X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fviewmodel%2FAlignmentViewport.java;h=063d4ab6e563fb6fad7de7045250e4f00fc92988;hb=f7c18c26f79036d16740e3077f172f8e9a9c2d32;hp=1ae879b0b4bfc545392c9d7371cfffd84f4f0d31;hpb=1f0742002d457b49733648b9369922bb0b78d2f0;p=jalview.git

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index 1ae879b..063d4ab 100644
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -662,7 +662,8 @@ public abstract class AlignmentViewport
          * retain any colour thresholds per group while
          * changing choice of colour scheme (JAL-2386)
          */
-        sg.setColourScheme(cs);
+        sg.setColourScheme(
+                cs == null ? null : cs.getInstance(this, sg));
         if (cs != null)
         {
           sg.getGroupColourScheme().alignmentChanged(sg,
@@ -958,6 +959,7 @@ public abstract class AlignmentViewport
     ranges = null;
     currentTree = null;
     selectionGroup = null;
+    colSel = null;
     setAlignment(null);
   }
 
@@ -1636,6 +1638,7 @@ public abstract class AlignmentViewport
   public void invertColumnSelection()
   {
     colSel.invertColumnSelection(0, alignment.getWidth(), alignment);
+    isColSelChanged(true);
   }
 
   @Override
@@ -2978,4 +2981,68 @@ public abstract class AlignmentViewport
   {
     return currentTree;
   }
+
+  /**
+   * flag set to indicate if structure views might be out of sync with sequences
+   * in the alignment
+   */
+
+  private boolean needToUpdateStructureViews = false;
+
+  @Override
+  public boolean isUpdateStructures()
+  {
+    return needToUpdateStructureViews;
+  }
+
+  @Override
+  public void setUpdateStructures(boolean update)
+  {
+    needToUpdateStructureViews = update;
+  }
+
+  @Override
+  public boolean needToUpdateStructureViews()
+  {
+    boolean update = needToUpdateStructureViews;
+    needToUpdateStructureViews = false;
+    return update;
+  }
+
+  @Override
+  public void addSequenceGroup(SequenceGroup sequenceGroup)
+  {
+    alignment.addGroup(sequenceGroup);
+
+    Color col = sequenceGroup.idColour;
+    if (col != null)
+    {
+      col = col.brighter();
+
+      for (SequenceI sq : sequenceGroup.getSequences())
+      {
+        setSequenceColour(sq, col);
+      }
+    }
+
+    if (codingComplement != null)
+    {
+      SequenceGroup mappedGroup = MappingUtils
+              .mapSequenceGroup(sequenceGroup, this, codingComplement);
+      if (mappedGroup.getSequences().size() > 0)
+      {
+        codingComplement.getAlignment().addGroup(mappedGroup);
+
+        if (col != null)
+        {
+          for (SequenceI seq : mappedGroup.getSequences())
+          {
+            codingComplement.setSequenceColour(seq, col);
+          }
+        }
+      }
+      // propagate the structure view update flag according to our own setting
+      codingComplement.setUpdateStructures(needToUpdateStructureViews);
+    }
+  }
 }