X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FSplitFrame.java;h=9b5865906f12275dd0d8e47edb3606a63eba4a5f;hb=838e4f91d4a53dd315640dbc9ff6ef7a815ee576;hp=bdda465535bebcd36fd7dd4c65e1cb3f771496fe;hpb=4d7f98a6dd54d9863ba449ec79dcd95d25ed863d;p=jalview.git

diff --git a/src/jalview/appletgui/SplitFrame.java b/src/jalview/appletgui/SplitFrame.java
index bdda465..9b58659 100644
--- a/src/jalview/appletgui/SplitFrame.java
+++ b/src/jalview/appletgui/SplitFrame.java
@@ -1,6 +1,25 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
+ * Copyright (C) 2015 The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.appletgui;
 
-import jalview.analysis.AlignmentUtils;
 import jalview.api.AlignmentViewPanel;
 import jalview.api.ViewStyleI;
 import jalview.bin.JalviewLite;
@@ -24,12 +43,14 @@ public class SplitFrame extends EmbmenuFrame
   private Panel outermost;
 
   /**
-   * Constructor
+   * Constructs the split frame placing cdna in the top half. No 'alignment' is
+   * performed here, this should be done by the calling client if wanted.
    */
   public SplitFrame(AlignFrame af1, AlignFrame af2)
   {
-    topFrame = af1;
-    bottomFrame = af2;
+    boolean af1IsNucleotide = af1.viewport.getAlignment().isNucleotide();
+    topFrame = af1IsNucleotide ? af1 : af2;
+    bottomFrame = topFrame == af1 ? af2 : af1;
     init();
   }
 
@@ -55,20 +76,15 @@ public class SplitFrame extends EmbmenuFrame
     AlignmentViewport protein = !topAlignment.isNucleotide() ? topViewport
             : (!bottomAlignment.isNucleotide() ? bottomViewport : null);
 
-    boolean mapped = AlignmentUtils.mapProteinToCdna(
-            protein.getAlignment(), cdna.getAlignment());
-    if (mapped)
-    {
-      final StructureSelectionManager ssm = StructureSelectionManager
-              .getStructureSelectionManager(topViewport.applet);
-      ssm.registerMappings(protein.getAlignment().getCodonFrames());
-      topViewport.setCodingComplement(bottomViewport);
-      ssm.addCommandListener(cdna);
-      ssm.addCommandListener(protein);
-    }
+    final StructureSelectionManager ssm = StructureSelectionManager
+            .getStructureSelectionManager(topViewport.applet);
+    ssm.registerMappings(protein.getAlignment().getCodonFrames());
+    topViewport.setCodingComplement(bottomViewport);
+    ssm.addCommandListener(cdna);
+    ssm.addCommandListener(protein);
 
     /*
-     * Now mappings exist, can compute cDNA consensus on protein alignment
+     * Compute cDNA consensus on protein alignment
      */
     protein.initComplementConsensus();
     AlignmentViewPanel ap = topAlignment.isNucleotide() ? bottomFrame.alignPanel