JAL-1925 update source version in license

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

diff --git a/src/jalview/datamodel/BinarySequence.java b/src/jalview/datamodel/BinarySequence.java
index 2b4ce6b..fccd84c 100755 (executable)
--- a/src/jalview/datamodel/BinarySequence.java
+++ b/src/jalview/datamodel/BinarySequence.java
@@ -1,23 +1,27 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * 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.
- * 
+ * 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/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.datamodel;
 
-import jalview.schemes.*;
+import jalview.schemes.ResidueProperties;
+import jalview.schemes.ScoreMatrix;
 
 /**
  * Encode a sequence as a numeric vector using either classic residue binary
@@ -42,7 +46,8 @@ public class BinarySequence extends Sequence
 
   double[] dbinary;
 
-  boolean isNa=false;
+  boolean isNa = false;
+
   /**
    * Creates a new BinarySequence object.
    * 
@@ -52,16 +57,18 @@ public class BinarySequence extends Sequence
   public BinarySequence(String s, boolean isNa)
   {
     super("", s, 0, s.length());
-    this.isNa=isNa;
+    this.isNa = isNa;
   }
 
   /**
-   * clear the dbinary matrix 
+   * clear the dbinary matrix
+   * 
    * @return nores - dimension of sequence symbol encoding for this sequence
    */
   private int initMatrixGetNoRes()
   {
-    int nores=(isNa) ? ResidueProperties.maxNucleotideIndex : ResidueProperties.maxProteinIndex;
+    int nores = (isNa) ? ResidueProperties.maxNucleotideIndex
+            : ResidueProperties.maxProteinIndex;
     // Set all matrix to 0
     dbinary = new double[getSequence().length * nores];
 
@@ -71,32 +78,35 @@ public class BinarySequence extends Sequence
     }
     return nores;
   }
+
   private int[] getSymbolmatrix()
   {
-    return (isNa) ? ResidueProperties.nucleotideIndex : ResidueProperties.aaIndex;
+    return (isNa) ? ResidueProperties.nucleotideIndex
+            : ResidueProperties.aaIndex;
   }
+
   /**
    * DOCUMENT ME!
    */
   public void encode()
   {
-    int nores=initMatrixGetNoRes();
-    final int[] sindex=getSymbolmatrix();
+    int nores = initMatrixGetNoRes();
+    final int[] sindex = getSymbolmatrix();
     for (int i = 0; i < getSequence().length; i++)
     {
-      int aanum = nores-1;
+      int aanum = nores - 1;
 
       try
       {
         aanum = sindex[getCharAt(i)];
       } catch (NullPointerException e)
       {
-        aanum = nores-1;
+        aanum = nores - 1;
       }
 
       if (aanum >= nores)
       {
-        aanum = nores-1;
+        aanum = nores - 1;
       }
 
       dbinary[(i * nores) + aanum] = 1.0;
@@ -108,9 +118,10 @@ public class BinarySequence extends Sequence
    * 
    * @param matrix
    */
-  public void matrixEncode(final ScoreMatrix matrix) throws InvalidSequenceTypeException
+  public void matrixEncode(final ScoreMatrix matrix)
+          throws InvalidSequenceTypeException
   {
-    if (isNa!=matrix.isDNA())
+    if (isNa != matrix.isDNA())
     {
       throw new InvalidSequenceTypeException("matrix "
               + matrix.getClass().getCanonicalName()
@@ -131,21 +142,21 @@ public class BinarySequence extends Sequence
     // for (int i = 0; i < dbinary.length; i++) {
     // dbinary[i] = 0.0;
     // }
-    for (int i = 0,iSize=getSequence().length; i<iSize; i++)
+    for (int i = 0, iSize = getSequence().length; i < iSize; i++)
     {
-      int aanum = nores-1;
+      int aanum = nores - 1;
 
       try
       {
         aanum = aaIndex[getCharAt(i)];
       } catch (NullPointerException e)
       {
-        aanum = nores-1;
+        aanum = nores - 1;
       }
 
-      if (aanum >=nores)
+      if (aanum >= nores)
       {
-        aanum = nores-1;
+        aanum = nores - 1;
       }
 
       // Do the blosum^H^H^H^H^H score matrix summation thing