     'description' => 'Import a GFF3 file into Chado',
     'page callback' => 'drupal_get_form',
     'page arguments' => array('tripal_core_gff3_load_form'),
     'access arguments' => array('access administration pages'),
     'type' => MENU_NORMAL_ITEM,
   );  

  // Adding Secondary Properties


  $items['node/%tf_node/tf_properties'] = array(       
    'title' => t('Add Properties & Synonyms'),                         
    'description' => t('Settings for Features'),
    'page callback' => 'tripal_feature_add_ALL_property_page',           
    'page arguments' => array(1), 
    'access arguments' => array('create chado_feature content'),
    'type' => MENU_CALLBACK
  ); 

  $items['node/%tf_node/tf_db_references'] = array(                        
    'title' => t('Add Database References'),                   
    'description' => t('Settings for Features'),              
    'page callback' => 'tripal_feature_add_ALL_dbreferences_page',                         
    'page arguments' => array(1),
    'access arguments' => array('create chado_feature content'),
    'type' => MENU_CALLBACK
  ); 

  $items['node/%tf_node/tf_relationships'] = array(                      
    'title' => t('Add Relationships'),                      
    'description' => t('Settings for Features'),               
    'page callback' => 'tripal_feature_add_ALL_relationships_page',                          
    'page arguments' => array(1),
    'access arguments' => array('create chado_feature content'),
    'type' => MENU_CALLBACK
  );
  //Edit/Deleting Secondary Properties-------------
/**
  $items['node/%tf_node/tf_edit_properties'] = array(
    'title' => t('Edit Properties'),
    'description' => t('Settings for Features'),
    'page callback' => 'tripal_feature_edit_ALL_properties_page',
    'page arguments' => array(1),
    'access arguments' => array('edit chado_feature content'),
    'type' => MENU_LOCAL_TASK,
    'weight' => 8,
  );

    $items['node/%tf_node/tf_edit_relationships'] = array(
    'title' => t('Edit Relationships'),
    'description' => t('Settings for Feature'), 
    'page callback' => 'tripal_feature_edit_ALL_relationships_page',
    'page arguments' => array(1),
    'access arguments' => array('edit chado_feature content'),
    'type' => MENU_LOCAL_TASK,
    'weight' => 9,
  );
*/
  $items['node/%tf_node/tf_edit_db_references'] = array(
    'title' => t('Edit References'),
    'description' => t('Settings for Feature'),
    'page callback' => 'tripal_feature_edit_ALL_dbreferences_page',
    'page arguments' => array(1),
    'access arguments' => array('edit chado_feature content'),
    'type' => MENU_LOCAL_TASK,
    'weight' => 10,
  );

 // managing relationship aggregates
   $items['admin/tripal/tripal_feature/aggregate'] = array(
     'title' => 'Feature Relationship Aggegators',
     'description' => t('Features have relationships with other features and it may be desirable to aggregate the content from one ore more child or parent feature.'),
     'page callback' => 'tripal_feature_aggregator_page',
     'access arguments' => array('manage chado_feature aggregator'),
     'type' => MENU_NORMAL_ITEM,
   );

   $items['admin/tripal/tripal_feature/aggregate/new'] = array(
     'title' => 'Add an Aggregator',
     'page callback' => 'drupal_get_form',
     'page arguments' => array('tripal_feature_aggregator_form'),
     'access arguments' => array('manage chado_feature aggregator'),
     'type' => MENU_NORMAL_ITEM,
   );
   $items['admin/tripal/tripal_feature/aggregate/edit/js'] = array(
     'title' => 'Edit an Aggegator',
     'page callback' => 'tripal_feature_aggregator_ajax_edit',
     'access arguments' => array('manage chado_feature aggregator'),
     'type' => MENU_CALLBACK,
   );

   return $items;
}

/**
 * Implements Menu wildcard_load hook
 * Purpose: Allows the node ID of a chado feature to be dynamically 
 *   pulled from the path. The node is loaded from this node ID
 *   and supplied to the page as an arguement
 *
 * @ingroup tripal_feature
 */
function tf_node_load($nid) {
  if (is_numeric($nid)) {
    $node = node_load($nid);
    if ($node->type == 'chado_feature') {
      return $node;
    }
  }
  return FALSE;
}
/**
 *
 *
 * @ingroup tripal_feature
 */
function tripal_feature_block($op = 'list', $delta = 0, $edit=array()){
   switch($op) {
      case 'list':
         $blocks['references']['info'] = t('Tripal Feature References');
         $blocks['references']['cache'] = BLOCK_NO_CACHE;

         $blocks['base']['info'] = t('Tripal Feature Details');
         $blocks['base']['cache'] = BLOCK_NO_CACHE;

         $blocks['sequence']['info'] = t('Tripal Feature Sequence');
         $blocks['sequence']['cache'] = BLOCK_NO_CACHE;

         $blocks['synonyms']['info'] = t('Tripal Feature Synonyms');
         $blocks['synonyms']['cache'] = BLOCK_NO_CACHE;

         $blocks['properties']['info'] = t('Tripal Feature Properties');
         $blocks['properties']['cache'] = BLOCK_NO_CACHE;;

         $blocks['featureloc_sequences']['info'] = t('Tripal Formatted Sequence');
         $blocks['featureloc_sequences']['cache'] = BLOCK_NO_CACHE;

         $blocks['alignments']['info'] = t('Tripal Feature Alignments');
         $blocks['alignments']['cache'] = BLOCK_NO_CACHE;

         $blocks['relationships']['info'] = t('Tripal Feature Relationships');
         $blocks['relationships']['cache'] = BLOCK_NO_CACHE;

         $blocks['org_feature_counts']['info'] = t('Tripal Organism Feature Counts');
         $blocks['org_feature_counts']['cache'] = BLOCK_NO_CACHE;

         $blocks['org_feature_browser']['info'] = t('Tripal Organism Feature Browser');
         $blocks['org_feature_browser']['cache'] = BLOCK_NO_CACHE;
         return $blocks;


      case 'view':
         if(user_access('access chado_feature content') and arg(0) == 'node' and is_numeric(arg(1))) {
            $nid = arg(1);
            $node = node_load($nid);
 
            $block = array();
            switch($delta){
               case 'references':
                  $block['subject'] = t('References');
                  $block['content'] = theme('tripal_feature_references',$node);
                  break;
               case 'base':
                  $block['subject'] = t('Feature Details');
                  $block['content'] = theme('tripal_feature_base',$node);
                  break;
               case 'synonyms':
                  $block['subject'] = t('Synonyms');
                  $block['content'] = theme('tripal_feature_synonyms',$node);
                  break;
               case 'properties':
                  $block['subject'] = t('Properties');
                  $block['content'] = theme('tripal_feature_properties',$node);
                  break;;
               case 'sequence':
                  $block['subject'] = t('Sequence');
                  $block['content'] = theme('tripal_feature_sequence',$node);
                  break;
               case 'featureloc_sequences':
                  $block['subject'] = t('Formatted Sequences');
                  $block['content'] = theme('tripal_feature_featureloc_sequences',$node);
                  break;
               case 'alignments':
                  $block['subject'] = t('Alignments');
                  $block['content'] = theme('tripal_feature_featurelocs',$node);
                  break;
               case 'relationships':
                  $block['subject'] = t('Relationships');
                  $block['content'] = theme('tripal_feature_relationships',$node);
                  break;
               case 'org_feature_counts':
                  $block['subject'] = t('Feature Type Summary');
                  $block['content'] = theme('tripal_organism_feature_counts', $node);
                  break;
               case 'org_feature_browser':
                  $block['subject'] = t('Feature Browser');
                  $block['content'] = theme('tripal_organism_feature_browser', $node);
                  break;
               default :
            }
            return $block;
         }

   }
}
/**
 *  When a new chado_feature node is created we also need to add information
 *  to our chado_feature table.  This function is called on insert of a new node
 *  of type 'chado_feature' and inserts the necessary information.
 *
 * @ingroup tripal_feature
 */
function chado_feature_insert($node){
   // remove spaces, newlines from residues
   $residues = preg_replace("/[\n\r\s]/","",$node->residues);
   $obsolete = 'FALSE';
   if($node->is_obsolete){
      $obsolete = 'TRUE';
   }
   $values = array(
      'cv_id' => array(
         'name' => 'sequence'
      ),
      'name' => $node->feature_type
   );
   $type = tripal_core_chado_select('cvterm',array('cvterm_id'),$values);
   $values = array(
      'organism_id' => $node->organism_id,
      'name' => $node->fname,
      'uniquename' => $node->uniquename,
      'residues' => $residues,
      'seqlen' => strlen($residues),
      'is_obsolete' => $obsolete,
      'type_id' => $type[0]->cvterm_id,
      'md5checksum' => md5($residues)
   );

