tripal/tripal_feature/theme/templates/tripal_feature_sequence.tpl.php

<?php
/*
 * There are two ways that sequences can be displayed.  They can come from the 
 * feature.residues column or they can come from an alignment with another feature.  
 * This template will show both or one or the other depending on the data available.
 * 
 * For retreiving the sequence from an alignment we would typically make a call to
 * chado_expand_var function.  For example, to retrieve all
 * of the featurelocs in order to get the sequences needed for this template, the
 * following function call would be made:
 *
 *   $feature = chado_expand_var($feature,'table','featureloc');
 *
 * Then all of the sequences would need to be retreived from the alignments and
 * formatted for display below.  However, to simplify this template, this has already
 * been done by the tripal_feature module and the sequences are made available in
 * the variable:
 *
 *   $feature->featureloc_sequences
 *
 */

$feature = $variables['node']->feature;

// we don't want to get the sequence for traditionally large types. They are
// too big,  bog down the web browser, take longer to load and it's not
// reasonable to print them on a page.
$residues ='';
if(strcmp($feature->type_id->name,'scaffold') !=0 and
   strcmp($feature->type_id->name,'chromosome') !=0 and
   strcmp($feature->type_id->name,'supercontig') !=0 and
   strcmp($feature->type_id->name,'pseudomolecule') !=0) {
  $feature = chado_expand_var($feature,'field','feature.residues');
  $residues = $feature->residues;
} 

// get the sequence derived from alignments
$feature = $variables['node']->feature;
$featureloc_sequences = $feature->featureloc_sequences;

if ($residues or count($featureloc_sequences) > 0) { 

  $sequences_html = '';  // a variable for holding all sequences HTML text
  $list_items = array(); // a list to be used for theming of content on this page ?>
  
  <div class="tripal_feature-data-block-desc tripal-data-block-desc">The following sequences are available for this feature:</div> <?php
  
  // ADD IN RESIDUES FOR THIS FEATURE
  // add in the residues if they are present
  if ($residues) {
    $list_items[] = '<a href="#residues">Current ' . $feature->type_id->name . ' sequence</a>';
     
    // format the sequence to break every 50 residues
    $sequences_html .= '<a name="residues"></a>';
    $sequences_html .= '<div class="tripal_feature-sequence-item">';
    $sequences_html .= '<p><b>Current ' . $feature->type_id->name . ' sequence</b></p>';
    $sequences_html .= '<pre class="tripal_feature-sequence">';
    $sequences_html .= '>' . tripal_get_fasta_defline($feature) . "\n";
    $sequences_html .= preg_replace("/(.{50})/","\\1<br>",$feature->residues);
    $sequences_html .= '</pre>';
    $sequences_html .= '<a href="#sequences-top">back to top</a>';
    $sequences_html .= '</div>';
    
  }
  
  // ADD IN RELATIONSHIP SEQUENCES (e.g. proteins)
  // see the explanation in the tripal_feature_relationships.tpl.php 
  // template for how the 'all_relationships' is provided. It is this
  // variable that we use to get the proteins.
  $all_relationships = $feature->all_relationships;
  $object_rels = $all_relationships['object'];
  foreach ($object_rels as $rel_type => $rels){
    foreach ($rels as $subject_type => $subjects){
      foreach ($subjects as $subject){
        if ($rel_type == 'derives from' and $subject_type == 'polypeptide') {
          $protein = $subject->record->subject_id;
          $protein = chado_expand_var($protein, 'field', 'feature.residues');
          
          $list_items[] = '<a href="#residues">Protein sequence of ' . $protein->name . '</a>';
          $sequences_html .= '<a name="protein-' . $protein->feature_id . '"></a>';
          $sequences_html .= '<div class="tripal_feature-sequence-item">';
          $sequences_html .= '<p><b>Protein sequence of ' . $protein->name . '</b></p>';
          $sequences_html .= '<pre class="tripal_feature-sequence">';
          $sequences_html .= '>' . tripal_get_fasta_defline($protein) . "\n";
          $sequences_html .= preg_replace("/(.{50})/","\\1<br>", $protein->residues);
          $sequences_html .= '</pre>';
          $sequences_html .= '<a href="#sequences-top">back to top</a>';
          $sequences_html .= '</div>';
        }
        // add any other sequences by by relationship in a similar way
      }
    }
  }
  
  // ADD IN ALIGNMENT SEQUENCES FOR THIS FEATURE
  // show the alignment sequences first as they are colored with child features
  if(count($featureloc_sequences) > 0){
    foreach($featureloc_sequences as $src => $attrs){
      // the $attrs array has the following keys
      //   * src:  a unique identifier combining the feature id with the cvterm id
      //   * type: the type of sequence (e.g. mRNA, etc)
      //   * location:  the alignment location
      //   * defline: the definition line
      //   * formatted_seq: the formatted sequences
      $list_items[] = '<a href="#' . $attrs['src'] . '">Alignment at  ' . $attrs['location'];
      $sequences_html .= '<a name="' . $attrs['src'] . '"></a>';
      $sequences_html .= '<div class="tripal_feature-sequence-item">';
      $sequences_html .= '<p><b>Alignment at  ' . $attrs['location'] .'</b></p>';
      $sequences_html .= $attrs['formatted_seq'];
      $sequences_html .= '<a href="#sequences-top">back to top</a>';
      $sequences_html .= '</div>';
    }
  }
  
  // first add a list at the top of the page that can be formatted as the
  // user desires.  We use the theme_item_list function of Drupal to create 
  // the list rather than hard-code the HTML here.  Instructions for how
  // to create the list can be found here:
  // https://api.drupal.org/api/drupal/includes%21theme.inc/function/theme_item_list/7
  print '<a name="sequences-top"></a>';
  print theme_item_list(array(
    'items' => $list_items,
    'title' => '',
    'type' => 'ul',
    'attributes' => array(),
  ));
  
  // now print the sequences
  print $sequences_html;
}