first patch for JAL-838 - allow new typed of PID calcs

diff --git a/src/jalview/util/Comparison.java b/src/jalview/util/Comparison.java
old mode 100755 (executable)
new mode 100644 (file)
index 32e049d..60f21c8
--- a/src/jalview/util/Comparison.java
+++ b/src/jalview/util/Comparison.java
@@ -133,7 +133,20 @@ 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 +162,16 @@ 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 !!!
@@ -171,14 +184,25 @@ public class Comparison
         // Faster than toUpperCase
         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;
   }
 
   /**