Issue #72: Updating API to include 2.1 improvements: d5e9bb1

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

@@ -1,10 +1,10 @@
 <?php
 /*
- * There are several ways that sequences can be displayed.  They can come from the 
+ * There are several ways that sequences can be displayed.  They can come from the
  * feature.residues column,  they can come from an alignment with another feature,
  * they can come from a protein sequence that has relationship with this sequence,
  * or they can come from sub children (e.g. CDS coding sequences).
- *   
+ *
  * This template will show all types depending on the data available.
  *
  */
@@ -12,7 +12,7 @@
 $feature = $variables['node']->feature;
 
 // number of bases per line in FASTA format
-$num_bases = 50; 
+$num_bases = 50;
 
 // 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
@@ -24,37 +24,37 @@ if(strcmp($feature->type_id->name,'scaffold') !=0 and
    strcmp($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) { 
+if ($residues or count($featureloc_sequences) > 0) {
 
   $sequences_html = '';  // a variable for holding all sequences HTML text
   $list_items = array(); // a list to be used for theming of content on this page
-  
+
   // ADD IN RESIDUES FOR THIS FEATURE
   // add in the residues if they are present
   if ($residues) {
     $list_items[] = '<a href="#residues">' . $feature->type_id->name . ' sequence</a>';
-     
+
     // format the sequence to break every 50 residues
     $sequences_html .= '<a name="residues"></a>';
     $sequences_html .= '<div id="residues" class="tripal_feature-sequence-item">';
     $sequences_html .= '<p><b>' . $feature->type_id->name . ' sequence</b></p>';
     $sequences_html .= '<pre class="tripal_feature-sequence">';
-    $sequences_html .= '>' . tripal_get_fasta_defline($feature, '', NULL, '', strlen($feature->residues)) . "\n";
+    $sequences_html .= '>' . tripal_get_fasta_defline($feature, '', NULL, '', strlen($feature->residues)) . "<br>";
     $sequences_html .= wordwrap($feature->residues, $num_bases, "<br>", TRUE);
     $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 
+  // 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 = $feature->all_relationships;
@@ -64,27 +64,27 @@ if ($residues or count($featureloc_sequences) > 0) {
   foreach ($object_rels as $rel_type => $rels){
     foreach ($rels as $subject_type => $subjects){
       foreach ($subjects as $subject){
-        
+
         // add in protein sequence if it has residues
         if ($rel_type == 'derives from' and $subject_type == 'polypeptide') {
           $protein = $subject->record->subject_id;
           $protein = chado_expand_var($protein, 'field', 'feature.residues');
-          
+
           if ($protein->residues) {
             $list_items[] = '<a href="#residues">protein sequence</a>';
             $sequences_html .= '<a name="protein-' . $protein->feature_id . '"></a>';
             $sequences_html .= '<div id="protein-' . $protein->feature_id . '" 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, '', NULL, '', strlen($protein->residues)) . "\n";
+            $sequences_html .= '>' . tripal_get_fasta_defline($protein, '', NULL, '', strlen($protein->residues)) . "<br>";
             $sequences_html .= wordwrap($protein->residues, $num_bases, "<br>", TRUE);
             $sequences_html .= '</pre>';
             $sequences_html .= '<a href="#sequences-top">back to top</a>';
             $sequences_html .= '</div>';
           }
         }
-        
-        // If the CDS has sequences then concatenate those. The objects 
+
+        // If the CDS has sequences then concatenate those. The objects
         // should be returned in order of rank
         if ($rel_type == 'part of' and $subject_type == 'CDS') {
           $cds = $subject->record->subject_id;
@@ -94,14 +94,14 @@ if ($residues or count($featureloc_sequences) > 0) {
             $coding_seq .= $cds->residues;
           }
         }
-        
+
         // add any other sequences that are related through a relationship
         // and that have values in the 'residues' column
-        
+
       }
     }
   }
-  
+
   // CODING SEQUENCES FROM RELATIONSHIPS
   // add in any CDS sequences.
   if ($has_coding_seq) {
@@ -115,7 +115,7 @@ if ($residues or count($featureloc_sequences) > 0) {
     $sequences_html .= '<a href="#sequences-top">back to top</a>';
     $sequences_html .= '</div>';
   }
-  
+
   /* ADD IN ALIGNMENT SEQUENCES FOR THIS FEATURE
    * For retreiving the sequence from an alignment we would typically make a call to
    * chado_expand_var function.  For example, to retrieve all
@@ -127,7 +127,7 @@ if ($residues or count($featureloc_sequences) > 0) {
    * 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: 
+   * the variable:
    *
    *   $feature->featureloc_sequences
    */
@@ -148,7 +148,7 @@ if ($residues or count($featureloc_sequences) > 0) {
       $sequences_html .= '<a href="#sequences-top">back to top</a>';
       $sequences_html .= '</div>';
     }
-    
+
     // check to see if this alignment has any CDS. If so, generate a CDS sequence
     $cds_sequence = tripal_get_feature_sequences(
         array(
@@ -183,14 +183,14 @@ if ($residues or count($featureloc_sequences) > 0) {
         $sequences_html .= '</div>';
       }
     }
-  } 
+  }
   ?>
 
-  <div class="tripal_feature-data-block-desc tripal-data-block-desc">The following sequences are available for this feature:</div> 
+  <div class="tripal_feature-data-block-desc tripal-data-block-desc">The following sequences are available for this feature:</div>
   <?php
-  
+
   // 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 
+  // 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
@@ -216,7 +216,7 @@ if ($residues or count($featureloc_sequences) > 0) {
           is associated with an mRNA feature and protein sequences will appear on the mRNA page.</li>
       <li>This feature has one or more CDS features associated via the "feature_relationship" table of Chado with a
           relationship of type "part of". If the CDS features have residues then those will be concatenated
-          and presented as a sequence. Typically, CDSs are associated with an mRNA feature and CDS sequences 
+          and presented as a sequence. Typically, CDSs are associated with an mRNA feature and CDS sequences
           will appear on the mRNA page.</li>
       <li>This feature is aligned to another feature (e.g. scaffold, or chromosome) and this feature has
           one or more CDS features associated.  The CDS sequenes underlying the alignment will be
@@ -224,7 +224,7 @@ if ($residues or count($featureloc_sequences) > 0) {
     </ul>
     </p>';
   print tripal_set_message($message, TRIPAL_INFO, array('return_html' => 1));
-  
+
   // now print the sequences
   print $sequences_html;
 }

tripal_chado/api/tripal_chado.query.api.inc

@@ -1683,7 +1683,9 @@ function chado_query($sql, $args = array()) {
  */
 function chado_pager_query($query, $args, $limit, $element, $count_query = '') {
   // get the page and offset for the pager
-  $page = isset($_GET['page']) ? $_GET['page'] : '0';
+  $page_arg = isset($_GET['page']) ? $_GET['page'] : '0';
+  $pages = explode(',', $page_arg);
+  $page = $pages[$element];
   $offset = $limit * $page;
   $q = $_GET['q'];