X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FBinarySequence.java;h=cea9de7ecec5c0095a40a0ccc7388f63067d525a;hb=9dabc02511e3a334a5749a504f57f69d6c9017bd;hp=ce969597976ad6c667c3b0e079f3f456f78da4ee;hpb=2de8acfae59aced665e4c37ad0f7dcc2ed68818e;p=jalview.git

diff --git a/src/jalview/datamodel/BinarySequence.java b/src/jalview/datamodel/BinarySequence.java
index ce96959..cea9de7 100755
--- a/src/jalview/datamodel/BinarySequence.java
+++ b/src/jalview/datamodel/BinarySequence.java
@@ -1,78 +1,108 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
- * 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 file is part of Jalview.
  * 
- * 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.
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * 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;
 
 /**
- * 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!
+   *          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()
   {
-    // Set all matrix to 0
-    dbinary = new double[getSequence().length * 21];
+    int nores = (isNa) ? ResidueProperties.maxNucleotideIndex
+            : ResidueProperties.maxProteinIndex;
 
-    int nores = 21;
+    dbinary = new double[getLength() * nores];
 
-    for (int i = 0; i < dbinary.length; i++)
-    {
-      dbinary[i] = 0.0;
-    }
+    return nores;
+  }
 
-    for (int i = 0; i < getSequence().length; i++)
+  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 < getLength(); 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;
@@ -82,52 +112,46 @@ public class BinarySequence extends Sequence
   /**
    * ancode using substitution matrix given in matrix
    * 
-   * @param matrix
-   */
-  public void matrixEncode(ScoreMatrix matrix)
-  {
-    matrixEncode(matrix.isDNA() ? ResidueProperties.nucleotideIndex
-            : ResidueProperties.aaIndex, matrix.getMatrix());
-  }
-
-  /**
-   * DOCUMENT ME!
+   * @param smtrx
    */
-  public void blosumEncode()
+  public void matrixEncode(final ScoreMatrix smtrx)
+          throws InvalidSequenceTypeException
   {
-    matrixEncode(ResidueProperties.aaIndex, ResidueProperties.getBLOSUM62());
+    if (isNa != smtrx.isDNA())
+    {
+      throw new InvalidSequenceTypeException(
+              "matrix " + smtrx.getClass().getCanonicalName()
+                      + " is not a valid matrix for "
+                      + (isNa ? "nucleotide" : "protein") + "sequences");
+    }
+    matrixEncode(smtrx.isDNA() ? ResidueProperties.nucleotideIndex
+            : ResidueProperties.aaIndex, smtrx.getMatrix());
   }
 
-  private void matrixEncode(int[] aaIndex, int[][] matrix)
+  private void matrixEncode(final int[] aaIndex, final float[][] matrix)
   {
-    // Set all matrix to 0
-    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 = getLength(); 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];
       }
@@ -145,7 +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))
       {