Merge branch 'develop' into trial_merge/JAL-1950

[jalview.git] / src / jalview / ws / seqfetcher / ASequenceFetcher.java

diff --git a/src/jalview/ws/seqfetcher/ASequenceFetcher.java b/src/jalview/ws/seqfetcher/ASequenceFetcher.java
index 31168b4..977f9da 100644 (file)
--- a/src/jalview/ws/seqfetcher/ASequenceFetcher.java
+++ b/src/jalview/ws/seqfetcher/ASequenceFetcher.java
@@ -98,8 +98,8 @@ public class ASequenceFetcher
     {
       return null;
     }
-    String[] sf = fetchableDbs.keySet().toArray(
-            new String[fetchableDbs.size()]);
+    String[] sf = fetchableDbs.keySet()
+            .toArray(new String[fetchableDbs.size()]);
     return sf;
   }
 
@@ -190,8 +190,8 @@ public class ASequenceFetcher
               seqset = fetcher.getSequenceRecords(qsb.toString());
             } catch (Exception ex)
             {
-              System.err.println("Failed to retrieve the following from "
-                      + db);
+              System.err.println(
+                      "Failed to retrieve the following from " + db);
               System.err.println(qsb);
               ex.printStackTrace(System.err);
             }
@@ -204,8 +204,9 @@ public class ASequenceFetcher
                 for (int is = 0; is < seqs.length; is++)
                 {
                   rseqs.addElement(seqs[is]);
-                  List<DBRefEntry> frefs = DBRefUtils.searchRefs(seqs[is]
-                          .getDBRefs(), new DBRefEntry(db, null, null));
+                  List<DBRefEntry> frefs = DBRefUtils.searchRefs(
+                          seqs[is].getDBRefs(),
+                          new DBRefEntry(db, null, null));
                   for (DBRefEntry dbr : frefs)
                   {
                     queriesFound.add(dbr.getAccessionId());
@@ -218,8 +219,8 @@ public class ASequenceFetcher
               {
                 if (fetcher.getRawRecords() != null)
                 {
-                  System.out.println("# Retrieved from " + db + ":"
-                          + qsb.toString());
+                  System.out.println(
+                          "# Retrieved from " + db + ":" + qsb.toString());
                   StringBuffer rrb = fetcher.getRawRecords();
                   /*
                    * for (int rr = 0; rr<rrb.length; rr++) {
@@ -275,8 +276,8 @@ public class ASequenceFetcher
           Exception ex)
   {
 
-    System.err.println("Failed to retrieve the following references from "
-            + db);
+    System.err.println(
+            "Failed to retrieve the following references from " + db);
     int n = 0;
     for (String qv : queriesMade)
     {
@@ -338,10 +339,8 @@ public class ASequenceFetcher
     } catch (Exception e)
     {
       // Serious problems if this happens.
-      throw new Error(
-              MessageManager
-                      .getString("error.dbrefsource_implementation_exception"),
-              e);
+      throw new Error(MessageManager
+              .getString("error.dbrefsource_implementation_exception"), e);
     }
     addDbRefSourceImpl(proxy);
   }
@@ -360,8 +359,8 @@ public class ASequenceFetcher
       {
         fetchableDbs = new Hashtable<String, Map<String, DbSourceProxy>>();
       }
-      Map<String, DbSourceProxy> slist = fetchableDbs.get(proxy
-              .getDbSource());
+      Map<String, DbSourceProxy> slist = fetchableDbs
+              .get(proxy.getDbSource());
       if (slist == null)
       {
         fetchableDbs.put(proxy.getDbSource(),
@@ -374,18 +373,18 @@ public class ASequenceFetcher
   /**
    * select sources which are implemented by instances of the given class
    * 
-   * @param class that implements DbSourceProxy
+   * @param class
+   *          that implements DbSourceProxy
    * @return null or vector of source names for fetchers
    */
   public String[] getDbInstances(Class class1)
   {
     if (!DbSourceProxy.class.isAssignableFrom(class1))
     {
-      throw new Error(
-              MessageManager
-                      .formatMessage(
-                              "error.implementation_error_dbinstance_must_implement_interface",
-                              new String[] { class1.toString() }));
+      throw new Error(MessageManager.formatMessage(
+              "error.implementation_error_dbinstance_must_implement_interface",
+              new String[]
+              { class1.toString() }));
     }
     if (fetchableDbs == null)
     {