X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FConsensus.java;h=ac895bbb6f90f460037bc0940a152d73948ba59b;hb=efc31b4a8d5cee63555586804a2b79c06bdb5a14;hp=8ca022389136d880b607ef11dc918c0640651166;hpb=9257b8510c7354cbd7e43a3fc2817978cc8e4ae9;p=jalview.git

diff --git a/src/jalview/schemes/Consensus.java b/src/jalview/schemes/Consensus.java
index 8ca0223..ac895bb 100755
--- a/src/jalview/schemes/Consensus.java
+++ b/src/jalview/schemes/Consensus.java
@@ -1,72 +1,80 @@
 /*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* 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., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
-*/
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * 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., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.schemes;
 
-
 ////////////////////////////////////////////
 // This does nothing at all at the moment!!!!!!!!!!
 // AW 15th Dec 2004
 /////////////////////////////////////////
-public class Consensus {
-    int[] mask;
-    double threshold;
-    String maskstr;
-
-    public Consensus(String mask, double threshold) {
-        // this.id = id;
-        //    this.mask = mask;
-        this.maskstr = mask;
-        setMask(mask);
-        this.threshold = threshold;
-    }
+public class Consensus
+{
+  int[] mask;
+  double threshold;
+  String maskstr;
 
-    public void setMask(String s) {
-        this.mask = setNums(s);
+  public Consensus(String mask, double threshold)
+  {
+    // this.id = id;
+    //    this.mask = mask;
+    this.maskstr = mask;
+    setMask(mask);
+    this.threshold = threshold;
+  }
 
-        //   for (int i=0; i < mask.length; i++) {
-        //  System.out.println(mask[i] + " " + ResidueProperties.aa[mask[i]]);
-        // }
-    }
+  public void setMask(String s)
+  {
+    this.mask = setNums(s);
 
-    public boolean isConserved(int[][] cons2, int col, int size) {
-        int tot = 0;
+    //   for (int i=0; i < mask.length; i++) {
+    //  System.out.println(mask[i] + " " + ResidueProperties.aa[mask[i]]);
+    // }
+  }
 
-        for (int i = 0; i < mask.length; i++)
-            tot += cons2[col][mask[i]];
+  public boolean isConserved(int[][] cons2, int col, int size)
+  {
+    int tot = 0;
 
-        if ((double) tot > ((threshold * size) / 100)) {
-            return true;
-        }
+    for (int i = 0; i < mask.length; i++)
+    {
+      tot += cons2[col][mask[i]];
+    }
 
-        return false;
+    if ( (double) tot > ( (threshold * size) / 100))
+    {
+      return true;
     }
 
-    int[] setNums(String s) {
-        int[] out = new int[s.length()];
-        int i = 0;
+    return false;
+  }
 
-        while (i < s.length()) {
-            out[i] = ((Integer) ResidueProperties.aaHash.get(s.substring(i,
-                        i + 1))).intValue();
-            i++;
-        }
+  int[] setNums(String s)
+  {
+    int[] out = new int[s.length()];
+    int i = 0;
 
-        return out;
+    while (i < s.length())
+    {
+      out[i] = ( (Integer) ResidueProperties.aaHash.get(s.substring(i,
+          i + 1))).intValue();
+      i++;
     }
+
+    return out;
+  }
 }