JAL-1953 2.11.2 with Archeopteryx!

[jalview.git] / src / jalview / ext / treeviewer / JalviewBinding.java

diff --git a/src/jalview/ext/treeviewer/JalviewBinding.java b/src/jalview/ext/treeviewer/JalviewBinding.java
index 630d586..fd1735e 100644 (file)
--- a/src/jalview/ext/treeviewer/JalviewBinding.java
+++ b/src/jalview/ext/treeviewer/JalviewBinding.java
@@ -177,11 +177,13 @@ public final class JalviewBinding
       TreeViewerUtils.associateNodesWithJalviewSequences(aptxFrame,
               parentAvport, sequencesBoundToNodes, nodesBoundToSequences);
 
+
       for (SequenceI seq : parentAvport.getAlignment().getSequencesArray())
       {
         if (!sequencesBoundToNodes.containsKey(seq))
         {
           parentAvport.hideSequence(new SequenceI[] { seq });
+
         }
       }
     }
@@ -466,7 +468,7 @@ public final class JalviewBinding
       }
       else
       {
-        cs = ColourSchemeProperty.getColourScheme(treeGroup,
+        cs = ColourSchemeProperty.getColourScheme(parentAvport,treeGroup,
                 ColourSchemeProperty.getColourName(
                         parentAvport.getGlobalColourScheme()));
       }
@@ -732,6 +734,28 @@ public final class JalviewBinding
     return nodesBoundToSequences;
   }
 
+  @Override
+  public void hideCollapsedSequences_actionPerformed()
+  {
+    parentAvport.showAllHiddenSeqs();
+
+    for (TreeNodeI node : treeView.getTree().getAllNodes())
+    {
+      if (node.isCollapsed())
+      {
+        SequenceI seqToHide = nodesBoundToSequences.get(node);
+        if (seqToHide != null)
+        {
+          parentAvport.hideSequence(new SequenceI[] { seqToHide });
+
+
+        }
+
+      }
+    }
+
+
+  }
 
 }