From 9360a7970c15aacc7e53eb3bdd2732d2c7bef9c8 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Wed, 15 Dec 2004 17:28:07 +0000
Subject: [PATCH] Added for the moment, only used by ClustalxColourScheme

---
 src/jalview/schemes/Consensus.java |   72 ++++++++++++++++++++++++++++++++++++
 1 file changed, 72 insertions(+)
 create mode 100755 src/jalview/schemes/Consensus.java

diff --git a/src/jalview/schemes/Consensus.java b/src/jalview/schemes/Consensus.java
new file mode 100755
index 0000000..7b0dbbb
--- /dev/null
+++ b/src/jalview/schemes/Consensus.java
@@ -0,0 +1,72 @@
+/* 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 jalview.datamodel.*;
+import java.util.*;
+////////////////////////////////////////////
+// This does nothing at all at the moment!!!!!!!!!!
+// AW 15th Dec 2004
+/////////////////////////////////////////
+public class Consensus {
+
+  int[] mask;
+  double threshold;
+
+  public Consensus(String m, double threshold)
+  {
+    mask = setNums(m);
+    this.threshold = threshold;
+  }
+
+
+  public boolean isConserved(int[][] cons2,int col, int res,int size)
+  {
+    int tot = 0;
+
+try{
+    for (int i=0; i < mask.length; i++)
+      tot += cons2[col][mask[i]];
+}catch(Exception ex)
+{ return true; }
+
+    if ((double)tot > threshold*size/100)
+      return true;
+
+    return false;
+  }
+
+  int[] setNums(String s)
+  {
+    int [] out = new int[s.length()];
+    int i = 0;
+    while (i < s.length())
+    {
+      out[i] = ( (Integer) ResidueProperties.aaHash.get(s.substring(i, i + 1))).intValue();
+      i++;
+    }
+    return out;
+  }
+
+
+}
+
+
+
+
-- 
1.7.10.2