X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FBinarySequence.java;h=04cfdc9ab712a60b21e51a242514802ff0107e3b;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=a351b04f18bbd219eb7e08a0ec65929c53548b13;hpb=588042b69abf8e60bcc950b24c283933c7dd422f;p=jalview.git

diff --git a/src/jalview/datamodel/BinarySequence.java b/src/jalview/datamodel/BinarySequence.java
index a351b04..04cfdc9 100755
--- a/src/jalview/datamodel/BinarySequence.java
+++ b/src/jalview/datamodel/BinarySequence.java
@@ -1,125 +1,168 @@
-/*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 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
-*/
-package jalview.datamodel;
-
-import jalview.analysis.PCA;
-
-import jalview.io.*;
-
-import jalview.jbgui.*;
-
-import jalview.schemes.*;
-
-import java.awt.*;
-
-
-public class BinarySequence extends Sequence {
-    int[] binary;
-    double[] dbinary;
-
-    public BinarySequence(SequenceI s) {
-        super(s.getName(), s.getSequence(), s.getStart(), s.getEnd());
-    }
-
-    public BinarySequence(String name, String sequence, int start, int end) {
-        super(name, sequence, start, end);
-    }
-
-    public void encode() {
-        // Set all matrix to 0
-        dbinary = new double[getSequence().length() * 21];
-
-        int nores = 21;
-
-        for (int i = 0; i < dbinary.length; i++) {
-            dbinary[i] = 0.0;
-        }
-
-        for (int i = 0; i < getSequence().length(); i++) {
-            int aanum = 20;
-
-            try {
-                aanum = ((Integer) ResidueProperties.getAAHash().get(getSequence()
-                                                                         .substring(i,
-                            i + 1))).intValue();
-            } catch (NullPointerException e) {
-                aanum = 20;
-            }
-
-            if (aanum > 20) {
-                aanum = 20;
-            }
-
-            dbinary[(i * nores) + aanum] = 1.0;
-        }
-    }
-
-    public void blosumEncode() {
-        // Set all matrix to 0
-        dbinary = new double[getSequence().length() * 21];
-
-        int nores = 21;
-
-        //for (int i = 0; i < dbinary.length; i++) {
-        //  dbinary[i] = 0.0;
-        //}
-        for (int i = 0; i < getSequence().length(); i++) {
-            int aanum = 20;
-
-            try {
-                aanum = ((Integer) ResidueProperties.getAAHash().get(getSequence()
-                                                                         .substring(i,
-                            i + 1))).intValue();
-            } catch (NullPointerException e) {
-                aanum = 20;
-            }
-
-            if (aanum > 20) {
-                aanum = 20;
-            }
-
-            // Do the blosum thing
-            for (int j = 0; j < 20; j++) {
-                dbinary[(i * nores) + j] = ResidueProperties.getBLOSUM62()[aanum][j];
-            }
-        }
-    }
-
-    public String toBinaryString() {
-        String out = "";
-
-        for (int i = 0; i < binary.length; i++) {
-            out += (new Integer(binary[i])).toString();
-
-            if (i < (binary.length - 1)) {
-                out += " ";
-            }
-        }
-
-        return out;
-    }
-
-    public double[] getDBinary() {
-        return dbinary;
-    }
-
-    public static void printMemory(Runtime rt) {
-        System.out.println("DEBUG: Free memory = " + rt.freeMemory()); // log.
-    }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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;
+
+import jalview.schemes.*;
+
+/**
+ * DOCUMENT ME!
+ * 
+ * @author $author$
+ * @version $Revision$
+ */
+public class BinarySequence extends Sequence
+{
+  int[] binary;
+
+  double[] dbinary;
+
+  /**
+   * Creates a new BinarySequence object.
+   * 
+   * @param s
+   *          DOCUMENT ME!
+   */
+  public BinarySequence(String s)
+  {
+    super("", s, 0, s.length());
+  }
+
+  /**
+   * DOCUMENT ME!
+   */
+  public void encode()
+  {
+    // Set all matrix to 0
+    dbinary = new double[getSequence().length * 21];
+
+    int nores = 21;
+
+    for (int i = 0; i < dbinary.length; i++)
+    {
+      dbinary[i] = 0.0;
+    }
+
+    for (int i = 0; i < getSequence().length; i++)
+    {
+      int aanum = 20;
+
+      try
+      {
+        aanum = ResidueProperties.aaIndex[getCharAt(i)];
+      } catch (NullPointerException e)
+      {
+        aanum = 20;
+      }
+
+      if (aanum > 20)
+      {
+        aanum = 20;
+      }
+
+      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());
+  }
+
+  /**
+   * DOCUMENT ME!
+   */
+  public void blosumEncode()
+  {
+    matrixEncode(ResidueProperties.aaIndex, ResidueProperties.getBLOSUM62());
+  }
+
+  private void matrixEncode(int[] aaIndex, int[][] matrix)
+  {
+    // Set all matrix to 0
+    dbinary = new double[getSequence().length * 21];
+
+    int nores = 21;
+
+    // for (int i = 0; i < dbinary.length; i++) {
+    // dbinary[i] = 0.0;
+    // }
+    for (int i = 0; i < getSequence().length; i++)
+    {
+      int aanum = 20;
+
+      try
+      {
+        aanum = aaIndex[getCharAt(i)];
+      } catch (NullPointerException e)
+      {
+        aanum = 20;
+      }
+
+      if (aanum > 20)
+      {
+        aanum = 20;
+      }
+
+      // Do the blosum thing
+
+      for (int j = 0; j < 20; j++)
+      {
+        dbinary[(i * nores) + j] = matrix[aanum][j];
+      }
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public String toBinaryString()
+  {
+    String out = "";
+
+    for (int i = 0; i < binary.length; i++)
+    {
+      out += (new Integer(binary[i])).toString();
+
+      if (i < (binary.length - 1))
+      {
+        out += " ";
+      }
+    }
+
+    return out;
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public double[] getDBinary()
+  {
+    return dbinary;
+  }
+
+}