X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fws%2Fseqfetcher%2FASequenceFetcher.java;h=2a27ccedd4142254485168d945ac60a4f0d9c684;hb=7459ed95f5ad213bafb1c691b193283850889e52;hp=977f9dad1fe8b8989c050806b9d64e2c90a672bf;hpb=3d0101179759ef157b088ea135423cd909512d9f;p=jalview.git

diff --git a/src/jalview/ws/seqfetcher/ASequenceFetcher.java b/src/jalview/ws/seqfetcher/ASequenceFetcher.java
index 977f9da..2a27cce 100644
--- a/src/jalview/ws/seqfetcher/ASequenceFetcher.java
+++ b/src/jalview/ws/seqfetcher/ASequenceFetcher.java
@@ -126,15 +126,16 @@ public class ASequenceFetcher
    */
   public SequenceI[] getSequences(List<DBRefEntry> refs, boolean dna)
   {
-    Vector<SequenceI> rseqs = new Vector<SequenceI>();
-    Hashtable<String, List<String>> queries = new Hashtable<String, List<String>>();
+    Vector<SequenceI> rseqs = new Vector<>();
+    Hashtable<String, List<String>> queries = new Hashtable<>();
     for (DBRefEntry ref : refs)
     {
-      if (!queries.containsKey(ref.getSource()))
+      String canonical = DBRefUtils.getCanonicalName(ref.getSource());
+      if (!queries.containsKey(canonical))
       {
-        queries.put(ref.getSource(), new ArrayList<String>());
+        queries.put(canonical, new ArrayList<String>());
       }
-      List<String> qset = queries.get(ref.getSource());
+      List<String> qset = queries.get(canonical);
       if (!qset.contains(ref.getAccessionId()))
       {
         qset.add(ref.getAccessionId());
@@ -154,14 +155,14 @@ public class ASequenceFetcher
         continue;
       }
 
-      Stack<String> queriesLeft = new Stack<String>();
+      Stack<String> queriesLeft = new Stack<>();
       queriesLeft.addAll(query);
 
       List<DbSourceProxy> proxies = getSourceProxy(db);
       for (DbSourceProxy fetcher : proxies)
       {
-        List<String> queriesMade = new ArrayList<String>();
-        HashSet<String> queriesFound = new HashSet<String>();
+        List<String> queriesMade = new ArrayList<>();
+        HashSet<String> queriesFound = new HashSet<>();
         try
         {
           if (fetcher.isDnaCoding() != dna)
@@ -204,9 +205,10 @@ public class ASequenceFetcher
                 for (int is = 0; is < seqs.length; is++)
                 {
                   rseqs.addElement(seqs[is]);
+                  // BH 2015.01.25 check about version/accessid being null here
                   List<DBRefEntry> frefs = DBRefUtils.searchRefs(
                           seqs[is].getDBRefs(),
-                          new DBRefEntry(db, null, null));
+                          new DBRefEntry(db, null, null), DBRefUtils.SEARCH_MODE_FULL);
                   for (DBRefEntry dbr : frefs)
                   {
                     queriesFound.add(dbr.getAccessionId());
@@ -306,13 +308,13 @@ public class ASequenceFetcher
     Map<String, DbSourceProxy> dblist = fetchableDbs.get(db);
     if (dblist == null)
     {
-      return new ArrayList<DbSourceProxy>();
+      return new ArrayList<>();
     }
 
     /*
      * sort so that primary sources precede secondary
      */
-    List<DbSourceProxy> dbs = new ArrayList<DbSourceProxy>(dblist.values());
+    List<DbSourceProxy> dbs = new ArrayList<>(dblist.values());
     Collections.sort(dbs, proxyComparator);
     return dbs;
   }
@@ -357,14 +359,14 @@ public class ASequenceFetcher
     {
       if (fetchableDbs == null)
       {
-        fetchableDbs = new Hashtable<String, Map<String, DbSourceProxy>>();
+        fetchableDbs = new Hashtable<>();
       }
       Map<String, DbSourceProxy> slist = fetchableDbs
               .get(proxy.getDbSource());
       if (slist == null)
       {
         fetchableDbs.put(proxy.getDbSource(),
-                slist = new Hashtable<String, DbSourceProxy>());
+                slist = new Hashtable<>());
       }
       slist.put(proxy.getDbName(), proxy);
     }
@@ -391,7 +393,7 @@ public class ASequenceFetcher
       return null;
     }
     String[] sources = null;
-    Vector<String> src = new Vector<String>();
+    Vector<String> src = new Vector<>();
     Enumeration<String> dbs = fetchableDbs.keys();
     while (dbs.hasMoreElements())
     {
@@ -413,7 +415,7 @@ public class ASequenceFetcher
 
   public DbSourceProxy[] getDbSourceProxyInstances(Class class1)
   {
-    List<DbSourceProxy> prlist = new ArrayList<DbSourceProxy>();
+    List<DbSourceProxy> prlist = new ArrayList<>();
     for (String fetchable : getSupportedDb())
     {
       for (DbSourceProxy pr : getSourceProxy(fetchable))