/*\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
*/\r
package jalview.datamodel;\r
\r
-import jalview.analysis.PCA;\r
-\r
-import jalview.io.*;\r
-\r
-import jalview.jbgui.*;\r
-\r
import jalview.schemes.*;\r
\r
-import java.awt.*;\r
\r
\r
/**\r
*\r
* @param s DOCUMENT ME!\r
*/\r
- public BinarySequence(SequenceI 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
+ public BinarySequence(String s)\r
{\r
- super(name, sequence, start, end);\r
+ super("", s, 0, s.length());\r
}\r
\r
/**\r
\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
\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
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