JAL-1452 nucleotide/protein default colour; JAL-845 SplitFrame refactor

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index cad90e3..93d8c19 100644 (file)
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -46,6 +46,7 @@ import jalview.api.AlignViewportI;
 import jalview.api.ViewStyleI;
 import jalview.bin.Cache;
 import jalview.commands.CommandI;
+import jalview.datamodel.AlignedCodonFrame;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.ColumnSelection;
@@ -300,10 +301,18 @@ public class AlignViewport extends AlignmentViewport implements
       showConsensus = Cache.getDefault("SHOW_IDENTITY", true);
     }
     initAutoAnnotation();
-    if (jalview.bin.Cache.getProperty(Preferences.DEFAULT_COLOUR) != null)
+    String colourProperty = alignment.isNucleotide() ? Preferences.DEFAULT_COLOUR_NUC
+            : Preferences.DEFAULT_COLOUR_PROT;
+    String propertyValue = Cache.getProperty(colourProperty);
+    if (propertyValue == null)
+    {
+      // fall back on this property for backwards compatibility
+      propertyValue = Cache.getProperty(Preferences.DEFAULT_COLOUR);
+    }
+    if (propertyValue != null)
     {
       globalColourScheme = ColourSchemeProperty.getColour(alignment,
-              jalview.bin.Cache.getProperty(Preferences.DEFAULT_COLOUR));
+              propertyValue);
 
       if (globalColourScheme instanceof UserColourScheme)
       {
@@ -1061,7 +1070,7 @@ public class AlignViewport extends AlignmentViewport implements
     if (openSplitPane)
     {
       protein = openSplitFrame(newAlignFrame,
-              thisAlignment.getSequencesArray());
+              thisAlignment.getSequencesArray(), protein.getCodonFrames());
     }
 
     /*
@@ -1083,10 +1092,11 @@ public class AlignViewport extends AlignmentViewport implements
    *          containing a new alignment to be shown
    * @param seqs
    *          'complementary' sequences to show in the other split half
+   * @param mappings
    * @return the protein alignment in the split frame
    */
   protected AlignmentI openSplitFrame(AlignFrame newAlignFrame,
-          SequenceI[] seqs)
+          SequenceI[] seqs, Set<AlignedCodonFrame> mappings)
   {
     AlignmentI complementAlignment = new Alignment(seqs);
     // TODO: move this to a factory/controller method ?
@@ -1103,6 +1113,7 @@ public class AlignViewport extends AlignmentViewport implements
     final AlignFrame cdnaFrame = al.isNucleotide() ? newAlignFrame
             : copyMe;
     AlignmentI protein = proteinFrame.viewport.getAlignment();
+    protein.setCodonFrames(mappings);
 
     cdnaFrame.setVisible(true);
     proteinFrame.setVisible(true);