X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FBinarySequence.java;h=9d6f5e84f4e51885a75d86c74f1dddc3f32a4251;hb=a45774ee31d9f35d4eff46d54d7deab719afb092;hp=1cdc934c09b8ab81063adcea6f0f6dd193f0e77c;hpb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;p=jalview.git

diff --git a/src/jalview/datamodel/BinarySequence.java b/src/jalview/datamodel/BinarySequence.java
index 1cdc934..9d6f5e8 100755
--- a/src/jalview/datamodel/BinarySequence.java
+++ b/src/jalview/datamodel/BinarySequence.java
@@ -1,20 +1,19 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 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 (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview 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 3 of the License, or (at your option) any later version.
+ * 
+ * Jalview 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 Jalview.  If not, see <http://www.gnu.org/licenses/>.
  */
 package jalview.datamodel;
 
@@ -22,20 +21,21 @@ 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 +64,7 @@ public class BinarySequence
       try
       {
         aanum = ResidueProperties.aaIndex[getCharAt(i)];
-      }
-      catch (NullPointerException e)
+      } catch (NullPointerException e)
       {
         aanum = 20;
       }
@@ -75,18 +74,19 @@ 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 +104,9 @@ 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 +114,7 @@ public class BinarySequence
       try
       {
         aanum = aaIndex[getCharAt(i)];
-      }
-      catch (NullPointerException e)
+      } catch (NullPointerException e)
       {
         aanum = 20;
       }
@@ -129,14 +128,14 @@ 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 +157,7 @@ public class BinarySequence
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   public double[] getDBinary()