   $istatus = tripal_core_chado_insert('feature', $values);
   if (!$istatus) {
		drupal_set_message('Unable to add feature.', 'warning');
		watchdog('tripal_organism', 
			'Insert feature: Unable to create feature where values: %values', 
			array('%values' => print_r($values, TRUE)),
			WATCHDOG_WARNING
		);
	}  
   $values = array(
      'organism_id' => $node->organism_id,
      'uniquename' => $node->uniquename,
      'type_id' => $type[0]->cvterm_id,
   );
   $feature = tripal_core_chado_select('feature',array('feature_id'),$values);   
   // add the genbank accession and synonyms
   chado_feature_add_synonyms($node->synonyms,$feature[0]->feature_id);

   // make sure the entry for this feature doesn't already exist in the chado_feature table
   // if it doesn't exist then we want to add it.
   $node_check_sql = "SELECT * FROM {chado_feature} ".
                     "WHERE feature_id = '%s'";
   $node_check = db_fetch_object(db_query($node_check_sql,$feature[0]->feature_id));
   if(!$node_check){
      // next add the item to the drupal table
      $sql = "INSERT INTO {chado_feature} (nid, vid, feature_id, sync_date) ".
             "VALUES (%d, %d, %d, " . time() . ")";
      db_query($sql,$node->nid,$node->vid,$feature[0]->feature_id);
   }
}
/**
 *
 *
 * @ingroup tripal_feature
 */
function chado_feature_update($node){
   if($node->revision){
      // TODO -- decide what to do about revisions
   } else {
      $residues = preg_replace("/[\n\r\s]/","",$node->residues);
      $obsolete = 'FALSE';
      if($node->is_obsolete){
         $obsolete = 'TRUE';
      }

      // get the feature type id
      $values = array(
         'cv_id' => array(
            'name' => 'sequence'
         ),
         'name' => $node->feature_type
      );
      $type = tripal_core_chado_select('cvterm',array('cvterm_id'),$values);

      $feature_id = chado_get_id_for_node('feature',$node) ;

      if(sizeof($type) > 0){
         $match = array(
            'feature_id' => $feature_id,
         );     
         $values = array(
            'organism_id' => $node->organism_id,
            'name' => $node->fname,
            'uniquename' => $node->uniquename,
            'residues' => $residues,
            'seqlen' => strlen($residues),
            'is_obsolete' => $obsolete,
            'type_id' => $type[0]->cvterm_id,
            'md5checksum' => md5($residues)
         );
         $status = tripal_core_chado_update('feature', $match,$values); 

         // add the genbank synonyms
         chado_feature_add_synonyms($node->synonyms,$feature_id);
      }    
      else {
		   drupal_set_message('Unable to update feature.', 'warning');
		   watchdog('tripal_organism', 
			   'Update feature: Unable to update feature where values: %values', 
			   array('%values' => print_r($values, TRUE)),
			   WATCHDOG_WARNING
		   );
      }
   }
}
/**
 *
 *
 * @ingroup tripal_feature
 */
function chado_feature_delete($node){

   $feature_id  = chado_get_id_for_node('feature',$node);

   // remove the drupal content  
   $sql_del = "DELETE FROM {chado_feature} ".
              "WHERE nid = %d ".
              "AND vid = %d";
   db_query($sql_del, $node->nid, $node->vid);
   $sql_del = "DELETE FROM {node} ".
              "WHERE nid = %d ".
              "AND vid = %d";
   db_query($sql_del, $node->nid, $node->vid);
   $sql_del = "DELETE FROM {node_revisions} ".
              "WHERE nid = %d ".
              "AND vid = %d";
   db_query($sql_del, $node->nid, $node->vid);


   // Remove data from feature tables of chado database.  This will
   // cause a cascade delete and remove all data in referencing tables
   // for this feature
   $previous_db = tripal_db_set_active('chado');
   db_query("DELETE FROM {feature} WHERE feature_id = %d", $feature_id);
   tripal_db_set_active($previous_db);
   
   drupal_set_message("The feature and all associated data were removed from ".
      "chado");

}
/**
 *
 *
 * @ingroup tripal_feature
 */
function chado_feature_add_synonyms($synonyms,$feature_id){

   // make sure we only have a single space between each synonym
   $synonyms = preg_replace("/[\s\n\r]+/"," ",$synonyms);
   // split the synonyms into an array based on a space as the delimieter
   $syn_array = array();
   $syn_array = explode(" ",$synonyms);

   // use the chado database
   $previous_db = tripal_db_set_active('chado');

   // remove any old synonyms
   $feature_syn_dsql = "DELETE FROM {feature_synonym} WHERE feature_id = %d";
   if(!db_query($feature_syn_dsql,$feature_id)){
      $error .= "Could not remove synonyms from feature. ";
   }

   // return if we don't have any synonmys to add
   if(!$synonyms){
      tripal_db_set_active($previous_db);
      return;
   }
   // iterate through each synonym and add it to the database
   foreach($syn_array as $syn){
      // skip this item if it's empty
      if(!$syn){ break; }

      // check to see if we have this accession number already in the database
      // if so then don't add it again. it messes up drupal if the insert fails.
      // It is possible for the accession number to be present and not the feature
      $synonym_sql = "SELECT synonym_id FROM {synonym} ".
                     "WHERE name = '%s'";
      $synonym = db_fetch_object(db_query($synonym_sql,$syn));
      if(!$synonym){
         $synonym_isql = "INSERT INTO {synonym} (name,synonym_sgml,type_id) ".
                         "VALUES ('%s','%s', ".
                         "   (SELECT cvterm_id ".
                         "    FROM {CVTerm} CVT ".
                         "    INNER JOIN CV ON CVT.cv_id = CV.cv_id ".
                         "    WHERE CV.name = 'feature_property' and CVT.name = 'synonym'))";
         if(!db_query($synonym_isql,$syn,$syn)){
            $error .= "Could not add synonym. ";
         }
         // now get the synonym we just added
         $synonym_sql = "SELECT synonym_id FROM {synonym} ".
                        "WHERE name = '%s'";
         $synonym = db_fetch_object(db_query($synonym_sql,$syn));
      }

      // now add in our new sysnonym
      $feature_syn_isql = "INSERT INTO {feature_synonym} (synonym_id,feature_id,pub_id) ".
                          "VALUES (%d,%d,1)";
      if(!db_query($feature_syn_isql,$synonym->synonym_id,$feature_id)){
         $error .= "Could not add synonyms to feature. ";
      }
   }

   // return to the drupal database
   tripal_db_set_active($previous_db);
   return $error;

}
/**
 *
 *
 * @ingroup tripal_feature
 */
function chado_feature_add_gbaccession($accession,$feature_id){

   // use chado database
   $previous_db = tripal_db_set_active('chado');

   // remove any old accession from genbank dbEST
   $fdbxref_dsql = "DELETE FROM {feature_dbxref} ".
                   "WHERE feature_id = %d and dbxref_id IN ".
                   "   (SELECT DBX.dbxref_id FROM {dbxref} DBX ".
                   "    INNER JOIN DB  ON DB.db_id = DBX.db_id ".
                   "    INNER JOIN feature_dbxref FDBX ON DBX.dbxref_id = FDBX.dbxref_id ".
                   "    WHERE DB.name = 'DB:Genbank' and FDBX.feature_id = %d)";
   if(!db_query($fdbxref_dsql,$feature_id,$feature_id)){
      $error .= "Could not remove accession from feature. ";
   }

   // if we don't have an accession number to add then just return
   if(!$accession){
      tripal_db_set_active($previous_db);
      return;
   }
   // get the db_id
   $db_sql = "SELECT db_id FROM {DB} ".
             "WHERE name = 'DB:Genbank_est'";
   $db = db_fetch_object(db_query($db_sql));

   // check to see if we have this accession number already in the database
   // if so then don't add it again. it messes up drupal if the insert fails.
   // It is possible for the accession number to be present and not the feature
   $dbxref_sql = "SELECT dbxref_id FROM {dbxref} ".
                 "WHERE db_id = %d and accession = '%s'";
   $dbxref = db_fetch_object(db_query($dbxref_sql,$db->db_id,$accession));
   if(!$dbxref){
      // add the accession number
      $dbxref_isql = "INSERT INTO {dbxref} (db_id,accession) ".
                     "  VALUES (%d, '%s') ";
      if(!db_query($dbxref_isql,$db->db_id,$accession)){
         $error .= 'Could not add accession as a database reference ';
      }
      // get the dbxref_id for the just added accession number
      $dbxref_sql = "SELECT dbxref_id FROM {dbxref} ".
                    "WHERE db_id = %d and accession = '%s'";
      $dbxref = db_fetch_object(db_query($dbxref_sql,$db->db_id,$accession));
   }


