X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=aedfe12c0e7aac5e49f4fa4cf2ba72ffb4a6a9e7;hb=405376d6d7002b3818d10aebc474f14134d5bbae;hp=b27518607159c03661be36f5cea17bbb4b8245d4;hpb=ba0bedafc61f5e83fa5a34f8ddbd0cd5222abe0e;p=jalview.git

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index b275186..aedfe12 100644
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -45,7 +45,6 @@ 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;
@@ -71,7 +70,6 @@ import java.awt.Rectangle;
 import java.util.ArrayList;
 import java.util.Hashtable;
 import java.util.List;
-import java.util.Set;
 import java.util.Vector;
 
 import javax.swing.JInternalFrame;
@@ -416,16 +414,43 @@ public class AlignViewport extends AlignmentViewport implements
    */
   public void setAlignment(AlignmentI align)
   {
-    if (alignment != null && alignment.getCodonFrames() != null)
+    replaceMappings(align);
+    this.alignment = align;
+  }
+
+  /**
+   * Replace any codon mappings for this viewport with those for the given
+   * viewport
+   * 
+   * @param align
+   */
+  public void replaceMappings(AlignmentI align)
+  {
+    StructureSelectionManager ssm = StructureSelectionManager
+            .getStructureSelectionManager(Desktop.instance);
+
+    /*
+     * Deregister current mappings (if any)
+     */
+    if (alignment != null)
     {
-      StructureSelectionManager.getStructureSelectionManager(
-              Desktop.instance).removeMappings(alignment.getCodonFrames());
+      ssm.removeMappings(alignment.getCodonFrames());
     }
-    this.alignment = align;
-    if (alignment != null && alignment.getCodonFrames() != null)
+
+    /*
+     * Register new mappings (if any)
+     */
+    if (align != null)
     {
-      StructureSelectionManager.getStructureSelectionManager(
-              Desktop.instance).addMappings(alignment.getCodonFrames());
+      ssm.addMappings(align.getCodonFrames());
+    }
+
+    /*
+     * replace mappings on our alignment
+     */
+    if (alignment != null && align != null)
+    {
+      alignment.setCodonFrames(align.getCodonFrames());
     }
   }
 
@@ -669,7 +694,7 @@ public class AlignViewport extends AlignmentViewport implements
       for (SequenceI sq : alignment.getSequences())
       {
         Vector<PDBEntry> pdbs = sq
-                .getDatasetSequence().getPDBId();
+                .getDatasetSequence().getAllPDBEntries();
         if (pdbs == null)
         {
           continue;
@@ -801,6 +826,17 @@ public class AlignViewport extends AlignmentViewport implements
      */
     if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
     {
+      if (al.getDataset() == null)
+      {
+        // need to create ds seqs
+        for (SequenceI sq : al.getSequences())
+        {
+          if (sq.getDatasetSequence() == null)
+          {
+            sq.createDatasetSequence();
+          }
+        }
+      }
       if (AlignmentUtils.isMappable(al, getAlignment()))
       {
         if (openLinkedAlignment(al, title))
@@ -873,9 +909,8 @@ public class AlignViewport extends AlignmentViewport implements
     AlignmentUtils.mapProteinToCdna(protein, cdna);
 
     /*
-     * Create the AlignFrame for the added alignment. Note this will include the
-     * cDNA consensus annotation if it is protein (because the alignment holds
-     * mappings to nucleotide)
+     * Create the AlignFrame for the added alignment. If it is protein, mappings
+     * are registered with StructureSelectionManager as a side-effect.
      */
     AlignFrame newAlignFrame = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
             AlignFrame.DEFAULT_HEIGHT);
@@ -909,18 +944,10 @@ public class AlignViewport extends AlignmentViewport implements
 
     if (openSplitPane)
     {
-      protein = openSplitFrame(newAlignFrame, thisAlignment,
-              protein.getCodonFrames());
+      al.alignAs(thisAlignment);
+      protein = openSplitFrame(newAlignFrame, thisAlignment);
     }
 
-    /*
-     * Register the mappings (held on the protein alignment) with the
-     * StructureSelectionManager (for mouseover linking).
-     */
-    final StructureSelectionManager ssm = StructureSelectionManager
-            .getStructureSelectionManager(Desktop.instance);
-    ssm.addMappings(protein.getCodonFrames());
-
     return true;
   }
 
@@ -932,16 +959,14 @@ public class AlignViewport extends AlignmentViewport implements
    *          containing a new alignment to be shown
    * @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 complement, Set<AlignedCodonFrame> mappings)
+          AlignmentI complement)
   {
     /*
      * Make a new frame with a copy of the alignment we are adding to. If this
-     * is protein, the new frame will have a cDNA consensus annotation row
-     * added.
+     * is protein, the mappings to cDNA will be registered with StructureSelectionManager as a side-effect.
      */
     AlignFrame copyMe = new AlignFrame(complement,
             AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
@@ -952,9 +977,6 @@ public class AlignViewport extends AlignmentViewport implements
             : newAlignFrame;
     final AlignFrame cdnaFrame = al.isNucleotide() ? newAlignFrame
             : copyMe;
-    AlignmentI protein = proteinFrame.viewport.getAlignment();
-    protein.setCodonFrames(mappings);
-
     cdnaFrame.setVisible(true);
     proteinFrame.setVisible(true);
     String linkedTitle = MessageManager
@@ -966,7 +988,7 @@ public class AlignViewport extends AlignmentViewport implements
     JInternalFrame splitFrame = new SplitFrame(cdnaFrame, proteinFrame);
     Desktop.addInternalFrame(splitFrame, linkedTitle, -1, -1);
 
-    return protein;
+    return proteinFrame.viewport.getAlignment();
   }
 
   public AnnotationColumnChooser getAnnotationColumnSelectionState()
@@ -1027,13 +1049,13 @@ public class AlignViewport extends AlignmentViewport implements
      * is found, the result will be empty.
      */
     SearchResults sr = new SearchResults();
-    int seqOffset = findComplementScrollTarget(sr);
+    int verticalOffset = findComplementScrollTarget(sr);
     if (!sr.isEmpty())
     {
       // TODO would like next line without cast but needs more refactoring...
       final AlignmentPanel complementPanel = ((AlignViewport) getCodingComplement()).getAlignPanel();
       complementPanel.setFollowingComplementScroll(true);
-      complementPanel.scrollToCentre(sr, seqOffset);
+      complementPanel.scrollToCentre(sr, verticalOffset);
     }
   }