* 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
-\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
- 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
+ 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
+ setMask(mask);\r
+ this.threshold = threshold;\r
+ }\r
\r
- public void setMask(String s) {\r
- this.mask = setNums(s);\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
+ 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
- tot += cons2[col][mask[i]];\r
+ // for (int i=0; i < mask.length; i++) {\r
+ // System.out.println(mask[i] + " " + ResidueProperties.aa[mask[i]]);\r
+ // }\r
+ }\r
\r
- if ( (double) tot > threshold * size / 100)\r
- return true;\r
+ public boolean isConserved(int[][] cons2, int col, int size) {\r
+ int tot = 0;\r
\r
- return false;\r
- }\r
+ for (int i = 0; i < mask.length; i++)\r
+ tot += cons2[col][mask[i]];\r
\r
- int[] setNums(String s)\r
- {\r
- int [] out = new int[s.length()];\r
- int i = 0;\r
- while (i < s.length())\r
- {\r
- out[i] = ( (Integer) ResidueProperties.aaHash.get(s.substring(i, i + 1))).intValue();\r
- i++;\r
+ if ((double) tot > ((threshold * size) / 100)) {\r
+ return true;\r
+ }\r
\r
+ return false;\r
}\r
\r
- return out;\r
- }\r
+ int[] setNums(String s) {\r
+ int[] out = new int[s.length()];\r
+ int i = 0;\r
\r
+ while (i < s.length()) {\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