Formatted source

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

diff --git a/src/jalview/schemes/Consensus.java b/src/jalview/schemes/Consensus.java
index 27c5906..8ca0223 100755 (executable)
--- a/src/jalview/schemes/Consensus.java
+++ b/src/jalview/schemes/Consensus.java
@@ -16,62 +16,57 @@
 * 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
-\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
-  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
+    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
+        setMask(mask);\r
+        this.threshold = threshold;\r
+    }\r
 \r
-  public void setMask(String s) {\r
-    this.mask = setNums(s);\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
+        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
-      tot += cons2[col][mask[i]];\r
+        //   for (int i=0; i < mask.length; i++) {\r
+        //  System.out.println(mask[i] + " " + ResidueProperties.aa[mask[i]]);\r
+        // }\r
+    }\r
 \r
-    if ( (double) tot > threshold * size / 100)\r
-      return true;\r
+    public boolean isConserved(int[][] cons2, int col, int size) {\r
+        int tot = 0;\r
 \r
-    return false;\r
-  }\r
+        for (int i = 0; i < mask.length; i++)\r
+            tot += cons2[col][mask[i]];\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
+        if ((double) tot > ((threshold * size) / 100)) {\r
+            return true;\r
+        }\r
 \r
+        return false;\r
     }\r
 \r
-    return out;\r
-  }\r
+    int[] setNums(String s) {\r
+        int[] out = new int[s.length()];\r
+        int i = 0;\r
 \r
+        while (i < s.length()) {\r
+            out[i] = ((Integer) ResidueProperties.aaHash.get(s.substring(i,\r
+                        i + 1))).intValue();\r
+            i++;\r
+        }\r
 \r
+        return out;\r
+    }\r
 }\r
-\r
-\r
-\r
-\r