From c3443e896f364ac09927f3faaf1401db12209ba0 Mon Sep 17 00:00:00 2001
From: Ben Soares <b.soares@dundee.ac.uk>
Date: Thu, 7 Nov 2024 12:57:02 +0000
Subject: [PATCH] JAL-4386 Demonstration of the ColorUtils HSB methods in the
 normal tree

---
 src/jalview/datamodel/BinaryNode.java |   32 ++++++++++++++++++++++++++++++++
 src/jalview/gui/TreeCanvas.java       |   24 ++++++++++--------------
 2 files changed, 42 insertions(+), 14 deletions(-)

diff --git a/src/jalview/datamodel/BinaryNode.java b/src/jalview/datamodel/BinaryNode.java
index ef543db..a842ddf 100755
--- a/src/jalview/datamodel/BinaryNode.java
+++ b/src/jalview/datamodel/BinaryNode.java
@@ -416,4 +416,36 @@ public class BinaryNode<T>
     }
     return hasLabel() ? label : "";
   }
+
+  /**
+   * get a concatenation of all node names under this node
+   */
+  public String getNodeName()
+  {
+    return getNodeName(0);
+  }
+
+  public String getNodeName(int depth)
+  {
+    StringBuilder sb = new StringBuilder();
+    if (getName() != null)
+    {
+      sb.append(getName());
+    }
+    if (left() != null)
+    {
+      sb.append("::L");
+      sb.append(depth);
+      sb.append("::");
+      sb.append(left().getNodeName(depth + 1));
+    }
+    if (right() != null)
+    {
+      sb.append("::R");
+      sb.append(depth);
+      sb.append("::");
+      sb.append(right.getNodeName(depth + 1));
+    }
+    return sb.toString();
+  }
 }
diff --git a/src/jalview/gui/TreeCanvas.java b/src/jalview/gui/TreeCanvas.java
index 494360f..fbb0a7d 100755
--- a/src/jalview/gui/TreeCanvas.java
+++ b/src/jalview/gui/TreeCanvas.java
@@ -61,7 +61,6 @@ import jalview.analysis.TreeModel;
 import jalview.api.AlignViewportI;
 import jalview.bin.Console;
 import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.Annotation;
 import jalview.datamodel.BinaryNode;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.ContactMatrixI;
@@ -424,10 +423,8 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
     }
     else
     {
-      drawNode(g, (BinaryNode) node.left(), chunk, wscale, width, offx,
-              offy);
-      drawNode(g, (BinaryNode) node.right(), chunk, wscale, width, offx,
-              offy);
+      drawNode(g, node.left(), chunk, wscale, width, offx, offy);
+      drawNode(g, node.right(), chunk, wscale, width, offx, offy);
 
       double height = node.height;
       double dist = node.dist;
@@ -683,8 +680,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
 
     if (top.count == 0)
     {
-      top.count = ((BinaryNode) top.left()).count
-              + ((BinaryNode) top.right()).count;
+      top.count = top.left().count + top.right().count;
     }
 
     float chunk = (float) (height - (offy)) / top.count;
@@ -743,10 +739,8 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
     }
     else
     {
-      pickNode(pickBox, (BinaryNode) node.left(), chunk, wscale, width,
-              offx, offy);
-      pickNode(pickBox, (BinaryNode) node.right(), chunk, wscale, width,
-              offx, offy);
+      pickNode(pickBox, node.left(), chunk, wscale, width, offx, offy);
+      pickNode(pickBox, node.right(), chunk, wscale, width, offx, offy);
     }
   }
 
@@ -778,8 +772,8 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
         }
       }
     }
-    setColor((BinaryNode) node.left(), c);
-    setColor((BinaryNode) node.right(), c);
+    setColor(node.left(), c);
+    setColor(node.right(), c);
   }
 
   /**
@@ -1271,7 +1265,9 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
     Map<BitSet, Color> colors = new HashMap();
     for (int i = 0; i < groups.size(); i++)
     {
-      Color col = ColorUtils.getARandomColor();
+      String colId = groups.get(i).getNodeName();
+      Color col = ColorUtils.getColourFromNameAndScheme(colId,
+              "AVOID_GREEN");
 
       setColor(groups.get(i), col.brighter());
 
-- 
1.7.10.2