apply version 2.7 copyright

[jalview.git] / src / jalview / schemes / Consensus.java

diff --git a/src/jalview/schemes/Consensus.java b/src/jalview/schemes/Consensus.java
index 7b0dbbb..0c010d5 100755 (executable)
--- a/src/jalview/schemes/Consensus.java
+++ b/src/jalview/schemes/Consensus.java
@@ -1,72 +1,94 @@
-/* Jalview - a java multiple alignment editor\r
- * Copyright (C) 1998  Michele Clamp\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., 59 Temple Place - Suite 330, Boston, MA  02111-1307, 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
-  int[] mask;\r
-  double threshold;\r
-\r
-  public Consensus(String m, double threshold)\r
-  {\r
-    mask = setNums(m);\r
-    this.threshold = threshold;\r
-  }\r
-\r
-\r
-  public boolean isConserved(int[][] cons2,int col, int res,int size)\r
-  {\r
-    int tot = 0;\r
-\r
-try{\r
-    for (int i=0; i < mask.length; i++)\r
-      tot += cons2[col][mask[i]];\r
-}catch(Exception ex)\r
-{ return true; }\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
-    return out;\r
-  }\r
-\r
-\r
-}\r
-\r
-\r
-\r
-\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * 
+ * 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/>.
+ */
+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;
+  }
+}