JAL-845 start cDNA consensus on 'add alignment' (as well as translate or

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

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 6c34479..289a0ea 100644 (file)
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -39,7 +39,6 @@
 package jalview.gui;
 
 import jalview.analysis.AlignmentUtils;
-import jalview.analysis.AlignmentUtils.MappingResult;
 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
 import jalview.analysis.NJTree;
 import jalview.api.AlignViewportI;
@@ -1036,21 +1035,11 @@ public class AlignViewport extends AlignmentViewport implements
     }
 
     /*
-     * Try to find mappings for at least one sequence. Any mappings made will be
-     * added to the protein alignment.
+     * Map sequences. At least one should get mapped as we have already passed
+     * the test for 'mappability'. Any mappings made will be added to the
+     * protein alignment.
      */
-    MappingResult mapped = AlignmentUtils.mapProteinToCdna(protein, cdna);
-    if (mapped != MappingResult.Mapped)
-    {
-      /*
-       * No mapping possible - warn the user, but leave window open.
-       */
-      final String msg = JvSwingUtils.wrapTooltip(true,
-              MessageManager.getString("label.mapping_failed"));
-      JOptionPane.showInternalMessageDialog(Desktop.desktop, msg,
-              MessageManager.getString("label.no_mappings"),
-              JOptionPane.WARNING_MESSAGE);
-    }
+    AlignmentUtils.mapProteinToCdna(protein, cdna);
 
     try
     {
@@ -1106,6 +1095,7 @@ public class AlignViewport extends AlignmentViewport implements
             : copyMe;
     AlignmentI protein = proteinFrame.viewport.getAlignment();
     protein.setCodonFrames(mappings);
+    proteinFrame.viewport.initComplementConsensus();
 
     cdnaFrame.setVisible(true);
     proteinFrame.setVisible(true);