From ebf33c3e8faceeba628466f69b39e6de7e102a9d Mon Sep 17 00:00:00 2001
From: kjvdheide <kjvanderheide@dundee.ac.uk>
Date: Wed, 29 Nov 2017 03:02:14 +0000
Subject: [PATCH] JAL-2844 start on colouring back onto the alignment

---
 src/jalview/ext/archaeopteryx/JalviewBinding.java |   38 +++++++++++++--------
 1 file changed, 24 insertions(+), 14 deletions(-)

diff --git a/src/jalview/ext/archaeopteryx/JalviewBinding.java b/src/jalview/ext/archaeopteryx/JalviewBinding.java
index 0e77243..66c348f 100644
--- a/src/jalview/ext/archaeopteryx/JalviewBinding.java
+++ b/src/jalview/ext/archaeopteryx/JalviewBinding.java
@@ -237,27 +237,17 @@ public final class JalviewBinding
       {
         Graphics g = treeView.getGraphics();
         int panelHeight = treeView.getHeight();
-        int viewWidth = treeView.getWidth();
         g.drawLine(x, 0, x, panelHeight);
 
         // double relativeTreeWidth = treeDepth / viewWidth;
-        //
-        // System.out.println(relativeTreeWidth);
 
         float rootX = tree.getRoot().getXcoord();
         double threshold = ((double) x - rootX) / longestBranch;
         List<PhylogenyNode> foundNodes = getNodesAboveThreshold(threshold,
                 longestBranch, tree.getRoot());
-        for (PhylogenyNode foundNode : foundNodes)
-        {
-          Color randomColor = new Color((int) (Math.random() * 255),
-                  (int) (Math.random() * 255), (int) (Math.random() * 255));
-          TreePanelUtil.colorizeSubtree(foundNode,
-                  new BranchColor(randomColor));
-        }
 
 
-        // groupNodes(threshold, tree.getRoot(), longestBranch);
+
 
 
 
@@ -274,13 +264,14 @@ public final class JalviewBinding
 
     List<PhylogenyNode> nodesAboveThreshold = new ArrayList<>();
 
-    iterateNodesAboveThreshold(nodesAboveThreshold, threshold, treeLength,
+    // could also use PhylogenyMethods.getAllDescendants
+    colourNodesAboveThreshold(nodesAboveThreshold, threshold, treeLength,
             node);
     return nodesAboveThreshold;
 
   }
 
-  private List<PhylogenyNode> iterateNodesAboveThreshold(
+  private List<PhylogenyNode> colourNodesAboveThreshold(
           List<PhylogenyNode> nodeList, double threshold,
           double treeLength, PhylogenyNode node)
   {
@@ -291,11 +282,29 @@ public final class JalviewBinding
       if (nodeCutoff > threshold)
       {
         nodeList.add(childNode);
+
+        Color randomColor = new Color((int) (Math.random() * 255),
+                (int) (Math.random() * 255), (int) (Math.random() * 255));
+        TreePanelUtil.colorizeSubtree(childNode,
+                new BranchColor(randomColor));
+        List<PhylogenyNode> descendantNodes = childNode
+                .getAllExternalDescendants();
+        List<SequenceI> descendantSeqs = new ArrayList<>();
+        for (PhylogenyNode descNode : descendantNodes)
+        {
+          descendantSeqs.add(nodesBoundToSequences.get(descNode));
+        }
+
+        SequenceGroup sg = new SequenceGroup(descendantSeqs, null, null,
+                true, true, false, 0,
+                parentAvport.getAlignment().getWidth() - 1);
+        sg.setIdColour(randomColor);
+
       }
 
       else
       {
-      iterateNodesAboveThreshold(nodeList, threshold, treeLength,
+      colourNodesAboveThreshold(nodeList, threshold, treeLength,
                 childNode);
       }
 
@@ -305,6 +314,7 @@ public final class JalviewBinding
 
 
 
+
   // public List<PhylogenyNode> groupNodes(float threshold, PhylogenyNode root,
   // double treeHeight)
   // {
-- 
1.7.10.2