X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FBinarySequence.java;h=49e35431f060805faf6fc6dc0a056b30ce3da8e3;hb=c766c1829042b039ea2ff56fc05f4a0100c2a73d;hp=7d034041258e80654a0721825f290d1ac572946a;hpb=b8b5c2410e8814caf24d216545f2266c8854f963;p=jalview.git

diff --git a/src/jalview/datamodel/BinarySequence.java b/src/jalview/datamodel/BinarySequence.java
index 7d03404..49e3543 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
@@ -49,7 +49,7 @@ public class BinarySequence extends Sequence
     public void encode()
     {
         // Set all matrix to 0
-        dbinary = new double[getSequence().length() * 21];
+        dbinary = new double[getSequence().length * 21];
 
         int nores = 21;
 
@@ -58,15 +58,13 @@ public class BinarySequence extends Sequence
             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();
+                aanum = ResidueProperties.aaIndex[getCharAt(i)];
             }
             catch (NullPointerException e)
             {
@@ -88,22 +86,20 @@ public class BinarySequence extends Sequence
     public void blosumEncode()
     {
         // Set all matrix to 0
-        dbinary = new double[getSequence().length() * 21];
+        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++)
+        for (int i = 0; i < getSequence().length; i++)
         {
             int aanum = 20;
 
             try
             {
-                aanum = ((Integer) ResidueProperties.getAAHash().get(getSequence()
-                                                                         .substring(i,
-                            i + 1))).intValue();
+                aanum = ResidueProperties.aaIndex[getCharAt(i)];
             }
             catch (NullPointerException e)
             {