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@@ -38,21 +38,93 @@ if(strcmp($feature->type_id->name,'scaffold') !=0 and
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$feature = $variables['node']->feature;
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$featureloc_sequences = $feature->featureloc_sequences;
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-if ($residues or count($featureloc_sequences) > 0) { ?>
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- <div class="tripal_feature-data-block-desc tripal-data-block-desc"></div> <?php
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+if ($residues or count($featureloc_sequences) > 0) {
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+
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+ $sequences_html = ''; // a variable for holding all sequences HTML text
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+ $list_items = array(); // a list to be used for theming of content on this page ?>
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+
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+ <div class="tripal_feature-data-block-desc tripal-data-block-desc">The following sequences are available for this feature:</div> <?php
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+
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+ // ADD IN RESIDUES FOR THIS FEATURE
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+ // add in the residues if they are present
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+ if ($residues) {
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+ $list_items[] = '<a href="#residues">Current ' . $feature->type_id->name . ' sequence</a>';
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+
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+ // format the sequence to break every 50 residues
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+ $sequences_html .= '<a name="residues"></a>';
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+ $sequences_html .= '<div class="tripal_feature-sequence-item">';
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+ $sequences_html .= '<p><b>Current ' . $feature->type_id->name . ' sequence</b></p>';
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+ $sequences_html .= '<pre class="tripal_feature-sequence">';
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+ $sequences_html .= '>' . tripal_get_fasta_defline($feature) . "\n";
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+ $sequences_html .= preg_replace("/(.{50})/","\\1<br>",$feature->residues);
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+ $sequences_html .= '</pre>';
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+ $sequences_html .= '<a href="#sequences-top">back to top</a>';
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+ $sequences_html .= '</div>';
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+
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+ }
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+ // ADD IN RELATIONSHIP SEQUENCES (e.g. proteins)
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+ // see the explanation in the tripal_feature_relationships.tpl.php
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+ // template for how the 'all_relationships' is provided. It is this
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+ // variable that we use to get the proteins.
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+ $all_relationships = $feature->all_relationships;
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+ $object_rels = $all_relationships['object'];
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+ foreach ($object_rels as $rel_type => $rels){
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+ foreach ($rels as $subject_type => $subjects){
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+ foreach ($subjects as $subject){
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+ if ($rel_type == 'derives from' and $subject_type == 'polypeptide') {
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+ $protein = $subject->record->subject_id;
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+ $protein = chado_expand_var($protein, 'field', 'feature.residues');
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+
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+ $list_items[] = '<a href="#residues">Protein sequence of ' . $protein->name . '</a>';
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+ $sequences_html .= '<a name="protein-' . $protein->feature_id . '"></a>';
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+ $sequences_html .= '<div class="tripal_feature-sequence-item">';
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+ $sequences_html .= '<p><b>Protein sequence of ' . $protein->name . '</b></p>';
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+ $sequences_html .= '<pre class="tripal_feature-sequence">';
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+ $sequences_html .= '>' . tripal_get_fasta_defline($protein) . "\n";
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+ $sequences_html .= preg_replace("/(.{50})/","\\1<br>", $protein->residues);
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+ $sequences_html .= '</pre>';
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+ $sequences_html .= '<a href="#sequences-top">back to top</a>';
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+ $sequences_html .= '</div>';
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+ }
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+ // add any other sequences by by relationship in a similar way
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+ }
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+ }
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+ }
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+
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+ // ADD IN ALIGNMENT SEQUENCES FOR THIS FEATURE
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// show the alignment sequences first as they are colored with child features
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if(count($featureloc_sequences) > 0){
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- foreach($featureloc_sequences as $src => $attrs){
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- print $attrs['formatted_seq'];
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- }
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+ foreach($featureloc_sequences as $src => $attrs){
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+ // the $attrs array has the following keys
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+ // * src: a unique identifier combining the feature id with the cvterm id
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+ // * type: the type of sequence (e.g. mRNA, etc)
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+ // * location: the alignment location
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+ // * defline: the definition line
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+ // * formatted_seq: the formatted sequences
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+ $list_items[] = '<a href="#' . $attrs['src'] . '">Alignment at ' . $attrs['location'];
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+ $sequences_html .= '<a name="' . $attrs['src'] . '"></a>';
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+ $sequences_html .= '<div class="tripal_feature-sequence-item">';
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+ $sequences_html .= '<p><b>Alignment at ' . $attrs['location'] .'</b></p>';
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+ $sequences_html .= $attrs['formatted_seq'];
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+ $sequences_html .= '<a href="#sequences-top">back to top</a>';
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+ $sequences_html .= '</div>';
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+ }
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}
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- // add in the residues if they are present
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- if ($residues) { ?>
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- <pre id="tripal_feature-sequence-residues"><?php
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- // format the sequence to break every 100 residues
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- print preg_replace("/(.{50})/","\\1<br>",$feature->residues); ?>
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- </pre> <?php
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- }
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+ // first add a list at the top of the page that can be formatted as the
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+ // user desires. We use the theme_item_list function of Drupal to create
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+ // the list rather than hard-code the HTML here. Instructions for how
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+ // to create the list can be found here:
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+ // https://api.drupal.org/api/drupal/includes%21theme.inc/function/theme_item_list/7
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+ print '<a name="sequences-top"></a>';
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+ print theme_item_list(array(
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+ 'items' => $list_items,
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+ 'title' => '',
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+ 'type' => 'ul',
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+ 'attributes' => array(),
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+ ));
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+
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+ // now print the sequences
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+ print $sequences_html;
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}
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Stephen Ficklin