Merge branch 'develop' into JAL-1705_trialMerge

[jalview.git] / src / jalview / controller / AlignViewController.java

diff --git a/src/jalview/controller/AlignViewController.java b/src/jalview/controller/AlignViewController.java
index a39dc80..151af0e 100644 (file)
--- a/src/jalview/controller/AlignViewController.java
+++ b/src/jalview/controller/AlignViewController.java
@@ -83,8 +83,7 @@ public class AlignViewController implements AlignViewControllerI
     SequenceGroup sg = viewport.getSelectionGroup();
     ColumnSelection cs = viewport.getColumnSelection();
     SequenceGroup[] gps = null;
-    if (sg != null
-            && (cs == null || cs.getSelected() == null || cs.size() == 0))
+    if (sg != null && (cs == null || cs.isEmpty()))
     {
       gps = jalview.analysis.Grouping.makeGroupsFrom(viewport
               .getSequenceSelection(), viewport.getAlignmentView(true)
@@ -394,7 +393,7 @@ public class AlignViewController implements AlignViewControllerI
     boolean featuresFile = false;
     try
     {
-      featuresFile = new FeaturesFile(file, protocol).parse(viewport
+      featuresFile = new FeaturesFile(false, file, protocol).parse(viewport
               .getAlignment().getDataset(), alignPanel.getFeatureRenderer()
               .getFeatureColours(), false, relaxedIdMatching);
     } catch (Exception ex)