X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FBinarySequence.java;h=af10e1d180a37114726ace7c78888867c4f25d5c;hb=d587f1aa61946dc14f6f089cf1dc2a3116cfb773;hp=a351b04f18bbd219eb7e08a0ec65929c53548b13;hpb=588042b69abf8e60bcc950b24c283933c7dd422f;p=jalview.git

diff --git a/src/jalview/datamodel/BinarySequence.java b/src/jalview/datamodel/BinarySequence.java
index a351b04..af10e1d 100755
--- a/src/jalview/datamodel/BinarySequence.java
+++ b/src/jalview/datamodel/BinarySequence.java
@@ -1,6 +1,6 @@
 /*
 * Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+* Copyright (C) 2006 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
@@ -18,51 +18,61 @@
 */
 package jalview.datamodel;
 
-import jalview.analysis.PCA;
-
-import jalview.io.*;
-
-import jalview.jbgui.*;
-
 import jalview.schemes.*;
 
-import java.awt.*;
 
 
-public class BinarySequence extends Sequence {
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+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);
+    /**
+     * Creates a new BinarySequence object.
+     *
+     * @param s DOCUMENT ME!
+     */
+    public BinarySequence(String s)
+    {
+        super("", s, 0, s.length());
     }
 
-    public void encode() {
+    /**
+     * 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++) {
+        for (int i = 0; i < dbinary.length; i++)
+        {
             dbinary[i] = 0.0;
         }
 
-        for (int i = 0; i < getSequence().length(); i++) {
+        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) {
+            try
+            {
+                aanum = ResidueProperties.aaIndex[getSequence().charAt(i)];
+            }
+            catch (NullPointerException e)
+            {
                 aanum = 20;
             }
 
-            if (aanum > 20) {
+            if (aanum > 20)
+            {
                 aanum = 20;
             }
 
@@ -70,7 +80,11 @@ public class BinarySequence extends Sequence {
         }
     }
 
-    public void blosumEncode() {
+    /**
+     * DOCUMENT ME!
+     */
+    public void blosumEncode()
+    {
         // Set all matrix to 0
         dbinary = new double[getSequence().length() * 21];
 
@@ -79,35 +93,47 @@ public class BinarySequence extends Sequence {
         //for (int i = 0; i < dbinary.length; i++) {
         //  dbinary[i] = 0.0;
         //}
-        for (int i = 0; i < getSequence().length(); i++) {
+        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) {
+            try
+            {
+                aanum = ResidueProperties.aaIndex[getSequence().charAt(i)];
+            }
+            catch (NullPointerException e)
+            {
                 aanum = 20;
             }
 
-            if (aanum > 20) {
+            if (aanum > 20)
+            {
                 aanum = 20;
             }
 
             // Do the blosum thing
-            for (int j = 0; j < 20; j++) {
+            for (int j = 0; j < 20; j++)
+            {
                 dbinary[(i * nores) + j] = ResidueProperties.getBLOSUM62()[aanum][j];
             }
         }
     }
 
-    public String toBinaryString() {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public String toBinaryString()
+    {
         String out = "";
 
-        for (int i = 0; i < binary.length; i++) {
+        for (int i = 0; i < binary.length; i++)
+        {
             out += (new Integer(binary[i])).toString();
 
-            if (i < (binary.length - 1)) {
+            if (i < (binary.length - 1))
+            {
                 out += " ";
             }
         }
@@ -115,11 +141,14 @@ public class BinarySequence extends Sequence {
         return out;
     }
 
-    public double[] getDBinary() {
+    /**
+     * 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.
-    }
 }