   // associate the accession number with the feature
   $feature_dbxref_isql = "INSERT INTO {feature_dbxref} (feature_id,dbxref_id) ".
                          "  VALUES (%d, %d) ";
   if(!db_query($feature_dbxref_isql,$feature_id,$dbxref->dbxref_id)){
      $error .= 'Could not add feature database reference. ';
   }

   tripal_db_set_active($previous_db);
   return $error;
}

/**
 *
 *
 * @ingroup tripal_feature
 */
function chado_feature_form ($node,$param){

   $type = node_get_types('type', $node);
   $form = array();

   $feature = $node->feature;

   // add the residues to the feature object
   $feature = tripal_core_expand_chado_vars($feature,'field','feature.residues');

   // if the node has synonyms then use that as the form may be returning
   // from an error.  Otherwise try to find synonyms from the database
   $synonyms = $node->synonyms;
   $feature = tripal_core_expand_chado_vars($feature,'table','feature_synonym');
   $feature_synonyms = $feature->feature_synonym;
   if(!$synonyms){
      if (!is_array($feature_synonyms)) {
         $synonyms = $feature_synonyms->synonym_id->name;
      } 
      elseif(is_array($feature_synonyms)) { 
         foreach($feature_synonyms as $index => $synonym){
            $synonyms .= $synonym->synonym_id->name ."\n";
         }
      }
   }

   $analyses = $node->analyses;
   $references = $node->references;

   // We need to pass above variables for preview to show
   $form['feature'] = array(
      '#type' => 'value',
      '#value' => $feature
   );
   // This field is read when previewing a node
   $form['synonyms'] = array(
      '#type' => 'value',
      '#value' => $synonyms
   );
   // This field is read when previewing a node
   $form['analyses'] = array(
      '#type' => 'value',
      '#value' => $analyses
   );
   // This field is read when previewing a node
   $form['references'] = array(
      '#type' => 'value',
      '#value' => $references
   );

   // keep track of the feature id if we have one.  If we do have one then
   // this would indicate an update as opposed to an insert.
   $form['feature_id'] = array(
      '#type' => 'value',
      '#value' => $feature->feature_id,
   );

   $form['title']= array(
      '#type' => 'textfield',
      '#title' => t('Title'),
      '#required' => TRUE,
      '#default_value' => $node->title,
      '#description' => t('The title must be a unique identifier for this feature.  It is recommended to use a combination of uniquename, organism and feature type in the title as this is guranteed to be unique.'),
      '#weight' => 1,
      '#maxlength' => 255
   );

   $form['uniquename']= array(
      '#type' => 'textfield',
      '#title' => t('Unique Feature Name'),
      '#required' => TRUE,
      '#default_value' => $feature->uniquename,
      '#description' => t('Enter a unique name for this feature.  This name must be unique for the organism and feature type.'),
      '#weight' => 1,
      '#maxlength' => 255
   );

   $form['fname']= array(
      '#type' => 'textfield',
      '#title' => t('Feature Name'),
      '#required' => TRUE,
      '#default_value' => $feature->name,
      '#description' => t('Enter the name used by humans to refer to this feature.'),
      '#weight' => 1,
      '#maxlength' => 255
   );

   // get the list of supported feature types
   $ftypes = array();
   $ftypes[''] = '';
   $supported_ftypes = split("[ \n]",variable_get('chado_feature_types','EST contig'));
   foreach($supported_ftypes as $ftype){
      $ftypes["$ftype"] = $ftype;
   }

   $form['feature_type'] = array (
     '#title'       => t('Feature Type'),
     '#type'        => t('select'),
     '#description' => t("Choose the feature type."),
     '#required'    => TRUE,
     '#default_value' => $feature->type_id->name,
     '#options'     => $ftypes,
     '#weight'      => 2
   );
   // get the list of organisms
   $sql = "SELECT * FROM {Organism} ORDER BY genus, species";
   $previous_db = tripal_db_set_active('chado');  // use chado database
   $org_rset = db_query($sql);
   tripal_db_set_active($previous_db);  // now use drupal database

   //
   $organisms = array();
   $organisms[''] = '';
   while($organism = db_fetch_object($org_rset)){
      $organisms[$organism->organism_id] = "$organism->genus $organism->species ($organism->common_name)";
   }

   $form['organism_id'] = array (
     '#title'       => t('Organism'),
     '#type'        => t('select'),
     '#description' => t("Choose the organism with which this feature is associated "),
     '#required'    => TRUE,
     '#default_value' => $feature->organism_id->organism_id,
     '#options'     => $organisms,
     '#weight'      => 3,
   );

   // Get synonyms
   if ($synonyms) {
      if (is_array($synonyms)) {
         foreach ($synonyms as $synonym){
            $syn_text .= "$synonym->name\n";
         }
      } else {
         $syn_text = $synonyms;
      }
   }
   $form['synonyms']= array(
      '#type' => 'textarea',
      '#title' => t('Synonyms'),
      '#required' => FALSE,
      '#default_value' => $syn_text,
      '#description' => t('Enter alternate names (synonmys) for this feature to help in searching and identification. You may enter as many alternate names as needed separated by spaces or on different lines.'),
      '#weight' => 5,
   );

   $form['residues']= array(
      '#type' => 'textarea',
      '#title' => t('Residues'),
      '#required' => FALSE,
      '#default_value' => $feature->residues,
      '#description' => t('Enter the nucelotide sequences for this feature'),
      '#weight' => 6
   );

   $checked = '';
   if($feature->is_obsolete == 't'){
      $checked = '1';
   }
   $form['is_obsolete']= array(
      '#type' => 'checkbox',
      '#title' => t('Is Obsolete'),
      '#required' => FALSE,
      '#default_value' => $checked,
      '#description' => t('Check this box if this sequence should be retired and no longer included in further analysis.'),
      '#weight' => 8
   );
   return $form;
}
/**
 *
 *
 * @ingroup tripal_feature
 */
function chado_feature_validate($node){
   $result = 0;

   // if this is an update, we want to make sure that a different feature for
   // the organism doesn't already have this uniquename. We don't want to give
   // two sequences the same uniquename
   if($node->feature_id){
      $sql = "SELECT * 
              FROM {Feature} F
                INNER JOIN {cvterm} CVT ON F.type_id = CVT.cvterm_id
              WHERE uniquename = '%s' 
               AND organism_id = %d AND CVT.name = '%s' AND NOT feature_id = %d";
      $previous_db = tripal_db_set_active('chado');
      $result = db_fetch_object(db_query($sql, $node->uniquename,$node->organism_id,$node->feature_type,$node->feature_id));
      tripal_db_set_active($previous_db);
      if($result){
         form_set_error('uniquename',t("Feature update cannot proceed. The feature name '$node->uniquename' is not unique for this organism. Please provide a unique name for this feature. "));
      }
   }

   // if this is an insert then we just need to make sure this name doesn't
   // already exist for this organism if it does then we need to throw an error
   else {
      $sql = "SELECT * 
              FROM {Feature} F
                INNER JOIN {cvterm} CVT ON F.type_id = CVT.cvterm_id
              WHERE uniquename = '%s' 
               AND organism_id = %d AND CVT.name = '%s'";
      $previous_db = tripal_db_set_active('chado');
      $result = db_fetch_object(db_query($sql, $node->uniquename,$node->organism_id,$node->feature_type));
      tripal_db_set_active($previous_db);
      if($result){
         form_set_error('uniquename',t("Feature insert cannot proceed. The feature name '$node->uniquename' already exists for this organism. Please provide a unique name for this feature. "));
      }
   }

   // we want to remove all characters except IUPAC nucleotide characters from the
   // the residues. however, residues are not required so if blank then we'll skip
   // this step
   if($node->residues){
      $residues = preg_replace("/[^\w]/",'',$node->residues);
      if(!preg_match("/^[ACTGURYMKSWBDHVN]+$/i",$residues)){
         form_set_error('residues',t("The residues in feature $node->name contains more than the nucleotide IUPAC characters. Only the following characters are allowed: A,C,T,G,U,R,Y,M,K,S,W,B,D,H,V,N: '" . $residues ."'"));
      }
   }

   // we don't allow a genbank accession number for a contig
   if($node->feature_type == 'contig' and $node->gbaccession){
      form_set_error('gbaccession',t("Contigs cannot have a genbank accession number.  Please change the feature type or remove the accession number"));
   }

