*/\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
+ 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
}\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
//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
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