JAL-3463 avoid Thread.sleep() as not supported in SwingJS

[jalview.git] / src / jalview / ws / DBRefFetcher.java

diff --git a/src/jalview/ws/DBRefFetcher.java b/src/jalview/ws/DBRefFetcher.java
index b1c987e..7daa7b4 100644 (file)
--- a/src/jalview/ws/DBRefFetcher.java
+++ b/src/jalview/ws/DBRefFetcher.java
@@ -20,7 +20,18 @@
  */
 package jalview.ws;
 
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Enumeration;
+import java.util.HashMap;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Map;
+import java.util.StringTokenizer;
+import java.util.Vector;
+
 import jalview.analysis.AlignSeq;
+import jalview.api.FeatureSettingsModelI;
 import jalview.bin.Cache;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefEntry;
@@ -35,15 +46,6 @@ import jalview.gui.OOMWarning;
 import jalview.util.DBRefUtils;
 import jalview.util.MessageManager;
 import jalview.ws.seqfetcher.DbSourceProxy;
-
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Enumeration;
-import java.util.Hashtable;
-import java.util.List;
-import java.util.StringTokenizer;
-import java.util.Vector;
-
 import uk.ac.ebi.picr.model.UPEntry;
 import uk.ac.ebi.www.picr.AccessionMappingService.AccessionMapperServiceLocator;
 
@@ -71,8 +73,6 @@ public class DBRefFetcher implements Runnable
 
   CutAndPasteTransfer output = new CutAndPasteTransfer();
 
-  boolean running = false;
-
   /**
    * picr client instance
    */
@@ -222,24 +222,13 @@ public class DBRefFetcher implements Runnable
    */
   public void fetchDBRefs(boolean waitTillFinished)
   {
-    // TODO can we not simply write
-    // if (waitTillFinished) { run(); } else { new Thread(this).start(); }
-
-    Thread thread = new Thread(this);
-    thread.start();
-    running = true;
-
     if (waitTillFinished)
     {
-      while (running)
-      {
-        try
-        {
-          Thread.sleep(500);
-        } catch (Exception ex)
-        {
-        }
-      }
+      run();
+    }
+    else
+    {
+      new Thread(this).start();
     }
   }
 
@@ -292,7 +281,6 @@ public class DBRefFetcher implements Runnable
       throw new Error(MessageManager
               .getString("error.implementation_error_must_init_dbsources"));
     }
-    running = true;
     long startTime = System.currentTimeMillis();
     if (progressWindow != null)
     {
@@ -317,6 +305,9 @@ public class DBRefFetcher implements Runnable
             Arrays.asList(dataset));
     List<String> warningMessages = new ArrayList<>();
 
+    // clear any old feature display settings recorded from past sessions
+    featureDisplaySettings = null;
+
     int db = 0;
     while (sdataset.size() > 0 && db < dbSources.length)
     {
@@ -383,7 +374,7 @@ public class DBRefFetcher implements Runnable
           }
           if (retrieved != null)
           {
-            transferReferences(sdataset, dbsource.getDbSource(), retrieved,
+            transferReferences(sdataset, dbsource, retrieved,
                     trimDsSeqs, warningMessages);
           }
         }
@@ -492,7 +483,6 @@ public class DBRefFetcher implements Runnable
     {
       listener.finished();
     }
-    running = false;
   }
 
   /**
@@ -512,7 +502,8 @@ public class DBRefFetcher implements Runnable
    * @param warningMessages
    *          a list of messages to add to
    */
-  boolean transferReferences(Vector<SequenceI> sdataset, String dbSource,
+  boolean transferReferences(Vector<SequenceI> sdataset,
+          DbSourceProxy dbSourceProxy,
           AlignmentI retrievedAl, boolean trimDatasetSeqs,
           List<String> warningMessages)
   {
@@ -522,6 +513,7 @@ public class DBRefFetcher implements Runnable
       return false;
     }
 
+    String dbSource = dbSourceProxy.getDbName();
     boolean modified = false;
     SequenceI[] retrieved = recoverDbSequences(
             retrievedAl.getSequencesArray());
@@ -593,6 +585,10 @@ public class DBRefFetcher implements Runnable
        * seqs.elementAt(jj); if (!sequenceMatches.contains(sequence)) {
        * sequenceMatches.addElement(sequence); } } } }
        */
+      if (sequenceMatches.size() > 0)
+      {
+        addFeatureSettings(dbSourceProxy);
+      }
       // sequenceMatches now contains the set of all sequences associated with
       // the returned db record
       final String retrievedSeqString = retrievedSeq.getSequenceAsString();
@@ -761,6 +757,33 @@ public class DBRefFetcher implements Runnable
     return modified;
   }
 
+  Map<String, FeatureSettingsModelI> featureDisplaySettings = null;
+
+  private void addFeatureSettings(DbSourceProxy dbSourceProxy)
+  {
+    FeatureSettingsModelI fsettings = dbSourceProxy
+            .getFeatureColourScheme();
+    if (fsettings != null)
+    {
+      if (featureDisplaySettings == null)
+      {
+        featureDisplaySettings = new HashMap<>();
+      }
+      featureDisplaySettings.put(dbSourceProxy.getDbName(), fsettings);
+    }
+  }
+
+  /**
+   * 
+   * @return any feature settings associated with sources that have provided sequences
+   */
+  public List<FeatureSettingsModelI>getFeatureSettingsModels()
+  {
+    return featureDisplaySettings == null
+            ? Arrays.asList(new FeatureSettingsModelI[0])
+            : Arrays.asList(featureDisplaySettings.values()
+                    .toArray(new FeatureSettingsModelI[1]));
+  }
   /**
    * Adds the message to the list unless it already contains it
    *