}
/**
 *  When a node is requested by the user this function is called to allow us
 *  to add auxiliary data to the node object.
 *
 * @ingroup tripal_feature
 */
function chado_feature_load($node){
   // get the feature details from chado
   $feature_id = chado_get_id_for_node('feature',$node);

   $values = array('feature_id' => $feature_id);
   $feature = tripal_core_generate_chado_var('feature',$values);

   $additions->feature = $feature;
   return $additions;
}
/**
 *  
 *
 * @ingroup tripal_feature
 */
function tripal_feature_load_organism ($organism_id){
   // add organism details
   $sql = "SELECT * FROM {organism} WHERE organism_id = %d";
   $previous_db = tripal_db_set_active('chado');  // use chado database
   $organism = db_fetch_object(db_query($sql,$organism_id));
   tripal_db_set_active($previous_db);  // now use drupal database
   return $organism;
}
/**
 *  
 *
 * @ingroup tripal_feature
 */
function tripal_feature_load_synonyms ($feature_id){

   $sql = "SELECT S.name ".
          "FROM {Feature_Synonym} FS ".
          "  INNER JOIN {Synonym} S ".
          "    ON FS.synonym_id = S.Synonym_id ".
          "WHERE FS.feature_id = %d ".
          "ORDER BY S.name ";
   $previous_db = tripal_db_set_active('chado');  // use chado database
   $results = db_query($sql,$feature_id);
   tripal_db_set_active($previous_db);  // now use drupal database
   $synonyms = array();
   $i=0;
   while($synonym = db_fetch_object($results)){
      $synonyms[$i++] = $synonym;
   }
   return $synonyms;
}
/**
 * 
 *
 * @ingroup tripal_feature
 */
function tripal_feature_load_properties ($feature_id){

   $sql = "SELECT CVT.name as cvname, FS.type_id, FS.value, FS.rank,
             CVT.definition, CVT.is_obsolete, 
             DBX.dbxref_id,DBX.accession,DB.name as dbname, 
             DB.urlprefix, DB.description as db_description, DB.url
           FROM {featureprop} FS 
             INNER JOIN {cvterm} CVT ON FS.type_id = CVT.cvterm_id
             INNER JOIN {dbxref} DBX ON CVT.dbxref_id = DBX.dbxref_id
             INNER JOIN {db} DB      ON DB.db_id = DBX.db_id
           WHERE FS.feature_id = %d
           ORDER BY FS.rank ASC";
   $previous_db = tripal_db_set_active('chado');  // use chado database
   $results = db_query($sql,$feature_id);
   tripal_db_set_active($previous_db);  // now use drupal database
   $i=0;
   $properties = array();
   while($property = db_fetch_object($results)){
      $properties[$i++] = $property;
   }
   return $properties;
}
/**
 *  
 *
 * @ingroup tripal_feature
 */
function tripal_feature_load_references ($feature_id){

   $sql = "SELECT F.uniquename,F.Feature_id,DBX.accession,DB.description as dbdesc, ".
          "   DB.db_id, DB.name as db_name, DB.urlprefix,DBX.dbxref_id ".
          "FROM {feature} F ".
          "  INNER JOIN {feature_dbxref} FDBX on F.feature_id = FDBX.feature_id ".
          "  INNER JOIN {dbxref} DBX on DBX.dbxref_id = FDBX.dbxref_id ".
          "  INNER JOIN {db} on DB.db_id = DBX.db_id ".
          "WHERE F.feature_id = %d ".
          "ORDER BY DB.name ";
   $previous_db = tripal_db_set_active('chado');  // use chado database
   $results = db_query($sql,$feature_id);
   tripal_db_set_active($previous_db);  // now use drupal database
   $references = array();
   $i=0;
   while($accession = db_fetch_object($results)){
      $references[$i++] = $accession;
   }
   return $references;
}
/**
 *  
 *
 * @ingroup tripal_feature
 */
function tripal_feature_load_featurelocs ($feature_id,$side = 'as_parent',$aggregate = 1){

   $sql = "SELECT 
             F.name, F.feature_id, F.uniquename,
             FS.name as src_name, 
             FS.feature_id as src_feature_id, 
             FS.uniquename as src_uniquename,
             CVT.name as cvname, CVT.cvterm_id,
             CVTS.name as src_cvname, CVTS.cvterm_id as src_cvterm_id,
             FL.fmin, FL.fmax, FL.is_fmin_partial, FL.is_fmax_partial,FL.strand, 
             FL.phase
           FROM {featureloc} FL
              INNER JOIN {feature} F on FL.feature_id = F.feature_id
              INNER JOIN {feature} FS on FS.feature_id = FL.srcfeature_id
              INNER JOIN {cvterm} CVT on F.type_id = CVT.cvterm_id
              INNER JOIN {cvterm} CVTS on FS.type_id = CVTS.cvterm_id
           ";
   if(strcmp($side,'as_parent')==0){
      $sql .= "WHERE FL.srcfeature_id = %d ";
   }
   if(strcmp($side,'as_child')==0){
      $sql .= "WHERE FL.feature_id = %d ";
   }

   $previous_db = tripal_db_set_active('chado');  // use chado database
   $flresults = db_query($sql, $feature_id);
   tripal_db_set_active($previous_db);  // now use drupal database 

   // copy the results into an array
   $i=0;
   $featurelocs = array();
   while($loc = db_fetch_object($flresults)){
      // if a drupal node exists for this feature then add the nid to the
      // results object
      $sql = 'SELECT nid FROM {chado_feature} WHERE feature_id = %d';

      $ffeature = db_fetch_object(db_query($sql, $loc->feature_id));
      $sfeature = db_fetch_object(db_query($sql, $loc->src_feature_id));
      $loc->fnid = $ffeature->nid;
      $loc->snid = $sfeature->nid;
      // add the result to the array
      $featurelocs[$i++] = $loc;
   }

   // Add the relationship feature locs if aggregate is turned on
   if($aggregate and strcmp($side,'as_parent')==0){ 
      // get the relationships for this feature without substituting any children
      // for the parent. We want all relationships
      $relationships = tripal_feature_get_aggregate_relationships($feature_id,0);
      foreach($relationships as $rindex => $rel){ 
         // get the featurelocs for each of the relationship features
         $rel_featurelocs = tripal_feature_load_featurelocs ($rel->subject_id,'as_child',0);
         foreach($rel_featurelocs as $findex => $rfloc){
            $featurelocs[$i++] = $rfloc;
         }
      }
   } 
   
   usort($featurelocs,'tripal_feature_sort_locations');
   return $featurelocs;
}
/**
 *  used to sort the feature locs by start position
 *
 * @ingroup tripal_feature
 */
function tripal_feature_sort_locations($a,$b){
   return strnatcmp($a->fmin, $b->fmin); 
}
/**
 *  
 *
 * @ingroup tripal_feature
 */
function tripal_feature_load_relationships ($feature_id,$side = 'as_subject'){
   // get the relationships for this feature.  The query below is used for both
   // querying the object and subject relationships
   $sql = "SELECT 
             FS.name as subject_name, 
             FS.uniquename as subject_uniquename, 
             CVTS.name as subject_type,
             CVTS.cvterm_id as subject_type_id,
             FR.subject_id,          
             FR.type_id as relationship_type_id,
             CVT.name as rel_type,     
             FO.name as object_name, 
             FO.uniquename as object_uniquename, 
             CVTO.name as object_type,
             CVTO.cvterm_id as object_type_id,
             FR.object_id, 
             FR.rank
           FROM {feature_relationship} FR
             INNER JOIN {cvterm} CVT ON FR.type_id = CVT.cvterm_id
             INNER JOIN {feature} FS ON FS.feature_id = FR.subject_id
             INNER JOIN {feature} FO ON FO.feature_id = FR.object_id
             INNER JOIN {cvterm} CVTO ON FO.type_id = CVTO.cvterm_id
             INNER JOIN {cvterm} CVTS ON FS.type_id = CVTS.cvterm_id
   ";
   if(strcmp($side,'as_object')==0){
      $sql .= " WHERE FR.object_id = %d";
   }
   if(strcmp($side,'as_subject')==0){
      $sql .= " WHERE FR.subject_id = %d";
   }
   $sql .= " ORDER BY FR.rank";

   // get the relationships 
   $previous_db = tripal_db_set_active('chado');  // use chado database
   $results = db_query($sql, $feature_id);
   tripal_db_set_active($previous_db);  // now use drupal database


