use organism for alignment links

README.md

@@ -27,3 +27,9 @@ services:
       APOLLO_LINKS: "SFRU_RICE>rice" # correspondance between contig name prefix and apollo organism id, example: "SFRU_RICE>rice_1;SFRU_CORN>corn_2"
     [...]
 ```
+
+If you prefer, you can also use the organism abbreviation in JBROWSE_LINKS:
+
+```
+    JBROWSE_LINKS: "S.frugiperda corn>corn;S.frugiperda rice>sfrice"
+```

templates/tripal_feature_alignments.tpl.php

@@ -104,11 +104,12 @@ if(count($alignments) > 0){ ?>
         $links = getenv(JBROWSE_LINKS);
         $found_link = false;
         if ($links) {
+            $cur_org = $feature->organism_id->abbreviation;
             $dlist = explode(';', $links);
 
             foreach ($dlist as $delem) {
                 $d = explode('>', $delem);
-                if (substr($alignment->name, 0, strlen($d[0])) === $d[0]) {
+                if ($cur_org === $d[0] || substr($alignment->name, 0, strlen($d[0])) === $d[0]) {
                     $url = "/jbrowse?data=data/".$d[1]."&";
                     $found_link = true;
                     break;
@@ -139,11 +140,12 @@ if(count($alignments) > 0){ ?>
         $links = getenv(JBROWSE_LINKS);
         $found_link = false;
         if ($links) {
+            $cur_org = $feature->organism_id->abbreviation;
             $dlist = explode(';', $links);
 
             foreach ($dlist as $delem) {
                 $d = explode('>', $delem);
-                if (substr($alignment->name, 0, strlen($d[0])) === $d[0]) {
+                if ($cur_org === $d[0] || substr($alignment->name, 0, strlen($d[0])) === $d[0]) {
                     $url = "/apollo/annotator/loadLink?organism=".$d[1]."&";
                     $found_link = true;
                     break;