Merge branch 'develop' into features/JAL-3010ontologyFeatureSettings

[jalview.git] / src / jalview / gui / SequenceFetcher.java

diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java
index 8d46792..0982dcc 100755 (executable)
--- a/src/jalview/gui/SequenceFetcher.java
+++ b/src/jalview/gui/SequenceFetcher.java
@@ -34,7 +34,6 @@ import jalview.io.gff.SequenceOntologyI;
 import jalview.util.DBRefUtils;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
-import jalview.ws.dbsources.das.api.DasSourceRegistryI;
 import jalview.ws.seqfetcher.DbSourceProxy;
 
 import java.awt.BorderLayout;
@@ -111,10 +110,6 @@ public class SequenceFetcher extends JPanel implements Runnable
 
   private static jalview.ws.SequenceFetcher sfetch = null;
 
-  private static long lastDasSourceRegistry = -3;
-
-  private static DasSourceRegistryI dasRegistry = null;
-
   private static boolean _initingFetcher = false;
 
   private static Thread initingThread = null;
@@ -165,11 +160,7 @@ public class SequenceFetcher extends JPanel implements Runnable
                 Thread.currentThread().hashCode());
       }
     }
-    if (sfetch == null || dasRegistry != Cache.getDasSourceRegistry()
-            || lastDasSourceRegistry != (Cache.getDasSourceRegistry()
-                    .getDasRegistryURL()
-                    + Cache.getDasSourceRegistry().getLocalSourceString())
-                            .hashCode())
+    if (sfetch == null)
     {
       _initingFetcher = true;
       initingThread = Thread.currentThread();
@@ -183,16 +174,12 @@ public class SequenceFetcher extends JPanel implements Runnable
                         "status.init_sequence_database_fetchers"),
                 Thread.currentThread().hashCode());
       }
-      dasRegistry = Cache.getDasSourceRegistry();
-      dasRegistry.refreshSources();
 
       jalview.ws.SequenceFetcher sf = new jalview.ws.SequenceFetcher();
       if (guiWindow != null)
       {
         guiWindow.setProgressBar(null, Thread.currentThread().hashCode());
       }
-      lastDasSourceRegistry = (dasRegistry.getDasRegistryURL()
-              + dasRegistry.getLocalSourceString()).hashCode();
       sfetch = sf;
       _initingFetcher = false;
       initingThread = null;
@@ -273,7 +260,7 @@ public class SequenceFetcher extends JPanel implements Runnable
         return Collections.emptyList();
       }
     }
-    sf.newAlframes = new ArrayList<AlignFrame>();
+    sf.newAlframes = new ArrayList<>();
     sf.run();
     return sf.newAlframes;
   }
@@ -564,15 +551,10 @@ public class SequenceFetcher extends JPanel implements Runnable
       dbeg.setText(MessageManager.formatMessage("label.example_query_param",
               new String[]
               { eq }));
+      // TODO this should be a property of the SequenceFetcher whether commas are and
+      // colons are allowed in the IDs...
+
       boolean enablePunct = !(eq != null && eq.indexOf(",") > -1);
-      for (DbSourceProxy dbs : database.getSelectedSources())
-      {
-        if (dbs instanceof jalview.ws.dbsources.das.datamodel.DasSequenceSource)
-        {
-          enablePunct = false;
-          break;
-        }
-      }
       replacePunctuation.setEnabled(enablePunct);
 
     } catch (Exception ex)
@@ -674,10 +656,10 @@ public class SequenceFetcher extends JPanel implements Runnable
     // TODO: Refactor to GUI independent code and write tests.
     // indicate if successive sources should be merged into one alignment.
     boolean addToLast = false;
-    List<String> aresultq = new ArrayList<String>();
-    List<String> presultTitle = new ArrayList<String>();
-    List<AlignmentI> presult = new ArrayList<AlignmentI>();
-    List<AlignmentI> aresult = new ArrayList<AlignmentI>();
+    List<String> aresultq = new ArrayList<>();
+    List<String> presultTitle = new ArrayList<>();
+    List<AlignmentI> presult = new ArrayList<>();
+    List<AlignmentI> aresult = new ArrayList<>();
     Iterator<DbSourceProxy> proxies = database.getSelectedSources()
             .iterator();
     String[] qries;
@@ -695,7 +677,7 @@ public class SequenceFetcher extends JPanel implements Runnable
         nqueries = nextFetch.size();
         // save the remaining queries in the original array
         qries = nextFetch.toArray(new String[nqueries]);
-        nextFetch = new ArrayList<String>();
+        nextFetch = new ArrayList<>();
       }
 
       DbSourceProxy proxy = proxies.next();
@@ -861,7 +843,7 @@ public class SequenceFetcher extends JPanel implements Runnable
           List<AlignmentI> aresult, List<String> nextFetch) throws Exception
   {
     StringBuilder multiacc = new StringBuilder();
-    List<String> tosend = new ArrayList<String>();
+    List<String> tosend = new ArrayList<>();
     while (accessions.hasNext())
     {
       String nel = accessions.next();
@@ -1047,7 +1029,7 @@ public class SequenceFetcher extends JPanel implements Runnable
         }
         if (Cache.getDefault("HIDE_INTRONS", true))
         {
-          af.hideFeatureColumns(SequenceOntologyI.EXON, false);
+          af.hideFeatureColumns(false, SequenceOntologyI.EXON);
         }
         if (newAlframes != null)
         {