   // iterate through the relationships, put these in an array and add
   // in the Drupal node id if one exists
   $i=0;
   $nodesql = "SELECT nid FROM {chado_feature} WHERE feature_id = %d";
   $relationships = array();
   while($rel = db_fetch_object($results)){
     $node = db_fetch_object(db_query($nodesql,$rel->subject_id));
     if($node){
        $rel->subject_nid = $node->nid;
     }  
     $node = db_fetch_object(db_query($nodesql,$rel->object_id));
     if($node){
        $rel->object_nid = $node->nid;
     }  
     $relationships[$i++] = $rel;      
   }
   return $relationships;
}
/**
 *  
 *
 * @ingroup tripal_feature
 */
function tripal_feature_get_aggregate_types($feature_id){
   // get the feature details
   $sql = 'SELECT type_id FROM {feature} WHERE feature_id = %d';
   $previous_db = tripal_db_set_active('chado');  // use chado database
   $feature = db_fetch_object(db_query($sql, $feature_id));
   tripal_db_set_active($previous_db);  // now use drupal database

   // check to see if this feature is of a type with an aggregate
   $sql = "SELECT * FROM {tripal_feature_relagg} WHERE type_id = %d";
   $types = array();
   $results = db_query($sql,$feature->type_id);
   while($agg = db_fetch_object($results)){
      $types[] = $agg->rel_type_id;
   }
   
   return $types;
}
/**
 *  
 *
 * @ingroup tripal_feature
 */
function tripal_feature_get_aggregate_relationships($feature_id, $substitute=1,
  $levels=0, $base_type_id=NULL, $depth=0)
{

   // we only want to recurse to as many levels deep as indicated by the 
   // $levels variable, but only if this variable is > 0. If 0 then we 
   // recurse until we reach the end of the relationships tree.
   if($levels > 0 and $levels == $depth){
      return NULL;
   }

   // first get the relationships for this feature
   $relationships = tripal_feature_load_relationships($feature_id,'as_object');

   // next, iterate through these relationships and descend, adding in those
   // that are specified by the aggregator.
   $i=0;
   $new_relationships = array();
   foreach($relationships as $rindex => $rel){

      // set the base type id 
      if(!$base_type_id){
         $base_type_id = $rel->object_type_id;
      } 
      // check to see if we have an aggregator for this base type
      $sql = "SELECT * FROM {tripal_feature_relagg} WHERE type_id = %d and rel_type_id = %d";
      $agg = db_fetch_object(db_query($sql,$base_type_id,$rel->subject_type_id));
      if($agg){
         // if we're not going to substitute the resulting relationships for the
         // parent then we need to add the parent to our list
         if(!$substitute){
            $new_relationships[$i++] = $rel;
         }
         // recurse all relationships 
         $agg_relationships = tripal_feature_get_aggregate_relationships(
            $rel->subject_id,$levels,$base_type_id,$depth++);
         // if we have an aggregate defined but we have no relationships beyond
         // this point then there's nothing we can substitute 
         if(!$agg_relationships and $substitute){
            $new_relationships[$i++] = $rel;
         }

         // merge all relationships into one array
         foreach($agg_relationships as $aindex => $arel){
            $new_relationships[$i++] = $arel;
         }  
      }  
      else {
         // if we don't have an aggregate then keep the current relationship
         $new_relationships[$i++] = $rel;
      }    
   } 
   return $new_relationships;
}
/**
 *  
 *
 * @ingroup tripal_feature
 */
function tripal_feature_load_featureloc_sequences($feature_id,$featurelocs){

   // if we don't have any featurelocs then no point in continuing
   if(!$featurelocs){
      return array();
   }

   // get the list of relationships (including any aggregators) and iterate
   // through each one to find information needed to color-code the reference sequence
   $relationships = tripal_feature_get_aggregate_relationships($feature_id);
   if(!$relationships){
      return array();
   }


   // iterate through each of the realtionships features and get their 
   // locations
   foreach($relationships as $rindex => $rel){
      // get the featurelocs for each of the relationship features
      $rel_featurelocs = tripal_feature_load_featurelocs ($rel->subject_id,'as_child',0);   
      foreach($rel_featurelocs as $rfindex => $rel_featureloc){
         // keep track of this unique source feature
         $src = $rel_featureloc->src_feature_id ."-". $rel_featureloc->src_cvterm_id;

         // copy over the results to the relationship object.  Since there can
         // be more than one feature location for each relationship feature we 
         // use the '$src' variable to keep track of these.
         $rel->featurelocs->$src->src_uniquename = $rel_featureloc->src_uniquename;
         $rel->featurelocs->$src->src_cvterm_id  = $rel_featureloc->src_cvterm_id;
         $rel->featurelocs->$src->src_cvname     = $rel_featureloc->src_cvname;
         $rel->featurelocs->$src->fmin           = $rel_featureloc->fmin;
         $rel->featurelocs->$src->fmax           = $rel_featureloc->fmax;
         $rel->featurelocs->$src->src_name       = $rel_featureloc->src_name;

         // keep track of the individual parts for each relationship 
         $start = $rel->featurelocs->$src->fmin;
         $end   = $rel->featurelocs->$src->fmax;
         $rel_locs[$src]['parts'][$start]['type']  = $rel->subject_type;
         $rel_locs[$src]['parts'][$start]['start'] = $start;
         $rel_locs[$src]['parts'][$start]['end']   = $end;
      }
   }

   // the featurelocs array provided to the function contains the locations
   // where this feature is found.   We want to get the sequence for each 
   // location and then annotate it with the parts found from the relationships
   // locations determiend above. 
   $sql = "SELECT residues FROM {feature} WHERE feature_id = %d";
   $floc_sequences = array();
   foreach ($featurelocs as $featureloc){
      // get the residues for this feature
      $previous_db = tripal_db_set_active('chado');  // use chado database
      $feature = db_fetch_object(db_query($sql,$featureloc->srcfeature_id->feature_id));
      tripal_db_set_active($previous_db);  // now use drupal database

      $src = $featureloc->srcfeature_id->feature_id ."-". $featureloc->srcfeature_id->type_id->cvterm_id;

      // orient the parts to the beginning of the feature sequence
      $parts = $rel_locs[$src]['parts'];
      usort($parts, 'tripal_feature_sort_rel_parts');
      foreach ($parts as $start => $attrs){
         $parts[$start]['start'] = $parts[$start]['start'] - $featureloc->fmin;
         $parts[$start]['end']   = $parts[$start]['end'] - $featureloc->fmin;
      }      
      $floc_sequences[$src]['src'] = $src;
      $floc_sequences[$src]['type'] = $featureloc->feature_id->type_id->name;
      $sequence = substr($feature->residues,$featureloc->fmin-1,($featureloc->fmax - $featureloc->fmin)+1);
      $floc_sequences[$src]['formatted_seq'] =  tripal_feature_color_sequence (
          $sequence,$parts);
   }
   return $floc_sequences;
}
/**
 *  
 *
 * @ingroup tripal_feature
 */
function tripal_feature_load_organism_feature_counts($organism){

   // don't show the browser if the settings in the admin page is turned off
   // instead return the array indicating the status of the browser
   $show_counts = variable_get('tripal_feature_summary_setting','show_feature_summary');
   if(strcmp($show_counts,'show_feature_summary')!=0){
      return array ('enabled' => false );
   }

   // get the feature counts.  This is dependent on a materialized view
   // installed with the organism module
   $sql = "
      SELECT OFC.num_features,OFC.feature_type,CVT.definition
      FROM {organism_feature_count} OFC
        INNER JOIN {cvterm} CVT on OFC.cvterm_id = CVT.cvterm_id
      WHERE organism_id = %d 
      ORDER BY num_features desc
   ";
   $previous_db = tripal_db_set_active('chado');  // use chado database
   $org_features = db_query($sql,$organism->organism_id);
   tripal_db_set_active($previous_db);  // now use drupal database

   $i=0;
   $types = array();
   while($type = db_fetch_object($org_features)){
      $types[$i++] = $type;
   }
   return array ( 'types' => $types, 'enabled' => true );
}
/**
 * 
 *
 * @ingroup tripal_feature
 */
function tripal_feature_load_organism_feature_browser($organism){

   // don't show the browser if the settings in the admin page is turned off
   // instead return the array indicating the status of the browser
   $show_browser = variable_get('tripal_feature_browse_setting','show_feature_browser');
   if(strcmp($show_browser,'show_feature_browser')!=0){
      return array ('enabled' => false);
   }

   # get the list of available sequence ontology terms for which
   # we will build drupal pages from features in chado.  If a feature
   # is not one of the specified typse we won't build a node for it.
   $allowed_types = variable_get('chado_feature_types','EST contig');
   $allowed_types = preg_replace("/[\s\n\r]+/"," ",$allowed_types);
   $so_terms = split(' ',$allowed_types);
   $where_cvt = "";
   foreach ($so_terms as $term){
      $where_cvt .= "CVT.name = '$term' OR ";
   }
   $where_cvt = substr($where_cvt,0,strlen($where_cvt)-3);  # strip trailing 'OR'

