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 4ba2113..289a0ea 100644 (file)
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -39,13 +39,13 @@
 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;
 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 +300,18 @@ public class AlignViewport extends AlignmentViewport implements
       showConsensus = Cache.getDefault("SHOW_IDENTITY", true);
     }
     initAutoAnnotation();
-    if (jalview.bin.Cache.getProperty("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("DEFAULT_COLOUR"));
+              propertyValue);
 
       if (globalColourScheme instanceof UserColourScheme)
       {
@@ -942,17 +950,11 @@ public class AlignViewport extends AlignmentViewport implements
      * If one alignment is protein and one nucleotide, with at least one
      * sequence name in common, offer to open a linked alignment.
      */
-    if (getAlignment().isNucleotide() != al.isNucleotide())
+    if (AlignmentUtils.isMappable(al, getAlignment()))
     {
-      // TODO: JAL-845 try a bit harder to link up imported sequences
-      final Set<String> sequenceNames = getAlignment().getSequenceNames();
-      sequenceNames.retainAll(al.getSequenceNames());
-      if (!sequenceNames.isEmpty()) // at least one sequence name in both
+      if (openLinkedAlignment(al, title))
       {
-        if (openLinkedAlignment(al, title))
-        {
-          return;
-        }
+        return;
       }
     }
     // TODO: JAL-407 regardless of above - identical sequences (based on ID and
@@ -1033,21 +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
     {
@@ -1060,7 +1052,8 @@ public class AlignViewport extends AlignmentViewport implements
 
     if (openSplitPane)
     {
-      protein = openSplitFrame(newAlignFrame, thisAlignment);
+      protein = openSplitFrame(newAlignFrame, thisAlignment,
+              protein.getCodonFrames());
     }
 
     /*
@@ -1080,18 +1073,18 @@ public class AlignViewport extends AlignmentViewport implements
    * 
    * @param newAlignFrame
    *          containing a new alignment to be shown
-   * @param existingAlignment
-   *          an existing alignment to be copied for display in the split frame
+   * @param complement
+   *          cdna/protein complement alignment to show in the other split half
+   * @param mappings
    * @return the protein alignment in the split frame
    */
   protected AlignmentI openSplitFrame(AlignFrame newAlignFrame,
-          AlignmentI existingAlignment)
+          AlignmentI complement, Set<AlignedCodonFrame> mappings)
   {
-    // TODO: move this to a factory/controller method ?
     /*
      * Open in split pane. DNA sequence above, protein below.
      */
-    AlignFrame copyMe = new AlignFrame(existingAlignment,
+    AlignFrame copyMe = new AlignFrame(complement,
             AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
     copyMe.setTitle(getAlignPanel().alignFrame.getTitle());
 
@@ -1101,6 +1094,8 @@ public class AlignViewport extends AlignmentViewport implements
     final AlignFrame cdnaFrame = al.isNucleotide() ? newAlignFrame
             : copyMe;
     AlignmentI protein = proteinFrame.viewport.getAlignment();
+    protein.setCodonFrames(mappings);
+    proteinFrame.viewport.initComplementConsensus();
 
     cdnaFrame.setVisible(true);
     proteinFrame.setVisible(true);
@@ -1109,20 +1104,6 @@ public class AlignViewport extends AlignmentViewport implements
     JInternalFrame splitFrame = new SplitFrame(cdnaFrame, proteinFrame);
     Desktop.addInternalFrame(splitFrame, linkedTitle, -1, -1);
 
-    /*
-     * Set the frames to listen for each other's edit and sort commands.
-     */
-    final StructureSelectionManager ssm = StructureSelectionManager
-            .getStructureSelectionManager(Desktop.instance);
-    ssm.addCommandListener(cdnaFrame.getViewport());
-    ssm.addCommandListener(proteinFrame.getViewport());
-
-    /*
-     * 'Coding complement' (dna/protein) views will mirror each others' edits,
-     * selections, sorting etc as decided from time to time by the relevant
-     * authorities.
-     */
-    proteinFrame.getViewport().setCodingComplement(cdnaFrame.getViewport());
     return protein;
   }