X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2FDBRefFetcher.java;h=6b8843da91fd92fb117becbb1ca2b5d242069c9b;hb=17e4ea278bc9a5fb280db1252ce78b7a295215f5;hp=241f443de05a344389ac542d6b4c1a5ce98825de;hpb=26b115b0a77d521da92a06572d9b7819c2d0d49a;p=jalview.git

diff --git a/src/jalview/ws/DBRefFetcher.java b/src/jalview/ws/DBRefFetcher.java
index 241f443..6b8843d 100644
--- a/src/jalview/ws/DBRefFetcher.java
+++ b/src/jalview/ws/DBRefFetcher.java
@@ -21,6 +21,7 @@
 package jalview.ws;
 
 import jalview.analysis.AlignSeq;
+import jalview.api.FeatureSettingsModelI;
 import jalview.bin.Cache;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefEntry;
@@ -39,8 +40,10 @@ import jalview.ws.seqfetcher.DbSourceProxy;
 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;
 
@@ -317,6 +320,9 @@ 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 +389,7 @@ public class DBRefFetcher implements Runnable
           }
           if (retrieved != null)
           {
-            transferReferences(sdataset, dbsource.getDbSource(), retrieved,
+            transferReferences(sdataset, dbsource, retrieved,
                     trimDsSeqs, warningMessages);
           }
         }
@@ -512,7 +518,8 @@ 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 +529,7 @@ public class DBRefFetcher implements Runnable
       return false;
     }
 
+    String dbSource = dbSourceProxy.getDbName();
     boolean modified = false;
     SequenceI[] retrieved = recoverDbSequences(
             retrievedAl.getSequencesArray());
@@ -593,6 +601,10 @@ 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();
@@ -756,13 +768,38 @@ public class DBRefFetcher implements Runnable
         // and remove it from the rest
         // TODO: decide if we should remove annotated sequence from set
         sdataset.remove(sequence);
-        // TODO: should we make a note of sequences that have received new DB
-        // ids, so we can query all enabled DAS servers for them ?
       }
     }
     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
    *