From 66340a2a1b9937fc8837c184e4998cbebe0e649d Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@issues.jalview.org>
Date: Mon, 24 Jun 2019 18:36:54 +0100
Subject: [PATCH] JAL-3330 dbreffetcher: record any feature display models
 associated with sources that provide sequences

---
 src/jalview/ws/DBRefFetcher.java |   43 ++++++++++++++++++++++++++++++++++++--
 1 file changed, 41 insertions(+), 2 deletions(-)

diff --git a/src/jalview/ws/DBRefFetcher.java b/src/jalview/ws/DBRefFetcher.java
index ae4207b..47d7bde 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;
 
@@ -318,6 +321,9 @@ 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)
     {
@@ -384,7 +390,7 @@ 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());
@@ -592,6 +600,10 @@ 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();
@@ -760,6 +772,33 @@ 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
    * 
-- 
1.7.10.2