From 50779cf7013a8db695c53637578ab135da3ce5b1 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Wed, 7 Jun 2006 12:57:38 +0000
Subject: [PATCH] Create random colour only if Colour is not specified

---
 src/jalview/gui/FeatureRenderer.java |   34 +++++++++++++++++++++++++++++-----
 1 file changed, 29 insertions(+), 5 deletions(-)

diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java
index fdbd7eb..591fa79 100755
--- a/src/jalview/gui/FeatureRenderer.java
+++ b/src/jalview/gui/FeatureRenderer.java
@@ -332,7 +332,7 @@ public class FeatureRenderer
       }
     }
 
-    void findAllFeatures()
+    synchronized void findAllFeatures()
     {
       av.featuresDisplayed = new Hashtable();
       Vector allfeatures = new Vector();
@@ -349,9 +349,19 @@ public class FeatureRenderer
         {
           if (!av.featuresDisplayed.containsKey(features[index].getType()))
           {
-            av.featuresDisplayed.put(features[index].getType(),
-                                  new Integer( getColour(features[index].getType()).getRGB()) );
-            allfeatures.addElement(features[index].getType());
+            if(!(features[index].begin == 0 && features[index].end ==0))
+            {
+              // If beginning and end are 0, the feature is for the whole sequence
+              // and we don't want to render the feature in the normal way
+
+              if (getColour(features[index].getType()) == null)
+                createRandomColour(features[index].getType());
+
+              av.featuresDisplayed.put(features[index].getType(),
+                                       new Integer(getColour(features[index].
+                  getType()).getRGB()));
+              allfeatures.addElement(features[index].getType());
+            }
           }
           index++;
         }
@@ -369,9 +379,11 @@ public class FeatureRenderer
 
     public Color getColour(String featureType)
     {
-      return (Color)featureColours.get(featureType);
+      Color colour = (Color)featureColours.get(featureType);
+      return colour;
     }
 
+
     public void addNewFeature(String name, Color col, String group)
     {
 
@@ -470,4 +482,16 @@ public class FeatureRenderer
       featureColours.put("zinc finger region", new Color(0, 65, 255));
     }
 
+    public Color createRandomColour(String name)
+    {
+      Random rg = new Random(System.currentTimeMillis());
+      Color color = new Color( (int) (Math.random() * 255),
+                                         (int) (Math.random() * 255),
+                                         (int) (Math.random() * 255));
+      featureColours.put(name, color); // java 1.2 here ?
+
+      return color;
+    }
+
+
 }
-- 
1.7.10.2