JAL-2843 add colour by attribute, and no value colour, to features file

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

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index b8f3a30..fe6b8d9 100644 (file)
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -1445,9 +1445,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     FeaturesFile formatter = new FeaturesFile();
     if (format.equalsIgnoreCase("Jalview"))
     {
-      features = formatter.printJalviewFormat(viewport.getAlignment()
-              .getSequencesArray(), getDisplayedFeatureCols(),
-              getDisplayedFeatureGroups(), true);
+      features = formatter.printJalviewFormat(
+              viewport.getAlignment().getSequencesArray(),
+              getDisplayedFeatureCols(), null, getDisplayedFeatureGroups(),
+              true);
     }
     else
     {
@@ -4149,7 +4150,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     {
       // register the association(s) and quit, don't create any windows.
       if (StructureSelectionManager.getStructureSelectionManager(applet)
-              .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
+              .setMapping(seqs, chains, pdb.getFile(), protocol, null) == null)
       {
         System.err.println("Failed to map " + pdb.getFile() + " ("
                 + protocol + ") to any sequences");