-/* Jalview - a java multiple alignment editor\r
- * Copyright (C) 1998 Michele Clamp\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
*\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
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package jalview.schemes;\r
\r
-import jalview.datamodel.*;\r
-import java.util.*;\r
////////////////////////////////////////////\r
// This does nothing at all at the moment!!!!!!!!!!\r
// AW 15th Dec 2004\r
/////////////////////////////////////////\r
-public class Consensus {\r
-\r
+public class Consensus\r
+{\r
int[] mask;\r
double threshold;\r
+ String maskstr;\r
\r
- public Consensus(String m, double threshold)\r
+ public Consensus(String mask, double threshold)\r
{\r
- mask = setNums(m);\r
+ // this.id = id;\r
+ // this.mask = mask;\r
+ this.maskstr = mask;\r
+ setMask(mask);\r
this.threshold = threshold;\r
}\r
\r
+ public void setMask(String s)\r
+ {\r
+ this.mask = setNums(s);\r
+\r
+ // for (int i=0; i < mask.length; i++) {\r
+ // System.out.println(mask[i] + " " + ResidueProperties.aa[mask[i]]);\r
+ // }\r
+ }\r
\r
- public boolean isConserved(int[][] cons2,int col, int res,int size)\r
+ public boolean isConserved(int[][] cons2, int col, int size)\r
{\r
int tot = 0;\r
\r
-try{\r
- for (int i=0; i < mask.length; i++)\r
+ for (int i = 0; i < mask.length; i++)\r
+ {\r
tot += cons2[col][mask[i]];\r
-}catch(Exception ex)\r
-{ return true; }\r
+ }\r
\r
- if ((double)tot > threshold*size/100)\r
+ if ( (double) tot > ( (threshold * size) / 100))\r
+ {\r
return true;\r
+ }\r
\r
return false;\r
}\r
\r
int[] setNums(String s)\r
{\r
- int [] out = new int[s.length()];\r
+ int[] out = new int[s.length()];\r
int i = 0;\r
+\r
while (i < s.length())\r
{\r
- out[i] = ( (Integer) ResidueProperties.aaHash.get(s.substring(i, i + 1))).intValue();\r
+ out[i] = ( (Integer) ResidueProperties.aaHash.get(s.substring(i,\r
+ i + 1))).intValue();\r
i++;\r
}\r
+\r
return out;\r
}\r
-\r
-\r
}\r
-\r
-\r
-\r
-\r