From d5b7f6f7d5774f2a2c96351e36a59c2a5f595da6 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Thu, 18 May 2017 14:57:37 +0100
Subject: [PATCH] JAL-2490 retrieve visible features only

---
 src/jalview/ext/rbvi/chimera/ChimeraCommands.java |   10 +++-------
 1 file changed, 3 insertions(+), 7 deletions(-)

diff --git a/src/jalview/ext/rbvi/chimera/ChimeraCommands.java b/src/jalview/ext/rbvi/chimera/ChimeraCommands.java
index 62aaa1c..e9ce49b 100644
--- a/src/jalview/ext/rbvi/chimera/ChimeraCommands.java
+++ b/src/jalview/ext/rbvi/chimera/ChimeraCommands.java
@@ -411,12 +411,8 @@ public class ChimeraCommands
           StructureMapping mapping, SequenceI seq,
           Map<String, Map<Object, AtomSpecModel>> theMap, int modelNumber)
   {
-    SequenceFeature[] sfs = seq.getSequenceFeatures();
-    if (sfs == null)
-    {
-      return;
-    }
-
+    List<SequenceFeature> sfs = seq.getFeatures().getPositionalFeatures(
+            visibleFeatures.toArray(new String[visibleFeatures.size()]));
     for (SequenceFeature sf : sfs)
     {
       String type = sf.getType();
@@ -427,7 +423,7 @@ public class ChimeraCommands
        */
       boolean isFromViewer = JalviewChimeraBinding.CHIMERA_FEATURE_GROUP
               .equals(sf.getFeatureGroup());
-      if (isFromViewer || !visibleFeatures.contains(type))
+      if (isFromViewer)
       {
         continue;
       }
-- 
1.7.10.2