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

diff --git a/src/jalview/datamodel/BinarySequence.java b/src/jalview/datamodel/BinarySequence.java
index a351b04..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
@@ -18,51 +18,61 @@
 */\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
-public class BinarySequence extends Sequence {\r
+/**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @author $author$\r
+ * @version $Revision$\r
+ */\r
+public class BinarySequence extends Sequence\r
+{\r
     int[] binary;\r
     double[] dbinary;\r
 \r
-    public BinarySequence(SequenceI s) {\r
-        super(s.getName(), s.getSequence(), s.getStart(), s.getEnd());\r
-    }\r
-\r
-    public BinarySequence(String name, String sequence, int start, int end) {\r
-        super(name, sequence, start, end);\r
+    /**\r
+     * Creates a new BinarySequence object.\r
+     *\r
+     * @param s DOCUMENT ME!\r
+     */\r
+    public BinarySequence(String s)\r
+    {\r
+        super("", s, 0, s.length());\r
     }\r
 \r
-    public void encode() {\r
+    /**\r
+     * DOCUMENT ME!\r
+     */\r
+    public void encode()\r
+    {\r
         // Set all matrix to 0\r
         dbinary = new double[getSequence().length() * 21];\r
 \r
         int nores = 21;\r
 \r
-        for (int i = 0; i < dbinary.length; i++) {\r
+        for (int i = 0; i < dbinary.length; i++)\r
+        {\r
             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
-                aanum = ((Integer) ResidueProperties.getAAHash().get(getSequence()\r
-                                                                         .substring(i,\r
-                            i + 1))).intValue();\r
-            } catch (NullPointerException e) {\r
+            try\r
+            {\r
+                aanum = ResidueProperties.aaIndex[getSequence().charAt(i)];\r
+            }\r
+            catch (NullPointerException e)\r
+            {\r
                 aanum = 20;\r
             }\r
 \r
-            if (aanum > 20) {\r
+            if (aanum > 20)\r
+            {\r
                 aanum = 20;\r
             }\r
 \r
@@ -70,7 +80,11 @@ public class BinarySequence extends Sequence {
         }\r
     }\r
 \r
-    public void blosumEncode() {\r
+    /**\r
+     * DOCUMENT ME!\r
+     */\r
+    public void blosumEncode()\r
+    {\r
         // Set all matrix to 0\r
         dbinary = new double[getSequence().length() * 21];\r
 \r
@@ -79,35 +93,47 @@ public class BinarySequence extends Sequence {
         //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
-                aanum = ((Integer) ResidueProperties.getAAHash().get(getSequence()\r
-                                                                         .substring(i,\r
-                            i + 1))).intValue();\r
-            } catch (NullPointerException e) {\r
+            try\r
+            {\r
+                aanum = ResidueProperties.aaIndex[getSequence().charAt(i)];\r
+            }\r
+            catch (NullPointerException e)\r
+            {\r
                 aanum = 20;\r
             }\r
 \r
-            if (aanum > 20) {\r
+            if (aanum > 20)\r
+            {\r
                 aanum = 20;\r
             }\r
 \r
             // Do the blosum thing\r
-            for (int j = 0; j < 20; j++) {\r
+            for (int j = 0; j < 20; j++)\r
+            {\r
                 dbinary[(i * nores) + j] = ResidueProperties.getBLOSUM62()[aanum][j];\r
             }\r
         }\r
     }\r
 \r
-    public String toBinaryString() {\r
+    /**\r
+     * DOCUMENT ME!\r
+     *\r
+     * @return DOCUMENT ME!\r
+     */\r
+    public String toBinaryString()\r
+    {\r
         String out = "";\r
 \r
-        for (int i = 0; i < binary.length; i++) {\r
+        for (int i = 0; i < binary.length; i++)\r
+        {\r
             out += (new Integer(binary[i])).toString();\r
 \r
-            if (i < (binary.length - 1)) {\r
+            if (i < (binary.length - 1))\r
+            {\r
                 out += " ";\r
             }\r
         }\r
@@ -115,11 +141,14 @@ public class BinarySequence extends Sequence {
         return out;\r
     }\r
 \r
-    public double[] getDBinary() {\r
+    /**\r
+     * DOCUMENT ME!\r
+     *\r
+     * @return DOCUMENT ME!\r
+     */\r
+    public double[] getDBinary()\r
+    {\r
         return dbinary;\r
     }\r
 \r
-    public static void printMemory(Runtime rt) {\r
-        System.out.println("DEBUG: Free memory = " + rt.freeMemory()); // log.\r
-    }\r
 }\r