3253-omnibus save

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

diff --git a/src/jalview/ext/ensembl/EnsemblInfo.java b/src/jalview/ext/ensembl/EnsemblInfo.java
index 71730de..97a8e74 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblInfo.java
+++ b/src/jalview/ext/ensembl/EnsemblInfo.java
@@ -2,7 +2,9 @@ package jalview.ext.ensembl;
 
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefSource;
+import jalview.util.JSONUtils;
 
+import java.io.BufferedReader;
 import java.io.IOException;
 import java.net.MalformedURLException;
 import java.net.URL;
@@ -17,20 +19,18 @@ import org.json.simple.parser.ParseException;
 public class EnsemblInfo extends EnsemblRestClient
 {
 
-  /**
+  /*
    * cached results of REST /info/divisions service, currently
-   * 
    * <pre>
    * { 
-   *  "ENSEMBLFUNGI", "http://rest.ensemblgenomes.org"},
-   *  "ENSEMBLBACTERIA", "http://rest.ensemblgenomes.org"},
-   *  "ENSEMBLPROTISTS", "http://rest.ensemblgenomes.org"},
-   *  "ENSEMBLMETAZOA", "http://rest.ensemblgenomes.org"},
-   *  "ENSEMBLPLANTS",  "http://rest.ensemblgenomes.org"},
-   *  "ENSEMBL", "http://rest.ensembl.org"
+   *  { "ENSEMBLFUNGI", "http://rest.ensemblgenomes.org"},
+   *    "ENSEMBLBACTERIA", "http://rest.ensemblgenomes.org"},
+   *    "ENSEMBLPROTISTS", "http://rest.ensemblgenomes.org"},
+   *    "ENSEMBLMETAZOA", "http://rest.ensemblgenomes.org"},
+   *    "ENSEMBLPLANTS",  "http://rest.ensemblgenomes.org"},
+   *    "ENSEMBL", "http://rest.ensembl.org" }
    *  }
    * </pre>
-   * 
    * The values for EnsemblGenomes are retrieved by a REST call, that for
    * Ensembl is added programmatically for convenience of lookup
    */
@@ -92,13 +92,9 @@ public class EnsemblInfo extends EnsemblRestClient
     try
     {
       @SuppressWarnings("unchecked")
-      Iterator<Object> rvals = (Iterator<Object>) getJSON(
-              getDivisionsUrl(ensemblGenomesDomain), null, -1,
-              MODE_ITERATOR, null);
+         Iterator<Object> rvals = (Iterator<Object>) getJSON(getDivisionsUrl(ensemblGenomesDomain), null, -1, MODE_ITERATOR, null);
       if (rvals == null)
-      {
-        return;
-      }
+         return;
       while (rvals.hasNext())
       {
         String division = rvals.next().toString();
@@ -128,8 +124,7 @@ public class EnsemblInfo extends EnsemblRestClient
    * 
    * @return
    */
-  public Set<String> getDivisions()
-  {
+  public Set<String> getDivisions() {
     if (divisions == null)
     {
       fetchDivisions();