blosum colour now displayed ok

diff --git a/src/jalview/schemes/ConservationColourScheme.java b/src/jalview/schemes/ConservationColourScheme.java
index f8db803..cef65c2 100755 (executable)
--- a/src/jalview/schemes/ConservationColourScheme.java
+++ b/src/jalview/schemes/ConservationColourScheme.java
@@ -24,7 +24,6 @@ import jalview.analysis.*;
 \r
 public class ConservationColourScheme extends ResidueColourScheme {\r
   public Conservation conserve;\r
-  boolean byResidue = true;\r
   public ColourSchemeI cs;\r
   public int inc = 30;\r
   int colourThreshold =  7;\r
@@ -38,24 +37,21 @@ public class ConservationColourScheme extends ResidueColourScheme {
   }\r
 \r
 \r
-   public Color findColour(String s, int i, java.util.Vector whatever)\r
+   public Color findColour(String s, int i, java.util.Vector v)\r
    {\r
-     Color c = null;\r
+     Color c = Color.white;\r
+     if(cs == null)\r
+       return c;\r
+\r
      if (colourThreshold > 0 && conserve.getConsSequence() != null)\r
      {\r
-       if (conserve.getConsSequence().getSequence().charAt(i)=='*'\r
-           || conserve.getConsSequence().getSequence().charAt(i)=='+')\r
+       if (conserve.getConsSequence().getSequence().charAt(i) == '*'\r
+           || conserve.getConsSequence().getSequence().charAt(i) == '+')\r
        {\r
-         if (byResidue)\r
-           c = findColour(s, i);\r
-         else\r
-           c = Color.red;\r
+           c = cs.findColour(s, i, v);\r
        }\r
        else\r
        {\r
-         if (byResidue)\r
-         {\r
-\r
            int tmp = 10;\r
            int t = 0;\r
            if (!jalview.util.Comparison.isGap(conserve.getConsSequence().\r
@@ -63,30 +59,17 @@ public class ConservationColourScheme extends ResidueColourScheme {
              t = Integer.parseInt(conserve.getConsSequence().getSequence().\r
                                   substring(i, i + 1));\r
 \r
-           c = findColour(s, i);\r
-\r
+           c = cs.findColour(s, i, v);\r
            while (tmp >= t)\r
            {\r
-             //      c = c.darker();\r
              c = lighter(c, inc);\r
              tmp--;\r
            }\r
-         }\r
-         else\r
-           c = Color.yellow;\r
        }\r
      }\r
      return c;\r
    }\r
 \r
-  public Color findColour(String s, int j) {\r
-    if(cs!=null)\r
-      return cs.findColour( s, j, null);\r
-    else\r
-      return Color.white;\r
-  }\r
-\r
-\r
 \r
   public Color lighter(Color c, int inc) {\r
     int red = c.getRed();\r