From ff665c68ddba84221ee3492911f9c0fd84ca0aac Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Thu, 28 Apr 2005 15:41:58 +0000
Subject: [PATCH] must set consensus in child colourscheme

---
 src/jalview/schemes/ConservationColourScheme.java |  170 +++++++++++----------
 1 file changed, 88 insertions(+), 82 deletions(-)

diff --git a/src/jalview/schemes/ConservationColourScheme.java b/src/jalview/schemes/ConservationColourScheme.java
index d418b4f..0a68682 100755
--- a/src/jalview/schemes/ConservationColourScheme.java
+++ b/src/jalview/schemes/ConservationColourScheme.java
@@ -1,82 +1,88 @@
-/* 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.*;
-
-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 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);
-  }
-
-}
+/* 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);
+  }
+
+}
-- 
1.7.10.2