2.08, not 2.07

[jalview.git] / src / jalview / schemes / Consensus.java

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