Added for the moment, only used by ClustalxColourScheme

diff --git a/src/jalview/schemes/Consensus.java b/src/jalview/schemes/Consensus.java
new file mode 100755 (executable)
index 0000000..7b0dbbb
--- /dev/null
+++ b/src/jalview/schemes/Consensus.java
@@ -0,0 +1,72 @@
+/* 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
+\r
+import jalview.datamodel.*;\r
+import java.util.*;\r
+////////////////////////////////////////////\r
+// This does nothing at all at the moment!!!!!!!!!!\r
+// AW 15th Dec 2004\r
+/////////////////////////////////////////\r
+public class Consensus {\r
+\r
+  int[] mask;\r
+  double threshold;\r
+\r
+  public Consensus(String m, double threshold)\r
+  {\r
+    mask = setNums(m);\r
+    this.threshold = threshold;\r
+  }\r
+\r
+\r
+  public boolean isConserved(int[][] cons2,int col, int res,int size)\r
+  {\r
+    int tot = 0;\r
+\r
+try{\r
+    for (int i=0; i < mask.length; i++)\r
+      tot += cons2[col][mask[i]];\r
+}catch(Exception ex)\r
+{ return true; }\r
+\r
+    if ((double)tot > threshold*size/100)\r
+      return true;\r
+\r
+    return false;\r
+  }\r
+\r
+  int[] setNums(String s)\r
+  {\r
+    int [] out = new int[s.length()];\r
+    int i = 0;\r
+    while (i < s.length())\r
+    {\r
+      out[i] = ( (Integer) ResidueProperties.aaHash.get(s.substring(i, i + 1))).intValue();\r
+      i++;\r
+    }\r
+    return out;\r
+  }\r
+\r
+\r
+}\r
+\r
+\r
+\r
+\r