Add canvas support #27

includes/blast_ui.linkouts.inc

@@ -64,7 +64,7 @@ function blast_ui_blast_linkout_info() {
     'require_regex' => FALSE,
     'require_db' => FALSE,
   );
-  
+
   $types['link'] = array(
     // Human-readable Type name to display to users in the BLAST Database
     // create/edit form.
@@ -73,7 +73,7 @@ function blast_ui_blast_linkout_info() {
     // This function will have full access to the blast hit and database
     // prefix information and is expected to return a URL.
     'process function' => 'tripal_blast_generate_linkout_link',
-    // Help text to show in the BLAST Database create/edit form so that 
+    // Help text to show in the BLAST Database create/edit form so that
     // users will know how to use this link-out type. Specifically, info
     // about your assumptions for the URL prefix are very helpful.
     // HTML is aloud but do not enclose in <p>.
@@ -197,13 +197,13 @@ function tripal_blast_generate_linkout_gbrowse($url_prefix, $hit, $info, $option
   // calculate the smallest and largest coordinate.
   $coords = array();
   foreach($info['HSPs'] as $hsp) {
-  
+
     $start = min($hsp['Hsp_hit-from'], $hsp['Hsp_hit-to']);
     $stop = max($hsp['Hsp_hit-from'], $hsp['Hsp_hit-to']);
-    
+
     // Format the hsp for inclusion in the new track later.
     array_push($ranges, "$start..$stop");
-    
+
     // Add both the start & stop to the coordinate list.
     array_push($coords, $start, $stop);
   }
@@ -228,7 +228,7 @@ function tripal_blast_generate_linkout_gbrowse($url_prefix, $hit, $info, $option
       '!hspcoords' => join ("," , $ranges),
     )
   );
-  
+
   // Highlight our newly added feature.
   $query['h_feat'] = 'BlastHit';
 
@@ -236,16 +236,16 @@ function tripal_blast_generate_linkout_gbrowse($url_prefix, $hit, $info, $option
   $url = l(
     $hit->{'linkout_id'},
     $hit_url,
-    array( 
+    array(
       'query' => $query,
       'attributes' => array('target' => '_blank')
     )
   );
-  
-  // For some reason GBrowse expects semi-colons (;&) to delineate query paramters 
+
+  // For some reason GBrowse expects semi-colons (;&) to delineate query paramters
   // whereas Drupal throws ampherstands (&) in. This is to fix that.
   $url = str_replace('&',';&', $url);
-  
+
   return $url;
 
 }
@@ -259,7 +259,7 @@ function tripal_blast_generate_linkout_gbrowse($url_prefix, $hit, $info, $option
  *  allow your default tracks to be visible and give contect to your blast hit. You
  *  should include "blast" in your jbrowse.conf default track list to ensure your
  *  users can always see their hits. If you don't have access to the jbrowse.conf,
- *  you can place the tracks you want to see including 'blast' in the url prefix 
+ *  you can place the tracks you want to see including 'blast' in the url prefix
  *  (see example below under @param $url_prefix).
  *
  * @param $url_prefix
@@ -268,7 +268,7 @@ function tripal_blast_generate_linkout_gbrowse($url_prefix, $hit, $info, $option
  *   For example,
  *     http://myserver.com/jbrowse/databasica/?
  *     http://myserver.com/jbrowse/databasica/?tracks=myfavtrack,anoktrack,blast&
- * 
+ *
  * @param $hit
  *   The blast XML hit object. This object has the following keys based on the
  *   XML: Hit_num, Hit_id, Hit_def, Hit_accession, Hit_len and Hit_hsps.
@@ -297,20 +297,22 @@ function tripal_blast_generate_linkout_jbrowse($url_prefix, $hit, $info, $option
   // calculate the smallest and largest coordinate.
   $coords = array();
   $count = 0;
+  $strands = array();
   foreach($info['HSPs'] as $hsp) {
     $count++;
-    
+
     $strand = '1';
     $hsp_start = $hsp['Hsp_hit-from'];
     $hsp_end = $hsp['Hsp_hit-to'];
-    
+    $strands[] = $strand;
+
     // Handle alignments on the negative strand.
     if (($hsp_end - $hsp_start) < 0) {
       $strand = '-1';
       $hsp_start = $hsp['Hsp_hit-to'];
       $hsp_end = $hsp['Hsp_hit-from'];
     }
-    
+
     // Add both the start & stop to the coordinate list.
     array_push($coords,$hsp['Hsp_hit-from'] , $hsp['Hsp_hit-to'] );
 
@@ -329,8 +331,8 @@ function tripal_blast_generate_linkout_jbrowse($url_prefix, $hit, $info, $option
   // Calculate the minimum & maximum coordinates.
   $min = min($coords);
   $max = max($coords);
-  
-  // We also want some white-space on either side of out hit 
+
+  // We also want some white-space on either side of out hit
   // when we show it in the JBrowse. To make this generic,
   // we want our blast hit to take up 2/3 of the screen thus
   // we have 1/6 per side for white-space.
@@ -350,19 +352,37 @@ function tripal_blast_generate_linkout_jbrowse($url_prefix, $hit, $info, $option
     )
   );
 
-  // Next we want to add our BLAST hit to the JBrowse.
-  $jbrowse_query['addFeatures'] = format_string(
-    'addFeatures=[{"seq_id":"!id","start":!min,"end":!max,"name":"!name","subfeatures":[!hspcoords]}]',
-    array(
-      '!id' => $hit->{'linkout_id'},
-      '!name' => $info['query_name'] . ' Blast Hit',
-      '!min' => $min,
-      '!max' => $max,
-      '!hspcoords' => join ("," , $ranges)
-    ));
+  $unique_strands = array_unique($strands);
+  if (count($unique_strands) === 1) {
+    $strand = end($strands);
+    // Next we want to add our BLAST hit to the JBrowse.
+    $jbrowse_query['addFeatures'] = format_string(
+      'addFeatures=[{"seq_id":"!id","start":!min,"end":!max,"name":"!name","strand":!strand,"subfeatures":[!hspcoords]}]',
+      array(
+        '!id' => $hit->{'linkout_id'},
+        '!name' => $info['query_name'] . ' Blast Hit',
+        '!min' => $min,
+        '!max' => $max,
+        '!hspcoords' => join(",", $ranges),
+        '!strand' => $strand,
+      )
+    );
+  }
+  else {
+    $jbrowse_query['addFeatures'] = format_string(
+      'addFeatures=[{"seq_id":"!id","start":!min,"end":!max,"name":"!name","subfeatures":[!hspcoords]}]',
+      array(
+        '!id' => $hit->{'linkout_id'},
+        '!name' => $info['query_name'] . ' Blast Hit',
+        '!min' => $min,
+        '!max' => $max,
+        '!hspcoords' => join(",", $ranges),
+      )
+    );
+  }
 
   // Then add a track to display our new feature.
-  $jbrowse_query['addTracks'] = 'addTracks=[{"label":"blast","key":"BLAST Result","type":"JBrowse/View/Track/HTMLFeatures","store":"url"}]';
+  $jbrowse_query['addTracks'] = 'addTracks=[{"label":"blast","key":"BLAST Result","type":"JBrowse/View/Track/CanvasFeatures","store":"url"}]';
 
   $url_postfix = implode('&', $jbrowse_query);