Merge branch 'develop' into features/JAL-2446NCList

[jalview.git] / src / jalview / appletgui / AlignFrame.java

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index b48dec9..ed04a0a 100644 (file)
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -1426,21 +1426,32 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     return null;
   }
 
+  private List<String> getDisplayedFeatureGroups()
+  {
+    if (alignPanel.getFeatureRenderer() != null
+            && viewport.getFeaturesDisplayed() != null)
+    {
+      return alignPanel.getFeatureRenderer().getDisplayedFeatureGroups();
+
+    }
+    return null;
+  }
+
   public String outputFeatures(boolean displayTextbox, String format)
   {
     String features;
     FeaturesFile formatter = new FeaturesFile();
     if (format.equalsIgnoreCase("Jalview"))
     {
-      features = formatter.printJalviewFormat(
-              viewport.getAlignment().getSequencesArray(),
-              getDisplayedFeatureCols());
+      features = formatter.printJalviewFormat(viewport.getAlignment()
+              .getSequencesArray(), getDisplayedFeatureCols(),
+              getDisplayedFeatureGroups(), true);
     }
     else
     {
-      features = formatter.printGffFormat(
-              viewport.getAlignment().getSequencesArray(),
-              getDisplayedFeatureCols());
+      features = formatter.printGffFormat(viewport.getAlignment()
+              .getSequencesArray(), getDisplayedFeatureCols(),
+              getDisplayedFeatureGroups(), true);
     }
 
     if (displayTextbox)
@@ -1725,7 +1736,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     {
       EditCommand editCommand = (EditCommand) command;
       al = editCommand.getAlignment();
-      Vector comps = (Vector) PaintRefresher.components
+      Vector comps = PaintRefresher.components
               .get(viewport.getSequenceSetId());
       for (int i = 0; i < comps.size(); i++)
       {
@@ -2485,7 +2496,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
             newaf.alignPanel.av.getSequenceSetId());
 
-    Vector comps = (Vector) PaintRefresher.components
+    Vector comps = PaintRefresher.components
             .get(viewport.getSequenceSetId());
     int viewSize = -1;
     for (int i = 0; i < comps.size(); i++)