JAL-1683 replace year/version strings with tokens in source

[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 316cf5b..1934583
--- a/src/jalview/util/Comparison.java
+++ b/src/jalview/util/Comparison.java
@@ -1,20 +1,22 @@
 /*
- * 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
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
- * 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 file is part of Jalview.
  * 
- * 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.
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.util;
 
@@ -35,9 +37,9 @@ public class Comparison
    * DOCUMENT ME!
    * 
    * @param ii
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param jj
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * 
    * @return DOCUMENT ME!
    */
@@ -50,13 +52,13 @@ public class Comparison
    * this was supposed to be an ungapped pid calculation
    * 
    * @param ii
-   *                SequenceI
+   *          SequenceI
    * @param jj
-   *                SequenceI
+   *          SequenceI
    * @param start
-   *                int
+   *          int
    * @param end
-   *                int
+   *          int
    * @return float
    */
   public static float compare(SequenceI ii, SequenceI jj, int start, int end)
@@ -119,9 +121,9 @@ public class Comparison
    * this is a gapped PID calculation
    * 
    * @param s1
-   *                SequenceI
+   *          SequenceI
    * @param s2
-   *                SequenceI
+   *          SequenceI
    * @return float
    */
   public final static float PID(String seq1, String seq2)
@@ -134,7 +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();
 
@@ -150,16 +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 !!!
@@ -173,20 +197,38 @@ 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;
   }
 
   /**
    * DOCUMENT ME!
    * 
    * @param c
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * 
    * @return DOCUMENT ME!
    */