must set consensus in child colourscheme

diff --git a/src/jalview/schemes/ConservationColourScheme.java b/src/jalview/schemes/ConservationColourScheme.java
index d418b4f..0a68682 100755 (executable)
--- a/src/jalview/schemes/ConservationColourScheme.java
+++ b/src/jalview/schemes/ConservationColourScheme.java
@@ -1,82 +1,88 @@
-/* Jalview - a java multiple alignment editor\r
- * Copyright (C) 1998  Michele Clamp\r
- *\r
- * This program is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
- *\r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
- * GNU General Public License for more details.\r
- *\r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.\r
- */\r
-\r
-package jalview.schemes;\r
-import java.awt.*;\r
-import jalview.gui.*;\r
-import jalview.datamodel.*;\r
-import jalview.analysis.*;\r
-\r
-public class ConservationColourScheme extends ResidueColourScheme {\r
-  public Conservation conserve;\r
-  public ColourSchemeI cs;\r
-  public int inc = 30;\r
-\r
-  public ConservationColourScheme(Conservation cons, ColourSchemeI oldcs)\r
-  {\r
-    super();\r
-    conserve = cons;\r
-    cs = oldcs;\r
-  }\r
-\r
-\r
-   public Color findColour(String s, int i)\r
-   {\r
-     Color c = Color.white;\r
-     if (cs == null)\r
-       return c;\r
-\r
-     char ch = conserve.getConsSequence().getSequence().charAt(i);\r
-     if (ch == '*' || ch == '+')\r
-     {\r
-       c = cs.findColour(s, i);\r
-     }\r
-     else\r
-     {\r
-       int tmp = 10;\r
-       int t = 0;\r
-       if (!jalview.util.Comparison.isGap(ch))\r
-         t = Integer.parseInt(ch + "");\r
-\r
-       c = cs.findColour(s, i);\r
-\r
-       while (tmp >= t)\r
-       {\r
-         c = lighter(c, inc);\r
-         tmp--;\r
-       }\r
-\r
-     }\r
-\r
-   return c;\r
-   }\r
-\r
-\r
-  public Color lighter(Color c, int inc) {\r
-    int red = c.getRed();\r
-    int blue = c.getBlue();\r
-    int green = c.getGreen();\r
-\r
-    if (red < 255-inc) { red = red +inc;} else {red = 255;}\r
-    if (blue < 255-inc) { blue = blue +inc;} else {blue = 255;}\r
-    if (green < 255-inc) { green = green +inc;} else {green = 255;}\r
-\r
-    return new Color(red,green,blue);\r
-  }\r
-\r
-}\r
+/* Jalview - a java multiple alignment editor
+ * Copyright (C) 1998  Michele Clamp
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
+ */
+
+package jalview.schemes;
+import java.awt.*;
+import jalview.gui.*;
+import jalview.datamodel.*;
+import jalview.analysis.*;
+import java.util.Vector;
+
+public class ConservationColourScheme extends ResidueColourScheme {
+  public Conservation conserve;
+  public ColourSchemeI cs;
+  public int inc = 30;
+
+  public ConservationColourScheme(Conservation cons, ColourSchemeI oldcs)
+  {
+    super();
+    conserve = cons;
+    cs = oldcs;
+  }
+
+  public void setConsensus(Vector consensus)
+  {
+    this.consensus = consensus;
+    cs.setConsensus(consensus);
+  }
+
+   public Color findColour(String s, int i)
+   {
+     Color c = Color.white;
+     if (cs == null)
+       return c;
+
+     char ch = conserve.getConsSequence().getSequence().charAt(i);
+     if (ch == '*' || ch == '+')
+     {
+       c = cs.findColour(s, i);
+     }
+     else
+     {
+       int tmp = 10;
+       int t = 0;
+       if (!jalview.util.Comparison.isGap(ch))
+         t = Integer.parseInt(ch + "");
+
+       c = cs.findColour(s, i);
+
+       while (tmp >= t)
+       {
+         c = lighter(c, inc);
+         tmp--;
+       }
+
+     }
+
+   return c;
+   }
+
+
+  public Color lighter(Color c, int inc) {
+    int red = c.getRed();
+    int blue = c.getBlue();
+    int green = c.getGreen();
+
+    if (red < 255-inc) { red = red +inc;} else {red = 255;}
+    if (blue < 255-inc) { blue = blue +inc;} else {blue = 255;}
+    if (green < 255-inc) { green = green +inc;} else {green = 255;}
+
+    return new Color(red,green,blue);
+  }
+
+}