X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FConsensus.java;h=af2be8da76686ee6358bfad2d02a57619b0eed14;hb=2de8acfae59aced665e4c37ad0f7dcc2ed68818e;hp=27c59066bca12a6f05b91bb8ba75f43993a318d8;hpb=99c58ee0ae2a848f982552e53feaf6d5cb9925e5;p=jalview.git

diff --git a/src/jalview/schemes/Consensus.java b/src/jalview/schemes/Consensus.java
index 27c5906..af2be8d 100755
--- a/src/jalview/schemes/Consensus.java
+++ b/src/jalview/schemes/Consensus.java
@@ -1,77 +1,95 @@
-/*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 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] = ( (Integer) ResidueProperties.aaHash.get(s.substring(i, i + 1))).intValue();
-      i++;
-
-    }
-
-    return out;
-  }
-
-
-}
-
-
-
-
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
+ * Copyright (C) 2009 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]]);
+    // }
+  }
+
+  /**
+   * @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;
+  }
+}