X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FConsensus.java;h=213621b36f436a27b9d875ca870b25d489ff9d3b;hb=59d682209891099d46b960509907c79e3fb276fe;hp=520196f532f20b7e130bb938eb93950b0185964a;hpb=c3c305755d392741176209a0274a47897ac4d8a8;p=jalview.git

diff --git a/src/jalview/schemes/Consensus.java b/src/jalview/schemes/Consensus.java
index 520196f..213621b 100755
--- a/src/jalview/schemes/Consensus.java
+++ b/src/jalview/schemes/Consensus.java
@@ -1,79 +1,94 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 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
- * 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.
- *
- * 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
- */
-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]]);
-    // }
-  }
-
-  public boolean isConserved(int[][] cons2, int col, int size)
-  {
-    int tot = 0;
-
-    for (int i = 0; i < mask.length; i++)
-    {
-      tot += cons2[col][mask[i]];
-    }
-
-    if ( (double) tot > ( (threshold * size) / 100))
-    {
-      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;
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, 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;
+  }
+}