merge from 2_4_Release branch

[jalview.git] / src / jalview / datamodel / BinarySequence.java

diff --git a/src/jalview/datamodel/BinarySequence.java b/src/jalview/datamodel/BinarySequence.java
index 1cdc934..52b0ece 100755 (executable)
--- a/src/jalview/datamodel/BinarySequence.java
+++ b/src/jalview/datamodel/BinarySequence.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
@@ -22,20 +22,21 @@ import jalview.schemes.*;
 
 /**
  * DOCUMENT ME!
- *
+ * 
  * @author $author$
  * @version $Revision$
  */
-public class BinarySequence
-    extends Sequence
+public class BinarySequence extends Sequence
 {
   int[] binary;
+
   double[] dbinary;
 
   /**
    * Creates a new BinarySequence object.
-   *
-   * @param s DOCUMENT ME!
+   * 
+   * @param s
+   *                DOCUMENT ME!
    */
   public BinarySequence(String s)
   {
@@ -64,8 +65,7 @@ public class BinarySequence
       try
       {
         aanum = ResidueProperties.aaIndex[getCharAt(i)];
-      }
-      catch (NullPointerException e)
+      } catch (NullPointerException e)
       {
         aanum = 20;
       }
@@ -75,18 +75,19 @@ public class BinarySequence
         aanum = 20;
       }
 
-      dbinary[ (i * nores) + aanum] = 1.0;
+      dbinary[(i * nores) + aanum] = 1.0;
     }
   }
 
   /**
    * ancode using substitution matrix given in matrix
+   * 
    * @param matrix
    */
   public void matrixEncode(ScoreMatrix matrix)
   {
-    matrixEncode(matrix.isDNA() ? ResidueProperties.nucleotideIndex :
-                 ResidueProperties.aaIndex, matrix.getMatrix());
+    matrixEncode(matrix.isDNA() ? ResidueProperties.nucleotideIndex
+            : ResidueProperties.aaIndex, matrix.getMatrix());
   }
 
   /**
@@ -104,9 +105,9 @@ public class BinarySequence
 
     int nores = 21;
 
-    //for (int i = 0; i < dbinary.length; i++) {
-    //  dbinary[i] = 0.0;
-    //}
+    // for (int i = 0; i < dbinary.length; i++) {
+    // dbinary[i] = 0.0;
+    // }
     for (int i = 0; i < getSequence().length; i++)
     {
       int aanum = 20;
@@ -114,8 +115,7 @@ public class BinarySequence
       try
       {
         aanum = aaIndex[getCharAt(i)];
-      }
-      catch (NullPointerException e)
+      } catch (NullPointerException e)
       {
         aanum = 20;
       }
@@ -129,14 +129,14 @@ public class BinarySequence
 
       for (int j = 0; j < 20; j++)
       {
-        dbinary[ (i * nores) + j] = matrix[aanum][j];
+        dbinary[(i * nores) + j] = matrix[aanum][j];
       }
     }
   }
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   public String toBinaryString()
@@ -158,7 +158,7 @@ public class BinarySequence
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   public double[] getDBinary()