Parse HTML links from jalview features file

[jalview.git] / src / jalview / appletgui / FeatureRenderer.java

diff --git a/src/jalview/appletgui/FeatureRenderer.java b/src/jalview/appletgui/FeatureRenderer.java
index aa3f830..0f9f393 100755 (executable)
--- a/src/jalview/appletgui/FeatureRenderer.java
+++ b/src/jalview/appletgui/FeatureRenderer.java
@@ -35,6 +35,7 @@ public class FeatureRenderer
 {\r
     AlignViewport av;\r
 \r
+    Hashtable featureColours = new Hashtable();\r
 \r
     // A higher level for grouping features of a\r
     // particular type\r
@@ -66,20 +67,11 @@ public class FeatureRenderer
     public FeatureRenderer(AlignViewport av)\r
     {\r
         this.av = av;\r
-        initColours();\r
 \r
         if(!System.getProperty("java.version").startsWith("1.1"))\r
              transparencySetter = new TransparencySetter();\r
     }\r
 \r
-    public void addFeatureLink(String feature, String link)\r
-    {\r
-      if(featureLinks == null)\r
-        featureLinks = new Hashtable();\r
-\r
-       featureLinks.put(feature, link);\r
-    }\r
-\r
 \r
     public void transferSettings(FeatureRenderer fr)\r
     {\r
@@ -402,50 +394,6 @@ public class FeatureRenderer
             renderOrder[data.length - i - 1] = type;\r
           }\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(185, 145, 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",\r
-                         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
 \r
   class TransparencySetter\r