   // get the features for this organism
   $sql  = "SELECT F.name,F.feature_id,F.uniquename,CVT.name as cvname ".
           "FROM {feature} F ".
              "  INNER JOIN {cvterm} CVT on F.type_id = CVT.cvterm_id ".
            "WHERE organism_id = %s and ($where_cvt) ".
            "ORDER BY feature_id ASC";

   // the counting SQL
   $csql  = "SELECT count(*) ".
            "FROM {feature} F".
            "  INNER JOIN {cvterm} CVT on F.type_id = CVT.cvterm_id ".
            "WHERE organism_id = %s and ($where_cvt) ".
            "GROUP BY organism_id ";

   $previous_db = tripal_db_set_active('chado');  // use chado database
   $org_features = pager_query($sql,10,0,$csql,$organism->organism_id);
   tripal_db_set_active($previous_db);  // now use drupal database
   $pager = theme('pager');

   // prepare the query that will lookup node ids
   $sql = "SELECT nid FROM {chado_feature} ".
           "WHERE feature_id = %d";
   $i=0;
   $features = array();
   while($feature = db_fetch_object($org_features)){
      $node = db_fetch_object(db_query($sql,$feature->feature_id));
      $feature->nid = $node->nid;
      $features[$i++] = $feature;
   }

   return array ( 'features' => $features, 'pager' => $pager, 'enabled' => true );
}

/**
 *  used to sort the list of relationship objects by start position
 *
 * @ingroup tripal_feature
 */
function tripal_feature_sort_rel_objects($a,$b){
   return strnatcmp($a->fmin, $b->fmin);
}

/**
 *  used to sort the list of relationship parts by start position
 *
 * @ingroup tripal_feature
 */
function tripal_feature_sort_rel_parts($a,$b){
   return strnatcmp($a['start'], $b['start']); 
}

/**
 * 
 *
 * @ingroup tripal_feature
 */
function tripal_feature_color_sequence ($sequence,$parts){

   $types = array();

   // first get the list of types so we can create a color legend
   foreach ($parts as $index => $child){ 
      $type = $child['type'];
      if(!in_array($type,$types)){
         $types[] = $type;
      }
   }
 
   $newseq .= "<div id=\"tripal_feature-featureloc_sequence-legend\">Legend: ";
   foreach($types as $type){
      $newseq .= "<span class=\"tripal_feature-featureloc_sequence-$type\">$type</span>";
   }
   $newseq .= "</div>";
   

   // set the background color of the rows based on the type
   $pos = 0;
   $newseq .= "<pre id=\"tripal_feature-featureloc_sequence\">";
   foreach ($parts as $index => $child){
      $type = $child['type'];
      $start = $child['start'];
      $end = $child['end']+1;
      
      $class = "class=\"tripal_feature-featureloc_sequence-$type\"";

      // iterate through the sequence up to the end of the child
      for ($i = $pos; $i < $end; $i++){ 
    
         // if we're at the beginning of the child sequence then set the
         // appropriate text color
         if($pos == $start){
            $newseq .= "<span $class>";
            $func = 'uc';  // nucleotides within the child should be uppercase
         }
         $newseq .= $sequence{$pos};
         $seqcount++;

         if($seqcount % 60 == 0){
            $newseq .= "\n";
         } 
         $pos++;  
         if($pos == $end){
            $newseq .= "</span>";
            $func = 'lc';
         }
      }
   }

   $newseq .= "</pre>";
   return $newseq;
}

/**
 *  This function customizes the view of the chado_feature node.  It allows
 *  us to generate the markup.
 *
 * @ingroup tripal_feature
 */
function chado_feature_view ($node, $teaser = FALSE, $page = FALSE) {

   if (!$teaser) {
      // use drupal's default node view:
      $node = node_prepare($node, $teaser);           

      // if we're building the node for searching then
      // we want to handle this within the module and
      // not allow theme customization.  We don't want to
      // index all items (such as DNA sequence).
      if($node->build_mode == NODE_BUILD_SEARCH_INDEX){
         $node->content['index_version'] = array(
            '#value' => theme('tripal_feature_search_index',$node),
            '#weight' => 1,
         );
      }
      elseif($node->build_mode == NODE_BUILD_SEARCH_RESULT){
         $node->content['index_version'] = array(
            '#value' => theme('tripal_feature_search_results',$node),
            '#weight' => 1,
         );
      }
      else {
         // do nothing here, let the theme derived template handle display
      }
   }

   return $node;
}

/**
 * Display feature information for associated organisms. This function also
 * provides contents for indexing
 *
 * @ingroup tripal_feature
 */
function tripal_feature_nodeapi(&$node, $op, $teaser, $page) {

   switch ($op) {
      // Note that this function only adds feature view to an organism node.
      // The view of a feature node is controled by the theme *.tpl file
      case 'view':
         switch($node->type){
            case 'chado_organism':
               // Show feature browser
               $types_to_show = array('chado_organism', 'chado_library');
               if (in_array($node->type, $types_to_show, TRUE)) {
                  $node->content['tripal_organism_feature_counts'] = array(
                    '#value' => theme('tripal_organism_feature_counts', $node),
                  );
                  $node->content['tripal_organism_feature_browser'] = array(
                    '#value' => theme('tripal_organism_feature_browser', $node),
                  );
               }
               break;
            case 'chado_library':
               break;
            default:           
         }
         break;
   }
}

/**
 *  We need to let drupal know about our theme functions and their arguments.
 *  We create theme functions to allow users of the module to customize the
 *  look and feel of the output generated in this module
 *
 * @ingroup tripal_feature
 */
function tripal_feature_theme () {
   return array(
      'tripal_feature_search_index' => array (
         'arguments' => array('node'),
      ),
      'tripal_feature_search_results' => array (
         'arguments' => array('node'),
      ),
      'tripal_organism_feature_browser' => array (
         'arguments' => array('node'=> null),
         'template' => 'tripal_organism_feature_browser',
      ),
      'tripal_organism_feature_counts' => array (
         'arguments' => array('node'=> null),
         'template' => 'tripal_organism_feature_counts',
      ),
      'tripal_feature_base' => array (
         'arguments' => array('node'=> null),
         'template' => 'tripal_feature_base',
      ),
      'tripal_feature_sequence' => array (
         'arguments' => array('node'=> null),
         'template' => 'tripal_feature_sequence',
      ),
      'tripal_feature_synonyms' => array (
         'arguments' => array('node'=> null),
         'template' => 'tripal_feature_synonyms',
      ),
      'tripal_feature_featureloc_sequences' => array (
         'arguments' => array('node'=> null),
         'template' => 'tripal_feature_featureloc_sequences',
      ),
      'tripal_feature_references' => array (
         'arguments' => array('node'=> null),
         'template' => 'tripal_feature_references',
      ),
      'tripal_feature_properties' => array (
         'arguments' => array('node'=> null),
         'template' => 'tripal_feature_properties',
      ),
      'tripal_feature_featurelocs' => array (
         'arguments' => array('node'=> null),
         'template' => 'tripal_feature_featurelocs',
      ),
      'tripal_feature_relationships' => array (
         'arguments' => array('node'=> null),
         'template' => 'tripal_feature_relationships',
      ),
   );
}


/**
 *
 *
 * @ingroup tripal_feature
 */
function tripal_feature_preprocess_tripal_organism_feature_counts(&$variables){
   $organism = $variables['node']->organism;
   $variables['tripal_feature']['feature_counts'] = tripal_feature_load_organism_feature_counts($organism);
}

/**
 *  
 *
 * @ingroup tripal_feature
 */
function tripal_feature_preprocess_tripal_organism_feature_browser(&$variables){
   $organism = $variables['node']->organism;
   $variables['tripal_feature']['browser'] = tripal_feature_load_organism_feature_browser($organism);
}


/**
 *
 *
 * @ingroup tripal_feature
 */
function tripal_feature_cv_chart($chart_id){

  // The CV module will create the JSON array necessary for buillding a
  // pie chart using jgChart and Google Charts.  We have to pass to it
  // a table that contains count information, tell it which column 
  // contains the cvterm_id and provide a filter for getting the
  // results we want from the table.
  $organism_id = preg_replace("/^tripal_feature_cv_chart_(\d+)$/","$1",$chart_id);
  $options = array(
     count_mview      => 'organism_feature_count',
     cvterm_id_column => 'cvterm_id',
     count_column     => 'num_features',
     size             => '550x200',
     filter           => "CNT.organism_id = $organism_id",
  );
  return $options;
}

/**
 *
 *
 * @ingroup tripal_feature
 */
function tripal_feature_cv_tree($tree_id){

