JAL-2136 merged develop into branch to fix build failure

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 507bfab..09537f2 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -3335,7 +3335,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
      */
     if (ResidueColourScheme.USER_DEFINED.equals(name))
     {
-      new UserDefinedColours(alignPanel, null);
+      new UserDefinedColours(alignPanel);
       return;
     }
 
@@ -3356,10 +3356,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   public void changeColour(ColourSchemeI cs)
   {
     // TODO: pull up to controller method
-    if (cs != null)
-    {
-      ColourMenuHelper.setColourSelected(colourMenu, cs.getSchemeName());
-    }
+    ColourMenuHelper.setColourSelected(colourMenu, cs);
 
     viewport.setGlobalColourScheme(cs);
 
@@ -4645,8 +4642,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
               // associating PDB files which have no IDs.
               for (SequenceI toassoc : (SequenceI[]) fm[2])
               {
-                PDBEntry pe = new AssociatePdbFileWithSeq()
-                        .associatePdbWithSeq((String) fm[0],
+                PDBEntry pe = new AssociateStructureFileWithSeq()
+                        .associateStructureWithSeq((String) fm[0],
                                 (DataSourceType) fm[1], toassoc, false,
                                 Desktop.instance);
                 if (pe != null)
@@ -5708,10 +5705,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     colourMenu.add(annotationColour);
 
     ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
-    String schemeName = colourScheme == null ? null : colourScheme
-            .getSchemeName();
-
-    ColourMenuHelper.setColourSelected(colourMenu, schemeName);
+    ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
   }
 }