X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FBinarySequence.java;h=9d6f5e84f4e51885a75d86c74f1dddc3f32a4251;hb=a45774ee31d9f35d4eff46d54d7deab719afb092;hp=dffa1a6d88c2c5201983e40c6a30e9690797dd2a;hpb=e5127e5f27f02c8f328539eaac68eabfbee1d135;p=jalview.git

diff --git a/src/jalview/datamodel/BinarySequence.java b/src/jalview/datamodel/BinarySequence.java
index dffa1a6..9d6f5e8 100755
--- a/src/jalview/datamodel/BinarySequence.java
+++ b/src/jalview/datamodel/BinarySequence.java
@@ -1,109 +1,168 @@
-/* Jalview - a java multiple alignment editor
- * Copyright (C) 1998  Michele Clamp
- *
- * 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., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
- */
-package jalview.datamodel;
-
-import jalview.io.*;
-import jalview.analysis.PCA;
-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, 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;
+  }
+
+}