JAL-3438 spotless for 2.11.2.0

[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 a07e88b..0d0a314 100644 (file)
--- a/src/jalview/ws/seqfetcher/ASequenceFetcher.java
+++ b/src/jalview/ws/seqfetcher/ASequenceFetcher.java
@@ -21,7 +21,7 @@
 package jalview.ws.seqfetcher;
 
 import jalview.api.FeatureSettingsModelI;
-import jalview.bin.Cache;
+import jalview.bin.Console;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.SequenceI;
@@ -112,7 +112,7 @@ public class ASequenceFetcher
         return true;
       }
     }
-    Cache.log.warn("isFetchable doesn't know about '" + source + "'");
+    Console.warn("isFetchable doesn't know about '" + source + "'");
     return false;
   }
 
@@ -130,11 +130,12 @@ public class ASequenceFetcher
     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());
@@ -204,9 +205,11 @@ 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());
@@ -363,8 +366,7 @@ public class ASequenceFetcher
               .get(proxy.getDbSource());
       if (slist == null)
       {
-        fetchableDbs.put(proxy.getDbSource(),
-                slist = new Hashtable<>());
+        fetchableDbs.put(proxy.getDbSource(), slist = new Hashtable<>());
       }
       slist.put(proxy.getDbName(), proxy);
     }