ColourScheme no longer requires sequence

diff --git a/src/jalview/gui/SequenceRenderer.java b/src/jalview/gui/SequenceRenderer.java
index e8cf340..82124ce 100755 (executable)
--- a/src/jalview/gui/SequenceRenderer.java
+++ b/src/jalview/gui/SequenceRenderer.java
@@ -27,9 +27,10 @@ public class SequenceRenderer implements RendererI
   public Color getResidueBoxColour(ColourSchemeI cs, SequenceI seq, int i)\r
   {\r
    Color c = Color.white;\r
-\r
+try{\r
      if (cs != null)\r
-       c = cs.findColour(seq, seq.getSequence(i, i + 1), i, av.getConsensus(false));\r
+       c = cs.findColour(seq.getSequence(i, i + 1), i, av.getConsensus(false));\r
+   }catch(Exception ex){}\r
 \r
     return c;\r
   }\r
@@ -54,8 +55,6 @@ public class SequenceRenderer implements RendererI
     int curStart = x1;\r
     int curWidth = width;\r
 \r
-  //  int threshold = 80;\r
-\r
     while (i <= end && i < length)\r
     {\r
       color = color.white;\r
@@ -69,34 +68,6 @@ public class SequenceRenderer implements RendererI
            color = getResidueBoxColour(av.getGlobalColourScheme(), seq, i);\r
 \r
 \r
-    //  Hashtable hash  = (Hashtable)freq.elementAt(i-start);\r
-    //  String    s     = (String)hash.get("maxResidue");\r
-    //  int       count = ((Integer)hash.get("maxCount")).intValue();\r
-  //    int       max   = ((Integer)hash.get("size")).intValue();\r
-   //   int       nongap = ((Integer)hash.get("nongap")).intValue();\r
-   //   float     frac  = (float)(count*1.0/(1.0*nongap));\r
-\r
-      //System.out.println("Frac/count/nongap " + frac + " " + count + " " + nongap);\r
-    /*  if (!seq.getSequence().substring(i,i+1).equals(s) ||\r
-         s.equals("-") ||\r
-         s.equals(".") ||\r
-         s.equals(" "))\r
-      {\r
-       c = Color.white;\r
-      } else {\r
-       if (frac > 0.9) {\r
-         c = Color.red;\r
-       } else if (frac > 0.8) {\r
-         c = Color.orange;\r
-       } else if (frac > 0.7) {\r
-         c = Color.pink;\r
-       } else if (frac > 0.5) {\r
-         c = Color.yellow;\r
-       } else if (frac> 0.3) {\r
-           c = Color.lightGray;\r
-       }\r
-      }*/\r
-\r
       if (color != currentColor || color != null)\r
       {\r
         g.fillRect(x1+width*(curStart-start),y1,curWidth,height);\r

diff --git a/src/jalview/gui/UserDefinedColours.java b/src/jalview/gui/UserDefinedColours.java
index 1fcc923..28f0474 100755 (executable)
--- a/src/jalview/gui/UserDefinedColours.java
+++ b/src/jalview/gui/UserDefinedColours.java
@@ -61,7 +61,7 @@ public class UserDefinedColours extends GUserDefinedColours implements ChangeLis
       cs = ap.av.getGlobalColourScheme();\r
 \r
     if(cs!=null)\r
-      col = cs.findColour(null, aa, -1, null);\r
+      col = cs.findColour( aa, -1, null);\r
 \r
     button.setBackground(  col );\r
     oldColours.addElement( col );\r