From befb1682d3f7d181e61d62adf20e31d53caf2671 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Wed, 31 Aug 2016 14:59:42 +0100
Subject: [PATCH] JAL-2077 check for isPopupTrigger() in mousePressed as well
 as mouseClicked.

---
 src/jalview/gui/TreeCanvas.java |   92 ++++++++++++++++++++++-----------------
 1 file changed, 52 insertions(+), 40 deletions(-)

diff --git a/src/jalview/gui/TreeCanvas.java b/src/jalview/gui/TreeCanvas.java
index f21c5e7..b300b5b 100755
--- a/src/jalview/gui/TreeCanvas.java
+++ b/src/jalview/gui/TreeCanvas.java
@@ -788,39 +788,52 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
   @Override
   public void mouseClicked(MouseEvent evt)
   {
-    if (highlightNode != null)
+    if (highlightNode == null)
     {
-      if (evt.isPopupTrigger())
-      {
-        Color col = JColorChooser.showDialog(this,
-                MessageManager.getString("label.select_subtree_colour"),
-                highlightNode.color);
-        if (col != null)
-        {
-          setColor(highlightNode, col);
-        }
-      }
-      else if (evt.getClickCount() > 1)
+      return;
+    }
+    if (evt.isPopupTrigger())
+    {
+      chooseSubtreeColour();
+    }
+    else if (evt.getClickCount() > 1)
+    {
+      tree.swapNodes(highlightNode);
+      tree.reCount(tree.getTopNode());
+      tree.findHeight(tree.getTopNode());
+    }
+    else
+    {
+      Vector leaves = new Vector();
+      tree.findLeaves(highlightNode, leaves);
+
+      for (int i = 0; i < leaves.size(); i++)
       {
-        tree.swapNodes(highlightNode);
-        tree.reCount(tree.getTopNode());
-        tree.findHeight(tree.getTopNode());
+        SequenceI seq = (SequenceI) ((SequenceNode) leaves.elementAt(i))
+                .element();
+        treeSelectionChanged(seq);
       }
-      else
-      {
-        Vector leaves = new Vector();
-        tree.findLeaves(highlightNode, leaves);
+      av.sendSelection();
+    }
 
-        for (int i = 0; i < leaves.size(); i++)
-        {
-          SequenceI seq = (SequenceI) ((SequenceNode) leaves.elementAt(i))
-                  .element();
-          treeSelectionChanged(seq);
-        }
-        av.sendSelection();
-      }
+    PaintRefresher.Refresh(tp, av.getSequenceSetId());
+    repaint();
+  }
 
-      PaintRefresher.Refresh(tp, av.getSequenceSetId());
+  /**
+   * Offer the user the option to choose a colour for the highlighted node and
+   * its children; this colour is also applied to the corresponding sequence ids
+   * in the alignment
+   */
+  void chooseSubtreeColour()
+  {
+    Color col = JColorChooser.showDialog(this,
+            MessageManager.getString("label.select_subtree_colour"),
+            highlightNode.color);
+    if (col != null)
+    {
+      setColor(highlightNode, col);
+      PaintRefresher.Refresh(tp, ap.av.getSequenceSetId());
       repaint();
     }
   }
@@ -866,6 +879,11 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
   public void mousePressed(MouseEvent e)
   {
     av.setCurrentTree(tree);
+    if (highlightNode != null && e.isPopupTrigger())
+    {
+      chooseSubtreeColour();
+      return;
+    }
 
     int x = e.getX();
     int y = e.getY();
@@ -993,17 +1011,14 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
                 .getCodingComplement();
         if (codingComplement != null)
         {
-          if (codingComplement != null)
+          SequenceGroup mappedGroup = MappingUtils.mapSequenceGroup(sg, av,
+                  codingComplement);
+          if (mappedGroup.getSequences().size() > 0)
           {
-            SequenceGroup mappedGroup = MappingUtils.mapSequenceGroup(sg,
-                    av, codingComplement);
-            if (mappedGroup.getSequences().size() > 0)
+            codingComplement.getAlignment().addGroup(mappedGroup);
+            for (SequenceI seq : mappedGroup.getSequences())
             {
-              codingComplement.getAlignment().addGroup(mappedGroup);
-              for (SequenceI seq : mappedGroup.getSequences())
-              {
-                codingComplement.setSequenceColour(seq, col.brighter());
-              }
+              codingComplement.setSequenceColour(seq, col.brighter());
             }
           }
         }
@@ -1022,11 +1037,8 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
       {
         ((AlignViewport) codingComplement).getAlignPanel()
                 .updateAnnotation();
-
       }
-
     }
-
   }
 
   /**
-- 
1.7.10.2