/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
* of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
* You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemes;
-////////////////////////////////////////////
+// //////////////////////////////////////////
// This does nothing at all at the moment!!!!!!!!!!
// AW 15th Dec 2004
-/////////////////////////////////////////
+// ///////////////////////////////////////
public class Consensus
{
int[] mask;
+
double threshold;
+
String maskstr;
public Consensus(String mask, double threshold)
{
// this.id = id;
- // this.mask = mask;
+ // this.mask = mask;
this.maskstr = mask;
setMask(mask);
this.threshold = threshold;
{
this.mask = setNums(s);
- // for (int i=0; i < mask.length; i++) {
- // System.out.println(mask[i] + " " + ResidueProperties.aa[mask[i]]);
+ // for (int i=0; i < mask.length; i++) {
+ // System.out.println(mask[i] + " " + ResidueProperties.aa[mask[i]]);
// }
}
/**
* @deprecated Use {@link #isConserved(int[][],int,int,boolean)} instead
*/
+ @Deprecated
public boolean isConserved(int[][] cons2, int col, int size)
{
+ System.out.println("DEPRECATED!!!!");
return isConserved(cons2, col, size, true);
}
- public boolean isConserved(int[][] cons2, int col, int size, boolean includeGaps)
+ public boolean isConserved(int[][] cons2, int col, int size,
+ boolean includeGaps)
{
int tot = 0;
if (!includeGaps)
{
- size -= cons2[col][cons2[col].length-1];
+ size -= cons2[col][cons2[col].length - 1];
}
for (int i = 0; i < mask.length; i++)
{
tot += cons2[col][mask[i]];
}
- if ( (double) tot > ( (threshold * size) / 100))
+ if (tot > ((threshold * size) / 100))
{
- // System.out.println("True conserved "+tot+" from "+threshold+" out of "+size+" : "+maskstr);
+ // System.out.println("True conserved "+tot+" from "+threshold+" out of
+ // "+size+" : "+maskstr);
return true;
}