createColourFromName if not specified

diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java
index 591fa79..628de4e 100755 (executable)
--- a/src/jalview/gui/FeatureRenderer.java
+++ b/src/jalview/gui/FeatureRenderer.java
@@ -41,11 +41,13 @@ public class FeatureRenderer
     FontMetrics fm;\r
     int charOffset;\r
 \r
+    Hashtable featureColours = new Hashtable();\r
+\r
+\r
     // A higher level for grouping features of a\r
    // particular type\r
     Hashtable featureGroups = null;\r
 \r
-\r
     // This is actually an Integer held in the hashtable,\r
     // Retrieved using the key feature type\r
     Object currentColour;\r
@@ -61,7 +63,6 @@ public class FeatureRenderer
     public FeatureRenderer(AlignViewport av)\r
     {\r
         this.av = av;\r
-        initColours();\r
     }\r
 \r
     public void transferSettings(FeatureRenderer fr)\r
@@ -334,7 +335,10 @@ public class FeatureRenderer
 \r
     synchronized void findAllFeatures()\r
     {\r
-      av.featuresDisplayed = new Hashtable();\r
+      jalview.schemes.UserColourScheme ucs = new\r
+          jalview.schemes.UserColourScheme();\r
+\r
+          av.featuresDisplayed = new Hashtable();\r
       Vector allfeatures = new Vector();\r
       for (int i = 0; i < av.alignment.getHeight(); i++)\r
       {\r
@@ -355,7 +359,11 @@ public class FeatureRenderer
               // and we don't want to render the feature in the normal way\r
 \r
               if (getColour(features[index].getType()) == null)\r
-                createRandomColour(features[index].getType());\r
+              {\r
+                 featureColours.put(features[index].getType(),\r
+                                   ucs.createColourFromName(features[index].\r
+                    getType()));\r
+              }\r
 \r
               av.featuresDisplayed.put(features[index].getType(),\r
                                        new Integer(getColour(features[index].\r
@@ -439,59 +447,7 @@ public class FeatureRenderer
 \r
     }\r
 \r
-    Hashtable featureColours = new Hashtable();\r
-    void initColours()\r
-    {\r
-      featureColours.put("active site", new Color(255, 75, 0));\r
-      featureColours.put("binding site", new Color(245, 85, 0));\r
-      featureColours.put("calcium-binding region", new Color(235, 95, 0));\r
-      featureColours.put("chain", new Color(225, 105, 0));\r
-      featureColours.put("coiled-coil region", new Color(215, 115, 0));\r
-      featureColours.put("compositionally biased region", new Color(205, 125, 0));\r
-      featureColours.put("cross-link", new Color(195, 135, 0));\r
-      featureColours.put("disulfide bond", new Color(230,230,0));\r
-      featureColours.put("DNA-binding region", new Color(175, 155, 0));\r
-      featureColours.put("domain", new Color(165, 165, 0));\r
-      featureColours.put("glycosylation site", new Color(155, 175, 0));\r
-      featureColours.put("helix", new Color(145, 185, 0));\r
-      featureColours.put("initiator methionine", new Color(135, 195, 5));\r
-      featureColours.put("lipid moiety-binding region", new Color(125, 205, 15));\r
-      featureColours.put("metal ion-binding site", new Color(115, 215, 25));\r
-      featureColours.put("modified residue", new Color(105, 225, 35));\r
-      featureColours.put("mutagenesis site", new Color(95, 235, 45));\r
-      featureColours.put("non-consecutive residues", new Color(85, 245, 55));\r
-      featureColours.put("non-terminal residue", new Color(75, 255, 65));\r
-      featureColours.put("nucleotide phosphate-binding region",new Color(65, 245, 75));\r
-      featureColours.put("peptide", new Color(55, 235, 85));\r
-      featureColours.put("propeptide", new Color(45, 225, 95));\r
-      featureColours.put("region of interest", new Color(35, 215, 105));\r
-      featureColours.put("repeat", new Color(25, 205, 115));\r
-      featureColours.put("selenocysteine", new Color(15, 195, 125));\r
-      featureColours.put("sequence conflict", new Color(5, 185, 135));\r
-      featureColours.put("sequence variant", new Color(0, 175, 145));\r
-      featureColours.put("short sequence motif", new Color(0, 165, 155));\r
-      featureColours.put("signal peptide", new Color(0, 155, 165));\r
-      featureColours.put("site", new Color(0, 145, 175));\r
-      featureColours.put("splice variant", new Color(0, 135, 185));\r
-      featureColours.put("strand", new Color(0, 125, 195));\r
-      featureColours.put("topological domain", new Color(0, 115, 205));\r
-      featureColours.put("transit peptide", new Color(0, 105, 215));\r
-      featureColours.put("transmembrane region", new Color(0, 95, 225));\r
-      featureColours.put("turn", new Color(0, 85, 235));\r
-      featureColours.put("unsure residue", new Color(0, 75, 245));\r
-      featureColours.put("zinc finger region", new Color(0, 65, 255));\r
-    }\r
 \r
-    public Color createRandomColour(String name)\r
-    {\r
-      Random rg = new Random(System.currentTimeMillis());\r
-      Color color = new Color( (int) (Math.random() * 255),\r
-                                         (int) (Math.random() * 255),\r
-                                         (int) (Math.random() * 255));\r
-      featureColours.put(name, color); // java 1.2 here ?\r
-\r
-      return color;\r
-    }\r
 \r
 \r
 }\r