X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fcontroller%2FAlignViewController.java;fp=src%2Fjalview%2Fcontroller%2FAlignViewController.java;h=d992e4e6a804f0f83fa6272a4cfa537bd91c1ddf;hb=14b1b2a878190d5fffda298c4b9a901c72c74ad3;hp=5662d0c11cb1eaa26560ab17b3b4f3e020a7b6b3;hpb=4073e96c3cb60f28c01cd91ec7f847cafbf01f78;p=jalview.git

diff --git a/src/jalview/controller/AlignViewController.java b/src/jalview/controller/AlignViewController.java
index 5662d0c..d992e4e 100644
--- a/src/jalview/controller/AlignViewController.java
+++ b/src/jalview/controller/AlignViewController.java
@@ -352,25 +352,25 @@ public class AlignViewController implements AlignViewControllerI
   public boolean parseFeaturesFile(String file, DataSourceType protocol,
           boolean relaxedIdMatching)
   {
-    boolean featuresFile = false;
+    boolean featuresAdded = false;
+    FeatureRenderer fr = alignPanel.getFeatureRenderer();
     try
     {
-      featuresFile = new FeaturesFile(false, file, protocol).parse(
-              viewport.getAlignment().getDataset(),
-              alignPanel.getFeatureRenderer().getFeatureColours(), false,
-              relaxedIdMatching);
+      featuresAdded = new FeaturesFile(false, file, protocol).parse(
+              viewport.getAlignment().getDataset(), fr.getFeatureColours(),
+              fr.getFeatureFilters(), false, relaxedIdMatching);
     } catch (Exception ex)
     {
       ex.printStackTrace();
     }
 
-    if (featuresFile)
+    if (featuresAdded)
     {
       avcg.refreshFeatureUI(true);
-      if (alignPanel.getFeatureRenderer() != null)
+      if (fr != null)
       {
         // update the min/max ranges where necessary
-        alignPanel.getFeatureRenderer().findAllFeatures(true);
+        fr.findAllFeatures(true);
       }
       if (avcg.getFeatureSettingsUI() != null)
       {
@@ -379,7 +379,7 @@ public class AlignViewController implements AlignViewControllerI
       alignPanel.paintAlignment(true, true);
     }
 
-    return featuresFile;
+    return featuresAdded;
 
   }