Merge remote-tracking branch 'origin/releases/Release_2_10_4_Branch' into merges...

[jalview.git] / src / jalview / ext / ensembl / EnsemblSymbol.java

diff --git a/src/jalview/ext/ensembl/EnsemblSymbol.java b/src/jalview/ext/ensembl/EnsemblSymbol.java
index 7862fce..40d6cad 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblSymbol.java
+++ b/src/jalview/ext/ensembl/EnsemblSymbol.java
@@ -44,8 +44,6 @@ public class EnsemblSymbol extends EnsemblXref
 {
   private static final String GENE = "gene";
   private static final String TYPE = "type";
-  private static final String ID = "id";
-
   /**
    * Constructor given the target domain to fetch data from
    * 
@@ -77,7 +75,7 @@ public class EnsemblSymbol extends EnsemblXref
       while (rvals.hasNext())
       {
         JSONObject val = (JSONObject) rvals.next();
-        String id = val.get(ID).toString();
+        String id = val.get(JSON_ID).toString();
         String type = val.get(TYPE).toString();
         if (id != null && GENE.equals(type))
         {
@@ -143,22 +141,18 @@ public class EnsemblSymbol extends EnsemblXref
     {
       for (String query : queries)
       {
-        for (Species taxon : Species.values())
+        for (Species taxon : Species.getModelOrganisms())
         {
-          if (taxon.isModelOrganism())
+          URL url = getUrl(query, taxon, GENE);
+          if (url != null)
           {
-            URL url = getUrl(query, taxon, GENE);
-            if (url != null)
+            br = getHttpResponse(url, ids);
+            if (br != null)
             {
-              br = getHttpResponse(url, ids);
-              if (br != null)
+              String geneId = parseSymbolResponse(br);
+              if (geneId != null && !result.contains(geneId))
               {
-                String geneId = parseSymbolResponse(br);
-                System.out.println(url + " returned " + geneId);
-                if (geneId != null && !result.contains(geneId))
-                {
-                  result.add(geneId);
-                }
+                result.add(geneId);
               }
             }
           }