Formatting changes

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

diff --git a/src/jalview/datamodel/BinarySequence.java b/src/jalview/datamodel/BinarySequence.java
index a351b04..3cc6910 100755 (executable)
--- a/src/jalview/datamodel/BinarySequence.java
+++ b/src/jalview/datamodel/BinarySequence.java
@@ -29,40 +29,72 @@ import jalview.schemes.*;
 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
+    /**\r
+     * Creates a new BinarySequence object.\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
-    public BinarySequence(String name, String sequence, int start, int end) {\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
     }\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
+            try\r
+            {\r
                 aanum = ((Integer) ResidueProperties.getAAHash().get(getSequence()\r
                                                                          .substring(i,\r
                             i + 1))).intValue();\r
-            } catch (NullPointerException e) {\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 +102,11 @@ 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 +115,49 @@ 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
+            try\r
+            {\r
                 aanum = ((Integer) ResidueProperties.getAAHash().get(getSequence()\r
                                                                          .substring(i,\r
                             i + 1))).intValue();\r
-            } catch (NullPointerException e) {\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 +165,23 @@ 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
+    /**\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