-/*\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
-\r
-package jalview.schemes;\r
-\r
-////////////////////////////////////////////\r
-// This does nothing at all at the moment!!!!!!!!!!\r
-// AW 15th Dec 2004\r
-/////////////////////////////////////////\r
-public class Consensus {\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
- this.maskstr = mask;\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
-\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
-\r
- if ( (double) tot > threshold * size / 100)\r
- return true;\r
-\r
- return false;\r
- }\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
-\r
- }\r
-\r
- return out;\r
- }\r
-\r
-\r
-}\r
-\r
-\r
-\r
-\r
+/*
+ * 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.
+ *
+ * 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 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.maskstr = mask;
+ setMask(mask);
+ this.threshold = threshold;
+ }
+
+ public void setMask(String s)
+ {
+ this.mask = setNums(s);
+
+ // 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
+ */
+ public boolean isConserved(int[][] cons2, int col, int size)
+ {
+ return isConserved(cons2, col, size, true);
+ }
+
+ public boolean isConserved(int[][] cons2, int col, int size,
+ boolean includeGaps)
+ {
+ int tot = 0;
+ if (!includeGaps)
+ {
+ 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))
+ {
+ // System.out.println("True conserved "+tot+" from "+threshold+" out of
+ // "+size+" : "+maskstr);
+ return true;
+ }
+
+ return false;
+ }
+
+ int[] setNums(String s)
+ {
+ int[] out = new int[s.length()];
+ int i = 0;
+
+ while (i < s.length())
+ {
+ out[i] = ResidueProperties.aaIndex[s.charAt(i)];
+ i++;
+ }
+
+ return out;
+ }
+}