theme_tripal/tripal_feature/tripal_feature_featurelocs_as_child.tpl.php

@@ -2,7 +2,7 @@
 
 $featurelocs_as_child = $variables['tripal_feature']['featurelocs_as_child'];
 $feature = $variables['node']->feature;
-
+dpm($featurelocs_as_child);
 ?>
 <div id="tripal_feature-featurelocs_as_child-box" class="tripal_feature-info-box tripal-info-box">
   <div class="tripal_feature-info-box-title tripal-info-box-title">Locations where <?php print $feature->featurename;?> is found</div>
@@ -23,15 +23,15 @@ $feature = $variables['node']->feature;
          if($i % 2 == 0 ){
             $class = 'tripal_feature-table-odd-row tripal-table-even-row';
          } 
-         $locname = $loc->name;
+         $src_name = $loc->src_name;
          if($loc->snid){
-           $locname = "<a href=\"" . url("node/$loc->snid") . "\">$loc->name</a> ";
+           $src_name = "<a href=\"" . url("node/$loc->snid") . "\">".$loc->src_name .":".$loc->fmin . ".." . $loc->fmax ."</a> ";
          }
          ?>
          <tr class="<?php print $class ?>">
-           <td><?php print $locname ?></td>
+           <td><?php print $loc->name ?></td>
            <td><?php print $loc->cvname ?></td>
-           <td><?php print $loc->src_name .":".$loc->fmin . ".." . $loc->fmax ?></td>
+           <td><?php print $src_name</td>
            <td><?php print $loc->phase ?></td>
            <td><?php 
               if($loc->strand == -1){

tripal_analysis_blast/tripal_analysis_blast.module

@@ -556,24 +556,6 @@ function chado_analysis_blast_load($node){
    $query_type      = tripal_analysis_get_property($analysis->analysis_id,'analysis_blast_query_type');	
    $query_uniquename= tripal_analysis_get_property($analysis->analysis_id,'analysis_blast_query_uniquename');	
    $blastfile_ext   = tripal_analysis_get_property($analysis->analysis_id,'analysis_blast_blastfile_ext');	
-	
-   // check if there exists a best hit report. if yes, reuturn the report url
-   $select = array(
-      'analysisfeature_id' => array(
-         'analysis_id' => $analysis_id,
-      ), 
-      'type_id' => array(
-         'name' => 'analysis_blast_besthit_query',
-         'cv_id' => array(
-            'name' => 'tripal'
-         ),
-      ),         
-   );
-   $blast_report = tripal_core_chado_select('analysisfeatureprop',array('analysisfeatureprop_id'),$select);
-	if ($blast_report) {
-		$report_url = url("tripal_blast_report/".$analysis->analysis_id."/1/0/0/20");
-		$analysis->blast_report = $report_url;
-	}
 
    $analysis->tripal_analysis_blast->blastdb         = $blastdb->value;
    $analysis->tripal_analysis_blast->blastfile       = $blastfile->value;	
@@ -597,6 +579,27 @@ function chado_analysis_blast_load($node){
       $analysis->tripal_analysis_blast->blastfile = $prop_values[1];
       $analysis->tripal_analysis_blast->blastparameters = $prop_values[2];
    }
+
+return $additions;
+
+   // check if there exists a best hit report. if yes, reuturn the report url
+   $select = array(
+      'analysisfeature_id' => array(
+         'analysis_id' => $analysis_id,
+      ), 
+      'type_id' => array(
+         'name' => 'analysis_blast_besthit_query',
+         'cv_id' => array(
+            'name' => 'tripal'
+         ),
+      ),         
+   );
+   $blast_report = tripal_core_chado_select('analysisfeatureprop',array('analysisfeatureprop_id'),$select);
+	if ($blast_report) {
+		$report_url = url("tripal_blast_report/".$analysis->analysis_id."/1/0/0/20");
+		$analysis->blast_report = $report_url;
+	}
+
 	return $additions;
 }
 /**

tripal_feature/tripal_feature.module

@@ -1291,7 +1291,7 @@ function tripal_feature_load_featureloc_sequences($feature_id,$featurelocs){
       }      
       $floc_sequences[$src]['src'] = $src;
       $floc_sequences[$src]['type'] = $featureloc->cvname;
-      $sequence = substr($feature->residues,$featureloc->fmin,$featureloc->fmax - $featureloc->fmin);
+      $sequence = substr($feature->residues,$featureloc->fmin-1,($featureloc->fmax - $featureloc->fmin)+1);
       $floc_sequences[$src]['formatted_seq'] =  tripal_feature_color_sequence (
           $sequence,$parts);
    }
@@ -1438,7 +1438,7 @@ function tripal_feature_color_sequence ($sequence,$parts){
    foreach ($parts as $index => $child){
       $type = $child['type'];
       $start = $child['start'];
-      $end = $child['end'];
+      $end = $child['end']+1;
       
       $class = "class=\"tripal_feature-featureloc_sequence-$type\"";