new file

diff --git a/src/jalview/schemes/ConservationColourScheme.java b/src/jalview/schemes/ConservationColourScheme.java
new file mode 100755 (executable)
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--- /dev/null
+++ b/src/jalview/schemes/ConservationColourScheme.java
@@ -0,0 +1,138 @@
+/* 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
+  boolean byResidue = true;\r
+  public ColourSchemeI cs;\r
+  public int inc = 30;\r
+  int colourThreshold =  7;\r
+\r
+  public ConservationColourScheme(SequenceGroup sg)\r
+  {\r
+    super();\r
+    this.conserve = sg.getConservation();\r
+    colourThreshold = 7;\r
+    this.cs = sg.cs;\r
+  }\r
+\r
+  public void setColours(DrawableSequence seq, int j) {\r
+    Color c = Color.white;\r
+    String s = seq.getSequence().substring(j,j+1);\r
+\r
+      if (colourThreshold > 0 && conserve.getConsSequence() != null) {\r
+        if (fullConservation(j)) {\r
+          if (byResidue) {\r
+            c = findColour(seq,s,j);\r
+           } else {\r
+             c = Color.red;\r
+           }\r
+        } else {\r
+          if (byResidue) {\r
+\r
+            int tmp = 10;\r
+            int t = Integer.parseInt(conserve.getConsSequence().getSequence().substring(j,j+1));\r
+            c = findColour(seq,s,j);\r
+\r
+             while (tmp >= t) {\r
+              //      c = c.darker();\r
+              c = lighter(c,inc);\r
+               tmp--;\r
+             }\r
+          } else {\r
+          c = Color.yellow;\r
+          }\r
+        }\r
+      }\r
+\r
+      seq.setColor(c);\r
+\r
+  }\r
+   public Color findColour(SequenceI seq, String s, int i, java.util.Vector whatever)\r
+   {\r
+     Color c = null;\r
+     if (colourThreshold > 0 && conserve.getConsSequence() != null)\r
+     {\r
+       if (fullConservation(i)) {\r
+         if (byResidue) {\r
+           c = findColour(null,s,i);\r
+          } else {\r
+            c = Color.red;\r
+          }\r
+       } else {\r
+         if (byResidue) {\r
+\r
+           int tmp = 10;\r
+           int t = 0;\r
+           try\r
+             {t=Integer.parseInt(conserve.getConsSequence().getSequence().substring(i,i+1));}\r
+             catch(NumberFormatException ex){\r
+               System.out.println("fix this bug, conserveColourScheme");\r
+               t=0;\r
+             }\r
+           c = findColour(null,s,i);\r
+\r
+            while (tmp >= t) {\r
+             //      c = c.darker();\r
+             c = lighter(c,inc);\r
+              tmp--;\r
+            }\r
+         } else {\r
+         c = Color.yellow;\r
+         }\r
+       }\r
+     }\r
+     return c;\r
+   }\r
+\r
+  public Color findColour(DrawableSequence seq, String s, int j) {\r
+    return cs.findColour(null, s, -1, null);\r
+  }\r
+  public boolean fullConservation(int j) {\r
+    String tmp = conserve.getConsSequence().getSequence().substring(j,j+1);\r
+    if (tmp.equals("*")) return true; else return false;\r
+  }\r
+  public boolean aboveThreshold(DrawableSequence seq, int j, int threshold) {\r
+    String tmp = conserve.getConsSequence().getSequence().substring(j,j+1);\r
+\r
+    if (Integer.parseInt(tmp) >= threshold || tmp.equals("*")) {\r
+      return true;\r
+    } else {\r
+      return false;\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