JAL-1894 update year/version in copyright

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

diff --git a/src/jalview/datamodel/BinarySequence.java b/src/jalview/datamodel/BinarySequence.java
index dd4bb60..ceecb74 100755 (executable)
--- a/src/jalview/datamodel/BinarySequence.java
+++ b/src/jalview/datamodel/BinarySequence.java
@@ -1,77 +1,112 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
+ * 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;
 
 /**
- * DOCUMENT ME!
+ * Encode a sequence as a numeric vector using either classic residue binary
+ * encoding or convolved with residue substitution matrix.
  * 
  * @author $author$
  * @version $Revision$
  */
 public class BinarySequence extends Sequence
 {
+  public class InvalidSequenceTypeException extends Exception
+  {
+
+    public InvalidSequenceTypeException(String string)
+    {
+      super(string);
+    }
+
+  }
+
   int[] binary;
 
   double[] dbinary;
 
+  boolean isNa = false;
+
   /**
    * Creates a new BinarySequence object.
    * 
    * @param s
    *          DOCUMENT ME!
    */
-  public BinarySequence(String s)
+  public BinarySequence(String s, boolean isNa)
   {
     super("", s, 0, s.length());
+    this.isNa = isNa;
   }
 
   /**
-   * DOCUMENT ME!
+   * clear the dbinary matrix
+   * 
+   * @return nores - dimension of sequence symbol encoding for this sequence
    */
-  public void encode()
+  private int initMatrixGetNoRes()
   {
+    int nores = (isNa) ? ResidueProperties.maxNucleotideIndex
+            : ResidueProperties.maxProteinIndex;
     // Set all matrix to 0
-    dbinary = new double[getSequence().length * 21];
-
-    int nores = 21;
+    dbinary = new double[getSequence().length * nores];
 
     for (int i = 0; i < dbinary.length; i++)
     {
       dbinary[i] = 0.0;
     }
+    return nores;
+  }
 
+  private int[] getSymbolmatrix()
+  {
+    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 aanum = 20;
+      int aanum = nores - 1;
 
       try
       {
-        aanum = ResidueProperties.aaIndex[getCharAt(i)];
+        aanum = sindex[getCharAt(i)];
       } catch (NullPointerException e)
       {
-        aanum = 20;
+        aanum = nores - 1;
       }
 
-      if (aanum > 20)
+      if (aanum >= nores)
       {
-        aanum = 20;
+        aanum = nores - 1;
       }
 
       dbinary[(i * nores) + aanum] = 1.0;
@@ -83,50 +118,50 @@ public class BinarySequence extends Sequence
    * 
    * @param matrix
    */
-  public void matrixEncode(ScoreMatrix matrix)
+  public void matrixEncode(final ScoreMatrix matrix)
+          throws InvalidSequenceTypeException
   {
+    if (isNa != matrix.isDNA())
+    {
+      throw new InvalidSequenceTypeException("matrix "
+              + matrix.getClass().getCanonicalName()
+              + " is not a valid matrix for "
+              + (isNa ? "nucleotide" : "protein") + "sequences");
+    }
     matrixEncode(matrix.isDNA() ? ResidueProperties.nucleotideIndex
             : ResidueProperties.aaIndex, matrix.getMatrix());
   }
 
-  /**
-   * DOCUMENT ME!
-   */
-  public void blosumEncode()
-  {
-    matrixEncode(ResidueProperties.aaIndex, ResidueProperties.getBLOSUM62());
-  }
-
-  private void matrixEncode(int[] aaIndex, int[][] matrix)
+  private void matrixEncode(final int[] aaIndex, final int[][] matrix)
   {
     // Set all matrix to 0
-    dbinary = new double[getSequence().length * 21];
+    // dbinary = new double[getSequence().length * 21];
 
-    int nores = 21;
+    int nores = initMatrixGetNoRes();
 
     // for (int i = 0; i < dbinary.length; i++) {
     // dbinary[i] = 0.0;
     // }
-    for (int i = 0; i < getSequence().length; i++)
+    for (int i = 0, iSize = getSequence().length; i < iSize; i++)
     {
-      int aanum = 20;
+      int aanum = nores - 1;
 
       try
       {
         aanum = aaIndex[getCharAt(i)];
       } catch (NullPointerException e)
       {
-        aanum = 20;
+        aanum = nores - 1;
       }
 
-      if (aanum > 20)
+      if (aanum >= nores)
       {
-        aanum = 20;
+        aanum = nores - 1;
       }
 
-      // Do the blosum thing
+      // Do the blosum^H^H^H^H^H score matrix summation thing
 
-      for (int j = 0; j < 20; j++)
+      for (int j = 0; j < nores; j++)
       {
         dbinary[(i * nores) + j] = matrix[aanum][j];
       }