JAL-1620 version bump and release notes

[jalview.git] / src / jalview / util / Comparison.java

diff --git a/src/jalview/util/Comparison.java b/src/jalview/util/Comparison.java
old mode 100755 (executable)
new mode 100644 (file)
index 32e049d..9b2edba
--- a/src/jalview/util/Comparison.java
+++ b/src/jalview/util/Comparison.java
@@ -1,19 +1,22 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
+ * Copyright (C) 2014 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.
- * 
+ * 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/>.
+ * 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.util;
 
@@ -133,7 +136,29 @@ public class Comparison
   // Another pid with region specification
   public final static float PID(String seq1, String seq2, int start, int end)
   {
+    return PID(seq1, seq2, start, end, true, false);
+  }
 
+  /**
+   * Calculate percent identity for a pair of sequences over a particular range,
+   * with different options for ignoring gaps.
+   * 
+   * @param seq1
+   * @param seq2
+   * @param start
+   *          - position in seqs
+   * @param end
+   *          - position in seqs
+   * @param wcGaps
+   *          - if true - gaps match any character, if false, do not match
+   *          anything
+   * @param ungappedOnly
+   *          - if true - only count PID over ungapped columns
+   * @return
+   */
+  public final static float PID(String seq1, String seq2, int start,
+          int end, boolean wcGaps, boolean ungappedOnly)
+  {
     int s1len = seq1.length();
     int s2len = seq2.length();
 
@@ -149,16 +174,16 @@ public class Comparison
       start = len - 1; // we just use a single residue for the difference
     }
 
-    int bad = 0;
+    int elen = len - start, bad = 0;
     char chr1;
     char chr2;
-
+    boolean agap;
     for (int i = start; i < len; i++)
     {
       chr1 = seq1.charAt(i);
 
       chr2 = seq2.charAt(i);
-
+      agap = isGap(chr1) || isGap(chr2);
       if ('a' <= chr1 && chr1 <= 'z')
       {
         // TO UPPERCASE !!!
@@ -172,13 +197,31 @@ public class Comparison
         chr2 -= caseShift;
       }
 
-      if (chr1 != chr2 && !isGap(chr1) && !isGap(chr2))
+      if (chr1 != chr2)
       {
-        bad++;
+        if (agap)
+        {
+          if (ungappedOnly)
+          {
+            elen--;
+          }
+          else if (!wcGaps)
+          {
+            bad++;
+          }
+        }
+        else
+        {
+          bad++;
+        }
       }
-    }
 
-    return ((float) 100 * (len - bad)) / len;
+    }
+    if (elen < 1)
+    {
+      return 0f;
+    }
+    return ((float) 100 * (elen - bad)) / elen;
   }
 
   /**