deleteSequenceFeature

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

diff --git a/src/jalview/datamodel/BinarySequence.java b/src/jalview/datamodel/BinarySequence.java
index 89d3971..af10e1d 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
@@ -38,22 +38,9 @@ public class BinarySequence extends Sequence
      *\r
      * @param s DOCUMENT ME!\r
      */\r
-    public BinarySequence(SequenceI s)\r
+    public BinarySequence(String s)\r
     {\r
-        super(s.getName(), s.getSequence(), s.getStart(), s.getEnd());\r
-    }\r
-\r
-    /**\r
-     * Creates a new BinarySequence object.\r
-     *\r
-     * @param name DOCUMENT ME!\r
-     * @param sequence DOCUMENT ME!\r
-     * @param start DOCUMENT ME!\r
-     * @param end DOCUMENT ME!\r
-     */\r
-    public BinarySequence(String name, String sequence, int start, int end)\r
-    {\r
-        super(name, sequence, start, end);\r
+        super("", s, 0, s.length());\r
     }\r
 \r
     /**\r
@@ -77,9 +64,7 @@ public class BinarySequence extends Sequence
 \r
             try\r
             {\r
-                aanum = ((Integer) ResidueProperties.getAAHash().get(getSequence()\r
-                                                                         .substring(i,\r
-                            i + 1))).intValue();\r
+                aanum = ResidueProperties.aaIndex[getSequence().charAt(i)];\r
             }\r
             catch (NullPointerException e)\r
             {\r
@@ -114,9 +99,7 @@ public class BinarySequence extends Sequence
 \r
             try\r
             {\r
-                aanum = ((Integer) ResidueProperties.getAAHash().get(getSequence()\r
-                                                                         .substring(i,\r
-                            i + 1))).intValue();\r
+                aanum = ResidueProperties.aaIndex[getSequence().charAt(i)];\r
             }\r
             catch (NullPointerException e)\r
             {\r
@@ -168,13 +151,4 @@ public class BinarySequence extends Sequence
         return dbinary;\r
     }\r
 \r
-    /**\r
-     * DOCUMENT ME!\r
-     *\r
-     * @param rt DOCUMENT ME!\r
-     */\r
-    public static void printMemory(Runtime rt)\r
-    {\r
-        System.out.println("DEBUG: Free memory = " + rt.freeMemory()); // log.\r
-    }\r
 }\r