Set startRes 0 for switch to wrap view

[jalview.git] / src / jalview / datamodel / BinarySequence.java

diff --git a/src/jalview/datamodel/BinarySequence.java b/src/jalview/datamodel/BinarySequence.java
index 7d03404..49e3543 100755 (executable)
--- a/src/jalview/datamodel/BinarySequence.java
+++ b/src/jalview/datamodel/BinarySequence.java
@@ -1,6 +1,6 @@
 /*\r
 * Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
 *\r
 * This program is free software; you can redistribute it and/or\r
 * modify it under the terms of the GNU General Public License\r
@@ -49,7 +49,7 @@ public class BinarySequence extends Sequence
     public void encode()\r
     {\r
         // Set all matrix to 0\r
-        dbinary = new double[getSequence().length() * 21];\r
+        dbinary = new double[getSequence().length * 21];\r
 \r
         int nores = 21;\r
 \r
@@ -58,15 +58,13 @@ public class BinarySequence extends Sequence
             dbinary[i] = 0.0;\r
         }\r
 \r
-        for (int i = 0; i < getSequence().length(); i++)\r
+        for (int i = 0; i < getSequence().length; i++)\r
         {\r
             int aanum = 20;\r
 \r
             try\r
             {\r
-                aanum = ((Integer) ResidueProperties.getAAHash().get(getSequence()\r
-                                                                         .substring(i,\r
-                            i + 1))).intValue();\r
+                aanum = ResidueProperties.aaIndex[getCharAt(i)];\r
             }\r
             catch (NullPointerException e)\r
             {\r
@@ -88,22 +86,20 @@ public class BinarySequence extends Sequence
     public void blosumEncode()\r
     {\r
         // Set all matrix to 0\r
-        dbinary = new double[getSequence().length() * 21];\r
+        dbinary = new double[getSequence().length * 21];\r
 \r
         int nores = 21;\r
 \r
         //for (int i = 0; i < dbinary.length; i++) {\r
         //  dbinary[i] = 0.0;\r
         //}\r
-        for (int i = 0; i < getSequence().length(); i++)\r
+        for (int i = 0; i < getSequence().length; i++)\r
         {\r
             int aanum = 20;\r
 \r
             try\r
             {\r
-                aanum = ((Integer) ResidueProperties.getAAHash().get(getSequence()\r
-                                                                         .substring(i,\r
-                            i + 1))).intValue();\r
+                aanum = ResidueProperties.aaIndex[getCharAt(i)];\r
             }\r
             catch (NullPointerException e)\r
             {\r