tripal/tripal_featuremap/theme/tripal_feature/tripal_feature_featurepos.tpl.php

<?php

// expand the feature object to include the records from the featurepos table
// specify the number of features to show by default and the unique pager ID
$num_results_per_page = 25; 
$featurepos_pager_id = 20;

// get the maps associated with this feature
$feature = $variables['node']->feature;
$options = array(  
  'return_array' => 1,
  'order_by' => array(
    'map_feature_id' => 'ASC'
  ),
  'pager' => array(
    'limit' => $num_results_per_page, 
    'element' => $featurepos_pager_id
  ),
  'include_fk' => array(
    'map_feature_id' => array(
      'type_id' => 1,
      'organism_id' => 1,
    ),
    'featuremap_id' => array(
       'unittype_id' => 1,
    ),
  ),
);

$feature = tripal_core_expand_chado_vars($feature, 'table', 'featurepos', $options);

// because the featurepos table has  FK relationships with map_feature_id and feature_id with the feature table 
// the function call above will try to expand both and will create an array of matches for each FK.
// we only want to show the map that this feature belongs to
$map_positions = $feature->featurepos->map_feature_id;
dpm($feature);

// the total number of records for the paged query is stored in a session variable
$total_records = chado_pager_get_count($featurepos_pager_id);


if(count($map_positions) > 0){ ?>
  <div class="tripal_feature-data-block-desc tripal-data-block-desc">This feature is contained in the following <?php print number_format($total_records) ?> map(s):</div><?php 

  // the $headers array is an array of fields to use as the colum headers.
  // additional documentation can be found here
  // https://api.drupal.org/api/drupal/includes%21theme.inc/function/theme_table/7
  $headers = array('Map Name', 'Landmark', 'Type', 'Position');
  
  // the $rows array contains an array of rows where each row is an array
  // of values for each column of the table in that row.  Additional documentation
  // can be found here:
  // https://api.drupal.org/api/drupal/includes%21theme.inc/function/theme_table/7
  $rows = array();

  // iterate through our map positions    
  foreach ($map_positions as $position){
    $map_feature = $position->map_feature_id;

    // check if there are any values in the featureposprop table for the start and stop
    $mappos = $position->mappos;
    $options = array(
      'return_array' => 1,
      'include_fk' => array(
        'type_id' => 1,            
      ),
    );
    $position = tripal_core_expand_chado_vars($position, 'table', 'featureposprop', $options);
    $featureposprop = $position->featureposprop;
    $start = '';
    $stop = '';
    if (is_array($featureposprop)) {
      foreach ($featureposprop as $index => $property) {
         if ($property->type_id->name == 'start') {
           $start = $property->value;
         }
         if ($property->type_id->name == 'stop') {
           $stop = $property->value;
         }
      }      
    }  
    if ($start and $stop and $start != $stop) {
      $mappos = "$start-$stop";
    }
    if ($start and !$stop) {
      $mappos = $start;
    }
    if ($start and $stop and $start == $stop) {
      $mappos = $start;
    }
    
    // get the map name feature
    $map_name =  $position->featuremap_id->name;
    if (property_exists($position->featuremap_id, 'nid')) {
      $map_name = l($map_name, 'node/' . $position->featuremap_id->nid, array('attributes' => array('target' => '_blank')));
    }
    
    
    // get the landmark
    $landmark = $map_feature->name;
    if (property_exists($map_feature, 'nid')) {
      $landmark =  l($landmark, 'node/' . $map_feature->nid, array('attributes' => array('target' => '_blank')));
    }
    
    $rows[] = array(
      $map_name,
      $landmark,
      $map_feature->type_id->name,
      $mappos . ' ' . $position->featuremap_id->unittype_id->name,
    );
  }
  // the $table array contains the headers and rows array as well as other
  // options for controlling the display of the table.  Additional
  // documentation can be found here:
  // https://api.drupal.org/api/drupal/includes%21theme.inc/function/theme_table/7
  $table = array(
    'header' => $headers,
    'rows' => $rows,
    'attributes' => array(
      'id' => 'tripal_feature-table-featurepos',
    ),
    'sticky' => FALSE,
    'caption' => '',
    'colgroups' => array(),
    'empty' => '',
  );

  // once we have our table array structure defined, we call Drupal's theme_table()
  // function to generate the table.
  print theme_table($table); 
  
  // the $pager array values that control the behavior of the pager.  For
  // documentation on the values allows in this array see:
  // https://api.drupal.org/api/drupal/includes!pager.inc/function/theme_pager/7
  // here we add the paramter 'block' => 'features'. This is because
  // the pager is not on the default block that appears. When the user clicks a
  // page number we want the browser to re-appear with the page is loaded.
  $pager = array(
    'tags' => array(),
    'element' => $featurepos_pager_id,
    'parameters' => array(
      'block' => 'featurepos'
    ),
    'quantity' => $num_results_per_page,
  );
  print theme_pager($pager); 
}?>