  // The CV module will create the JSON array necessary for buillding a
  // pie chart using jgChart and Google Charts.  We have to pass to it
  // a table that contains count information, tell it which column 
  // contains the cvterm_id and provide a filter for getting the
  // results we want from the table.
  $organism_id = preg_replace("/^tripal_feature_cv_tree_(\d+)$/","$1",$tree_id);
  $options = array(
     cv_id            => tripal_cv_get_cv_id('sequence'),
     count_mview      => 'organism_feature_count',
     cvterm_id_column => 'cvterm_id',
     count_column     => 'num_features',
     filter           => "CNT.organism_id = $organism_id",
     label            => 'Features',
  );
  return $options;
}

/**
 *  This function is an extension of the chado_feature_view by providing
 *  the markup for the feature object THAT WILL BE INDEXED.
 *
 * @ingroup tripal_feature
 */
function theme_tripal_feature_search_index ($node) {
   $feature = $node->feature;
   $content = '';

   // get the accession prefix
   $aprefix = variable_get('chado_feature_accession_prefix','ID');

   $content .= "<h1>$feature->uniquename</h1>. ";
   $content .= "<strong>$aprefix$feature->feature_id.</strong> ";
   $content .= "$feature->cvname ";
   $content .= "$feature->common_name ";

   // add the synonyms of this feature to the text for searching
   $synonyms = $node->synonyms;
   if(count($synonyms) > 0){
      foreach ($synonyms as $result){
         $content .= "$result->name ";
      }
   }

   return $content;
}

/**
 *  This function is an extension of the chado_feature_view by providing
 *  the markup for the feature object THAT WILL BE INDEXED.
 *
 * @ingroup tripal_feature
 */
function theme_tripal_feature_search_results ($node) {
   $feature = $node->feature;
   $content = '';

   // get the accession prefix
   $aprefix = variable_get('chado_feature_accession_prefix','ID');

   $content .= "Feature Name: <h1>$feature->uniquename</h1>. ";
   $content .= "<strong>Accession: $aprefix$feature->feature_id.</strong>";
   $content .= "Type: $feature->cvname. ";
   $content .= "Organism: $feature->common_name. ";

   // add the synonyms of this feature to the text for searching
   $synonyms = $node->synonyms;
   if(count($synonyms) > 0){
      $content .= "Synonyms: ";
      foreach ($synonyms as $result){
         $content .= "$result->name, ";
      }
   }

   return $content;
}

/**
 *
 *
 * @ingroup tripal_feature
 */
function tripal_feature_set_vocabulary (){

   //include the file containing the required functions for adding taxonomy vocabs
   module_load_include('inc', 'taxonomy', 'taxonomy.admin');

   // get the vocabularies so that we make sure we don't recreate
   // the vocabs that already exist
   $vocabularies = taxonomy_get_vocabularies();
   $ft_vid = NULL;
   $op_vid = NULL;
   $lb_vid = NULL;
   $an_vid = NULL;

   // These taxonomic terms are hard coded because we
   // konw we have these relationships in the chado tables
   // through foreign key relationships.  The tripal
   // modules that correspond to these chado "modules" don't
   // need to be installed for the taxonomy to work.
   foreach($vocabularies as $vocab){
      if($vocab->name == 'Feature Type'){
         $ft_vid = $vocab->vid;
      }
      if($vocab->name == 'Organism'){
         $op_vid = $vocab->vid;
      }
      if($vocab->name == 'Library'){
         $lb_vid = $vocab->vid;
      }
      if($vocab->name == 'Analysis'){
         $an_vid = $vocab->vid;
      }
   }

   if(!$ft_vid){
      $form_state = array();
      $values = array(
         'name' => t('Feature Type'),
         'nodes' => array('chado_feature' => 'chado_feature'),
         'description' => t('The feature type (or SO cvterm for this feature).'),
         'help' => t('Select the term that matches the feature '),
         'tags' => 0,
         'hierarchy' => 1,
         'relations' => 1,
         'multiple' => 0,
         'required' => 0,
         'weight' => 1,
      );
      drupal_execute('taxonomy_form_vocabulary', $form_state,$values);
      drupal_execute('taxonomy_form_vocabulary', $form_state);
   }

   if(!$op_vid){
      $form_state = array();
      $values = array(
         'name' => t('Organism'),
         'nodes' => array('chado_feature' => 'chado_feature'),
         'description' => t('The organism to which this feature belongs.'),
         'help' => t('Select the term that matches the feature '),
         'tags' => 0,
         'hierarchy' => 1,
         'relations' => 1,
         'multiple' => 0,
         'required' => 0,
         'weight' => 2,
      );
      drupal_execute('taxonomy_form_vocabulary', $form_state,$values);
      drupal_execute('taxonomy_form_vocabulary', $form_state);
   }

   if(!$lb_vid){
      $form_state = array();
      $values = array(
         'name' => t('Library'),
         'nodes' => array('chado_feature' => 'chado_feature'),
         'description' => t('Chado features associated with a library are assigned the term associated with the library'),
         'help' => t('Select the term that matches the feature '),
         'tags' => 0,
         'hierarchy' => 1,
         'relations' => 1,
         'multiple' => 0,
         'required' => 0,
         'weight' => 3,
      );
      drupal_execute('taxonomy_form_vocabulary', $form_state, $values);
      drupal_execute('taxonomy_form_vocabulary', $form_state);
   }

   if(!$an_vid){
      $form_state = array();
      $values = array(
         'name' => t('Analysis'),
         'nodes' => array('chado_feature' => 'chado_feature'),
         'description' => t('Any analysis to which this feature belongs.'),
         'help' => t('Select the term that matches the feature '),
         'tags' => 0,
         'hierarchy' => 1,
         'relations' => 1,
         'multiple' => 1,
         'required' => 0,
         'weight' => 4,
      );
      drupal_execute('taxonomy_form_vocabulary', $form_state,$values);
      drupal_execute('taxonomy_form_vocabulary', $form_state);
   }
}

/**
 *
 *
 * @ingroup tripal_feature
 */
function tripal_feature_del_vocabulary(){
   //include the file containing the required functions for adding taxonomy vocabs
   module_load_include('inc', 'taxonomy', 'taxonomy.admin');

   // get the vocabularies
   $vocabularies = taxonomy_get_vocabularies();

   // These taxonomic terms are hard coded because we
   // know we have these relationships in the chado tables
   // through foreign key relationships.  The tripal
   // modules that correspond to these chado "modules" don't
   // need to be installed for the taxonomy to work.
   foreach($vocabularies as $vocab){
      if($vocab->name == 'Feature Type'){
         taxonomy_del_vocabulary($vocab->vid);
      }
      if($vocab->name == 'Organism'){
         taxonomy_del_vocabulary($vocab->vid);
      }
      if($vocab->name == 'Library'){
         taxonomy_del_vocabulary($vocab->vid);
      }
      if($vocab->name == 'Analysis'){
         taxonomy_del_vocabulary($vocab->vid);
      }
   }

}

/**
 *
 *
 * @ingroup tripal_feature
 */
function tripal_features_set_taxonomy($max_sync = 0,$job_id = NULL){

   // make sure our vocabularies are cleaned and reset before proceeding
   tripal_feature_del_vocabulary();
   tripal_feature_set_vocabulary();

   // iterate through all drupal feature nodes and set the taxonomy
   $results = db_query("SELECT * FROM {chado_feature}");
   $nsql =  "SELECT * FROM {node} ".
            "WHERE nid = %d";
   $i = 0;

   // load into ids array
   $count = 0;
   $chado_features = array();
   while($chado_feature = db_fetch_object($results)){
      $chado_features[$count] = $chado_feature;
      $count++;
   }

   // Iterate through features that need to be synced
   $interval = intval($count * 0.01);
   foreach($chado_features as $chado_feature){

      // update the job status every 1% features
      if($job_id and $i % $interval == 0){
         tripal_job_set_progress($job_id,intval(($i/$count)*100));
      }
      print "$i of $count: ";
      $node = db_fetch_object(db_query($nsql,$chado_feature->nid));
      tripal_feature_set_taxonomy($node,$chado_feature->feature_id);

      $i++;
   }
}

/**
 *
 *
 * @ingroup tripal_feature
 */
function tripal_feature_set_taxonomy ($node,$feature_id){

   // iterate through the taxonomy classes that have been
   // selected by the admin user and make sure we only set those
   $tax_classes = variable_get('tax_classes', '');
   $do_ft = 0;
   $do_op = 0;
   $do_lb = 0;
   $do_an = 0;
   foreach($tax_classes as $class){
      if(strcmp($class ,'organism')==0){
         $do_op = 1;
      }
      if(strcmp($class,'feature_type')==0){
         $do_ft = 1;
      }
      if(strcmp($class,'library')==0){
         $do_lb = 1;
      }
      if(strcmp($class,'analysis')==0){
         $do_an = 1;
      }
   }


