JAL-2089 patch broken merge to master for Release 2.10.0b1

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

diff --git a/src/jalview/schemes/Consensus.java b/src/jalview/schemes/Consensus.java
index 8ca0223..f0d1990 100755 (executable)
--- a/src/jalview/schemes/Consensus.java
+++ b/src/jalview/schemes/Consensus.java
@@ -1,72 +1,97 @@
-/*\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
-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
-    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
-\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
-\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
-\r
-        return false;\r
-    }\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
+/*
+ * 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;
+  }
+}