JAL-2375 JAL-2376 First commit of implementation for Phyre2 result browsing, template...

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 8ca9085..c3102ed 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -857,7 +857,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     modifyConservation.setEnabled(!nucleotide);
     showGroupConservation.setEnabled(!nucleotide);
     rnahelicesColour.setEnabled(nucleotide);
+    nucleotideColour.setEnabled(nucleotide);
     purinePyrimidineColour.setEnabled(nucleotide);
+    RNAInteractionColour.setEnabled(nucleotide);
     showComplementMenuItem.setText(nucleotide ? MessageManager
             .getString("label.protein") : MessageManager
             .getString("label.nucleotide"));
@@ -1112,11 +1114,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   public void saveAs_actionPerformed(ActionEvent e)
   {
+    String format = currentFileFormat == null ? null : currentFileFormat
+            .toString();
     JalviewFileChooser chooser = JalviewFileChooser.forWrite(
-            Cache.getProperty("LAST_DIRECTORY"),
-            // AppletFormatAdapter.WRITABLE_EXTENSIONS,
-            // AppletFormatAdapter.WRITABLE_FNAMES,
-            currentFileFormat.toString(), false);
+            Cache.getProperty("LAST_DIRECTORY"), format);
 
     chooser.setFileView(new JalviewFileView());
     chooser.setDialogTitle(MessageManager
@@ -4934,8 +4935,8 @@ 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)