   // get the list of vocabularies and find our two vocabularies of interest
   $vocabularies = taxonomy_get_vocabularies();
   $ft_vid = NULL;
   $op_vid = NULL;
   $lb_vid = NULL;
   $an_vid = NULL;
   foreach($vocabularies as $vocab){
      if($vocab->name == 'Feature Type'){
         $ft_vid = $vocab->vid;
      }
      if($vocab->name == 'Organism'){
         $op_vid = $vocab->vid;
      }
      if($vocab->name == 'Library'){
         $lb_vid = $vocab->vid;
      }
      if($vocab->name == 'Analysis'){
         $an_vid = $vocab->vid;
      }
   }

   // get the cvterm and the organism for this feature
   $sql = "SELECT CVT.name AS cvname, O.genus, O.species ".
          "FROM {CVTerm} CVT ".
          "  INNER JOIN Feature F on F.type_id = CVT.cvterm_id ".
          "  INNER JOIN Organism O ON F.organism_id = O.organism_id ".
          "WHERE F.feature_id = $feature_id";
   $previous_db = tripal_db_set_active('chado');  // use chado database
   $feature = db_fetch_object(db_query($sql));
   tripal_db_set_active($previous_db);  // now use drupal database

   // Set the feature type for this feature
   if($do_ft && $ft_vid){
      $tags["$ft_vid"] = "$feature->cvname";
   }
   // Set the organism for this feature type
   if($do_op && $op_vid){
      $tags["$op_vid"] = "$feature->genus $feature->species";
   }

   // get the library that this feature may belong to and add it as taxonomy
   if($do_lb && $lb_vid){
      $sql = "SELECT L.name ".
             "FROM {Library} L ".
             "  INNER JOIN Library_feature LF ON LF.library_id = L.library_id ".
             "WHERE LF.feature_id = %d ";
      $previous_db = tripal_db_set_active('chado');  // use chado database
      $library = db_fetch_object(db_query($sql,$feature_id));
      tripal_db_set_active($previous_db);  // now use drupal database
      $tags["$lb_vid"] = "$library->name";
   }

   // now add the taxonomy to the node
   $terms['tags'] = $tags;
   taxonomy_node_save($node,$terms);
   //   print "Setting $node->name: " . implode(", ",$tags) . "\n";

   // get the analysis that this feature may belong to and add it as taxonomy
   // We'll add each one individually since there may be more than one analysis
   if($do_an && $an_vid){
      $sql = "SELECT A.name ".
             "FROM {Analysis} A ".
             "  INNER JOIN Analysisfeature AF ON AF.analysis_id = A.analysis_id ".
             "WHERE AF.feature_id = $feature_id ";
      $results = db_query($sql);
      $previous_db = tripal_db_set_active('chado');  // use chado database
      $analysis_terms = array();
      while($analysis=db_fetch_object($results)){
         $tags2["$an_vid"] = "$analysis->name";
         $terms['tags'] = $tags2;
         taxonomy_node_save($node,$terms);
      }
      tripal_db_set_active($previous_db);  // now use drupal database
   }

}

/**
 *
 *
 * @ingroup tripal_feature
 */
function tripal_features_cleanup($dummy = NULL, $job_id = NULL) {

   // build the SQL statments needed to check if nodes point to valid features
   $dsql = "SELECT * FROM {node} WHERE type = 'chado_feature' order by nid";
   $nsql = "SELECT * FROM {node} WHERE nid = %d";
   $csql = "SELECT * FROM {chado_feature} where nid = %d ";
   $cfsql= "SELECT * FROM {chado_feature}";
   $tsql = "SELECT * FROM {feature} F ".
          "  INNER JOIN CVTerm CVT ON F.type_id = CVT.cvterm_id ".
          "WHERE feature_id = %d  AND (";
   $supported_ftypes = split("[ \n]",variable_get('chado_feature_types','EST contig'));
   foreach($supported_ftypes as $ftype){
      $tsql .= " CVT.name = '$ftype' OR ";
   }
   $tsql .= " 0=1) ";  // add a 0=1 just as a filler so we don't have to remove a trailing 'OR'

   // load into nodes array
   $results = db_query($dsql);
   $count = 0;
   $nodes = array();
   while($node = db_fetch_object($results)){
      $nodes[$count] = $node;
      $count++;
   }

   // load the chado_features into an array
   $results = db_query($cfsql);
   $cnodes = array();
   while($node = db_fetch_object($results)){
      $cnodes[$count] = $node;
      $count++;
   }
   $interval = intval($count * 0.01);

   // iterate through all of the chado_feature nodes and delete those  that aren't valid
   foreach($nodes as $nid){

      // update the job status every 1% features
      if($job_id and $i % $interval == 0){
         tripal_job_set_progress($job_id,intval(($i/$count)*100));
      }

      // first check to see if the node has a corresponding entry
      // in the chado_feature table. If not then delete the node.
      $feature = db_fetch_object(db_query($csql,$nid->nid));
      if(!$feature){
         node_delete($nid->nid);
         $message = "Missing in chado_feature table.... DELETING: $nid->nid\n";
         watchdog('tripal_feature',$message,array(),WATCHDOG_WARNING);
         continue;
      }

      // second check to see if the node is for a feature of an allowed type.
      // if not, then delete the node.  This check will also take care of the
      // case when a node exists and an entry in the chado_feature table exists
      // but no feature with a matching feature_id exists
      $previous_db = tripal_db_set_active('chado');  // use chado database
      $ftype = db_fetch_object(db_query($tsql,$feature->feature_id));
      tripal_db_set_active($previous_db);  // now use drupal database

      if(!$ftype){
         node_delete($nid->nid);
         db_query("DELETE FROM {chado_feature} WHERE feature_id = $feature->feature_id");
         $message = "Node of the wrong feature type.... DELETING: $nid->nid\n";
         watchdog('tripal_feature',$message,array(),WATCHDOG_WARNING);
      }
      $i++;
   }

   // iterate through all of the chado_feature nodes and delete those  that aren't valid
   foreach($cnodes as $nid){
      // update the job status every 1% features
      if($job_id and $i % $interval == 0){
         tripal_job_set_progress($job_id,intval(($i/$count)*100));
      }
      $node = db_fetch_object(db_query($nsql,$nid->nid));
      if(!$node){
         db_query("DELETE FROM {chado_feature} WHERE nid = $nid->nid");
         $message = "chado_feature missing node.... DELETING: $nid->nid\n";
         watchdog('tripal_feature',$message,array(),WATCHDOG_WARNING);
      }

      $i++;
   }
   return '';
}

/**
 *
 *
 * @ingroup tripal_feature
 */
function tripal_feature_return_fasta($feature,$desc){   
   $fasta  = ">" . variable_get('chado_feature_accession_prefix','ID') . "$feature->feature_id|$feature->name";
   $fasta .= " $desc\n";
   $fasta .= wordwrap($feature->residues, 50, "\n", true);
   $fasta .= "\n\n";
   return $fasta;
}
/**
 *
 *
 * @ingroup tripal_feature
 */
function tripal_feature_job_describe_args($callback,$args){

   $new_args = array();
   if($callback == 'tripal_feature_load_fasta'){
      $new_args['FASTA file'] = $args[0];
      $organism = tripal_core_chado_select('organism',array('genus','species'),array('organism_id' => $args[1]));
      $new_args['Organism'] = $organism[0]->genus." ". $organism[0]->species;
      $new_args['Sequence Type'] = $args[2];
      $new_args['Name RE'] = $args[4];
      $new_args['Unique Name RE'] = $args[5];

      // add in the relationship arguments
      $new_args['Relationship Type'] = $args[8];
      $new_args['Relationship Parent RE'] = $args[9];
      $new_args['Relationship Parent Type'] = $args[10];

      // add in the database reference arguments
      if($args[7]){
         $db = tripal_core_chado_select('db',array('name'),array('db_id' => $args[7]));
      }
      $new_args['Database Reference'] = $db[0]->name;
      $new_args['Accession RE'] = $args[6];
      if($args[11]){
         $new_args['Update and Insert'] = 'Yes';
      }
      else {
         $new_args['Insert Only New Features'] = 'Yes';
      }

      // add in the analysis 
      if($args[13]){
         $analysis = tripal_core_chado_select('analysis',array('name'),array('analysis_id' => $args[13]));
      }
      $new_args['Analysis'] = $analysis[0]->name;
   }
   return $new_args;
}