/*\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
+ * Jalview - A Sequence Alignment Editor and Viewer\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
+ * 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.schemes;\r
\r
-\r
////////////////////////////////////////////\r
// This does nothing at all at the moment!!!!!!!!!!\r
// AW 15th Dec 2004\r
/////////////////////////////////////////\r
-public class Consensus {\r
- int[] mask;\r
- double threshold;\r
- String maskstr;\r
-\r
- public Consensus(String mask, double threshold) {\r
- // this.id = id;\r
- // this.mask = mask;\r
- this.maskstr = mask;\r
- setMask(mask);\r
- this.threshold = threshold;\r
- }\r
+public class Consensus\r
+{\r
+ int[] mask;\r
+ double threshold;\r
+ String maskstr;\r
\r
- public void setMask(String s) {\r
- this.mask = setNums(s);\r
+ public Consensus(String mask, double threshold)\r
+ {\r
+ // this.id = id;\r
+ // this.mask = mask;\r
+ this.maskstr = mask;\r
+ setMask(mask);\r
+ this.threshold = threshold;\r
+ }\r
\r
- // for (int i=0; i < mask.length; i++) {\r
- // System.out.println(mask[i] + " " + ResidueProperties.aa[mask[i]]);\r
- // }\r
- }\r
+ public void setMask(String s)\r
+ {\r
+ this.mask = setNums(s);\r
\r
- public boolean isConserved(int[][] cons2, int col, int size) {\r
- int tot = 0;\r
+ // for (int i=0; i < mask.length; i++) {\r
+ // System.out.println(mask[i] + " " + ResidueProperties.aa[mask[i]]);\r
+ // }\r
+ }\r
\r
- for (int i = 0; i < mask.length; i++)\r
- tot += cons2[col][mask[i]];\r
+ public boolean isConserved(int[][] cons2, int col, int size)\r
+ {\r
+ int tot = 0;\r
\r
- if ((double) tot > ((threshold * size) / 100)) {\r
- return true;\r
- }\r
+ for (int i = 0; i < mask.length; i++)\r
+ {\r
+ tot += cons2[col][mask[i]];\r
+ }\r
\r
- return false;\r
+ if ( (double) tot > ( (threshold * size) / 100))\r
+ {\r
+ return true;\r
}\r
\r
- int[] setNums(String s) {\r
- int[] out = new int[s.length()];\r
- int i = 0;\r
+ return false;\r
+ }\r
\r
- while (i < s.length()) {\r
- out[i] = ((Integer) ResidueProperties.aaHash.get(s.substring(i,\r
- i + 1))).intValue();\r
- i++;\r
- }\r
+ int[] setNums(String s)\r
+ {\r
+ int[] out = new int[s.length()];\r
+ int i = 0;\r
\r
- return out;\r
+ while (i < s.length())\r
+ {\r
+ out[i] = ResidueProperties.aaIndex[s.charAt(i)];\r
+ i++;\r
}\r
+\r
+ return out;\r
+ }\r
}\r