-/* Jalview - a java multiple alignment editor\r
- * Copyright (C) 1998 Michele Clamp\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
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
- *\r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * GNU General Public License for more details.\r
- *\r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.\r
- */\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+* as published by the Free Software Foundation; either version 2\r
+* of the License, or (at your option) any later version.\r
+*\r
+* This program is distributed in the hope that it will be useful,\r
+* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+* GNU General Public License for more details.\r
+*\r
+* You should have received a copy of the GNU General Public License\r
+* along with this program; if not, write to the Free Software\r
+* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+*/\r
package jalview.datamodel;\r
\r
-import jalview.io.*;\r
-import jalview.analysis.PCA;\r
-import jalview.jbgui.*;\r
import jalview.schemes.*;\r
\r
-import java.awt.*;\r
-\r
-public class BinarySequence extends Sequence {\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
\r
- public void encode() {\r
- // Set all matrix to 0\r
- dbinary = new double[getSequence().length() * 21];\r
- int nores = 21;\r
- for (int i = 0; i < dbinary.length; i++) {\r
- dbinary[i] = 0.0;\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
+ /**\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
- for (int i=0; i < getSequence().length(); i++ ) {\r
- int aanum = 20;\r
- try {\r
- aanum = ((Integer)ResidueProperties.getAAHash().get(getSequence().substring(i,i+1))).intValue();\r
- } catch (NullPointerException e) {\r
- aanum = 20;\r
- }\r
- if (aanum > 20) {\r
- aanum = 20;\r
- }\r
-\r
- dbinary[i* nores + aanum] = 1.0;\r
-\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
+ {\r
+ dbinary[i] = 0.0;\r
+ }\r
+\r
+ for (int i = 0; i < getSequence().length(); i++)\r
+ {\r
+ int aanum = 20;\r
+\r
+ try\r
+ {\r
+ aanum = ((Integer) ResidueProperties.getAAHash().get(getSequence()\r
+ .substring(i,\r
+ i + 1))).intValue();\r
+ }\r
+ catch (NullPointerException e)\r
+ {\r
+ aanum = 20;\r
+ }\r
+\r
+ if (aanum > 20)\r
+ {\r
+ aanum = 20;\r
+ }\r
+\r
+ dbinary[(i * nores) + aanum] = 1.0;\r
+ }\r
}\r
- }\r
-\r
- public void blosumEncode() {\r
-\r
- // Set all matrix to 0\r
- dbinary = new double[getSequence().length() * 21];\r
- int nores = 21;\r
- //for (int i = 0; i < dbinary.length; i++) {\r
- // dbinary[i] = 0.0;\r
- //}\r
-\r
- for (int i=0; i < getSequence().length(); i++ ) {\r
- int aanum = 20;\r
- try {\r
- aanum = ((Integer)ResidueProperties.getAAHash().get(getSequence().substring(i,i+1))).intValue();\r
- } catch (NullPointerException e) {\r
- aanum = 20;\r
- }\r
- if (aanum > 20) {\r
- aanum = 20;\r
- }\r
-\r
- // Do the blosum thing\r
- for (int j = 0;j < 20;j++) {\r
- dbinary[i * nores + j] = ResidueProperties.getBLOSUM62()[aanum][j];\r
- }\r
\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
+ int nores = 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
+ {\r
+ int aanum = 20;\r
+\r
+ try\r
+ {\r
+ aanum = ((Integer) ResidueProperties.getAAHash().get(getSequence()\r
+ .substring(i,\r
+ i + 1))).intValue();\r
+ }\r
+ catch (NullPointerException e)\r
+ {\r
+ aanum = 20;\r
+ }\r
+\r
+ if (aanum > 20)\r
+ {\r
+ aanum = 20;\r
+ }\r
+\r
+ // Do the blosum thing\r
+ for (int j = 0; j < 20; j++)\r
+ {\r
+ dbinary[(i * nores) + j] = ResidueProperties.getBLOSUM62()[aanum][j];\r
+ }\r
+ }\r
}\r
- }\r
-\r
- public String toBinaryString() {\r
- String out = "";\r
- for (int i=0; i < binary.length;i++) {\r
- out += (new Integer(binary[i])).toString();\r
- if (i < binary.length-1) {\r
- out += " ";\r
- }\r
+\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
+ {\r
+ out += (new Integer(binary[i])).toString();\r
+\r
+ if (i < (binary.length - 1))\r
+ {\r
+ out += " ";\r
+ }\r
+ }\r
+\r
+ return out;\r
}\r
- return out;\r
- }\r
\r
- public double[] getDBinary() {\r
- return dbinary;\r
- }\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
git://source.jalview.org / jalview.git / blobdiff