X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FBinarySequence.java;h=cea9de7ecec5c0095a40a0ccc7388f63067d525a;hb=bc7c2cf5500c5a4124a69ef8e7b1374d8997558f;hp=2b4ce6b47376754c363adc67df37fd374fe20b96;hpb=b2824493add6517beee16bf7dc9066642c9bd26e;p=jalview.git

diff --git a/src/jalview/datamodel/BinarySequence.java b/src/jalview/datamodel/BinarySequence.java
index 2b4ce6b..cea9de7 100755
--- 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 ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.analysis.scoremodels.ScoreMatrix;
+import jalview.schemes.ResidueProperties;
 
 /**
  * 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.
    * 
@@ -52,51 +57,52 @@ 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;
-    // Set all matrix to 0
-    dbinary = new double[getSequence().length * nores];
+    int nores = (isNa) ? ResidueProperties.maxNucleotideIndex
+            : ResidueProperties.maxProteinIndex;
+
+    dbinary = new double[getLength() * nores];
 
-    for (int i = 0; i < dbinary.length; i++)
-    {
-      dbinary[i] = 0.0;
-    }
     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();
-    for (int i = 0; i < getSequence().length; i++)
+    int nores = initMatrixGetNoRes();
+    final int[] sindex = getSymbolmatrix();
+    for (int i = 0; i < getLength(); 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;
@@ -106,46 +112,41 @@ public class BinarySequence extends Sequence
   /**
    * ancode using substitution matrix given in matrix
    * 
-   * @param matrix
+   * @param smtrx
    */
-  public void matrixEncode(final ScoreMatrix matrix) throws InvalidSequenceTypeException
+  public void matrixEncode(final ScoreMatrix smtrx)
+          throws InvalidSequenceTypeException
   {
-    if (isNa!=matrix.isDNA())
+    if (isNa != smtrx.isDNA())
     {
-      throw new InvalidSequenceTypeException("matrix "
-              + matrix.getClass().getCanonicalName()
-              + " is not a valid matrix for "
-              + (isNa ? "nucleotide" : "protein") + "sequences");
+      throw new InvalidSequenceTypeException(
+              "matrix " + smtrx.getClass().getCanonicalName()
+                      + " is not a valid matrix for "
+                      + (isNa ? "nucleotide" : "protein") + "sequences");
     }
-    matrixEncode(matrix.isDNA() ? ResidueProperties.nucleotideIndex
-            : ResidueProperties.aaIndex, matrix.getMatrix());
+    matrixEncode(smtrx.isDNA() ? ResidueProperties.nucleotideIndex
+            : ResidueProperties.aaIndex, smtrx.getMatrix());
   }
 
-  private void matrixEncode(final int[] aaIndex, final int[][] matrix)
+  private void matrixEncode(final int[] aaIndex, final float[][] matrix)
   {
-    // Set all matrix to 0
-    // dbinary = new double[getSequence().length * 21];
-
     int nores = initMatrixGetNoRes();
 
-    // 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 = getLength(); 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
@@ -168,7 +169,7 @@ public class BinarySequence extends Sequence
 
     for (int i = 0; i < binary.length; i++)
     {
-      out += (new Integer(binary[i])).toString();
+      out += (Integer.valueOf(binary[i])).toString();
 
       if (i < (binary.length - 1))
       {