From 4b25259949fbc582a579aa91922cde6f838155ea Mon Sep 17 00:00:00 2001
From: kjvdheide <kjvanderheide@dundee.ac.uk>
Date: Fri, 10 Nov 2017 15:31:40 +0000
Subject: [PATCH] JAL-2794 reorganized node select code, added subtree
 selection support

---
 .../ext/archaeopteryx/JalviewAptxBinding.java      |   64 ++++++++++++++------
 1 file changed, 46 insertions(+), 18 deletions(-)

diff --git a/src/jalview/ext/archaeopteryx/JalviewAptxBinding.java b/src/jalview/ext/archaeopteryx/JalviewAptxBinding.java
index 6a6b3f1..e0a143c 100644
--- a/src/jalview/ext/archaeopteryx/JalviewAptxBinding.java
+++ b/src/jalview/ext/archaeopteryx/JalviewAptxBinding.java
@@ -13,9 +13,11 @@ import java.awt.event.ActionEvent;
 import java.awt.event.InputEvent;
 import java.awt.event.MouseEvent;
 import java.util.HashSet;
+import java.util.List;
 import java.util.Map;
 
 import org.forester.archaeopteryx.MainFrame;
+import org.forester.phylogeny.PhylogenyMethods;
 import org.forester.phylogeny.PhylogenyNode;
 
 /**
@@ -131,7 +133,8 @@ public final class JalviewAptxBinding implements JalviewTreeViewerBindingI
 
   /**
    * If a node is selected in the tree panel this method highlights the
-   * corresponding sequence in the Jalview alignment view.
+   * corresponding sequence in the Jalview alignment view. If an internal node
+   * is selected all child sequences get highlighted as well.
    */
   @Override
   public void showNodeSelectionOnAlign(final MouseEvent e)
@@ -139,32 +142,57 @@ public final class JalviewAptxBinding implements JalviewTreeViewerBindingI
     final PhylogenyNode node = treeView.findNode(e.getX(), e.getY());
     if (node != null)
     {
-      SequenceI matchingSequence = nodesBoundToSequences.get(node);
-      if (matchingSequence != null)
+      if ((e.getModifiers() & InputEvent.SHIFT_MASK) == 0) // clear previous
+      // selection if shift
+      // IS NOT pressed
       {
+        parentAvport.setSelectionGroup(null);
+      }
 
-        if ((e.getModifiers() & InputEvent.SHIFT_MASK) != 0) // shift is pressed
-        // (so multiple nodes
-        // can be selected)
-        {
-          // something?
+      if (node.isInternal())
+      {
+        showMatchingChildSequences(node);
 
-        }
-        else
-        {
-          parentAvport.setSelectionGroup(null); // reset selection if shift
-                                                // isn't pressed
-        }
+      }
+      else
+      {
+        showMatchingSequence(node);
 
-        treeSelectionChanged(matchingSequence);
-        parentAvport.sendSelection(); // not actually needed?
-        PaintRefresher.Refresh(treeView, parentAvport.getSequenceSetId());
+      }
 
+    }
+  }
 
-      }
+
+
+
+  public void showMatchingSequence(final PhylogenyNode nodeToMatch)
+  {
+    SequenceI matchingSequence = nodesBoundToSequences.get(nodeToMatch);
+    if (matchingSequence != null)
+    {
+      treeSelectionChanged(matchingSequence);
+      parentAvport.sendSelection();
+      PaintRefresher.Refresh(treeView, parentAvport.getSequenceSetId());
     }
+  }
+
+  public void showMatchingChildSequences(final PhylogenyNode parentNode)
+  {
+    final List<PhylogenyNode> childNodes = PhylogenyMethods
+            .getAllDescendants(parentNode);
 
+    for (PhylogenyNode childNode : childNodes)
+    {
+      SequenceI matchingSequence = nodesBoundToSequences.get(childNode);
+      if (matchingSequence != null)
+      {
+        treeSelectionChanged(matchingSequence);
+      }
+    }
 
+    parentAvport.sendSelection();
+    PaintRefresher.Refresh(treeView, parentAvport.getSequenceSetId());
   }
 
   /**
-- 
1.7.10.2