X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FBinarySequence.java;h=89d39716ba5dc3d4c54a89f4b41a091be0685c91;hb=0966c1ef3ea179ff8fbe7ced753c1dfc0d4fcb0a;hp=dffa1a6d88c2c5201983e40c6a30e9690797dd2a;hpb=e5127e5f27f02c8f328539eaac68eabfbee1d135;p=jalview.git

diff --git a/src/jalview/datamodel/BinarySequence.java b/src/jalview/datamodel/BinarySequence.java
index dffa1a6..89d3971 100755
--- a/src/jalview/datamodel/BinarySequence.java
+++ b/src/jalview/datamodel/BinarySequence.java
@@ -1,109 +1,180 @@
-/* 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.
- */
+/*
+* 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.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;
+/**
+ * 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(SequenceI s)
+    {
+        super(s.getName(), s.getSequence(), s.getStart(), s.getEnd());
     }
 
-    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;
+    /**
+     * Creates a new BinarySequence object.
+     *
+     * @param name DOCUMENT ME!
+     * @param sequence DOCUMENT ME!
+     * @param start DOCUMENT ME!
+     * @param end DOCUMENT ME!
+     */
+    public BinarySequence(String name, String sequence, int start, int end)
+    {
+        super(name, sequence, start, end);
+    }
 
+    /**
+     * 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 = ((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];
-      }
 
+    /**
+     * DOCUMENT ME!
+     */
+    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 += " ";
-      }
+
+    /**
+     * 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;
     }
-    return out;
-  }
 
-  public double[] getDBinary() {
-    return dbinary;
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public double[] getDBinary()
+    {
+        return dbinary;
+    }
 
-  public static void printMemory(Runtime rt) {
-    System.out.println("DEBUG: Free memory = " + rt.freeMemory()); // log.
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param rt DOCUMENT ME!
+     */
+    public static void printMemory(Runtime rt)
+    {
+        System.out.println("DEBUG: Free memory = " + rt.freeMemory()); // log.
+    }
 }