From bd37829796d6d9f9b8340967eea49eb0d98f70a7 Mon Sep 17 00:00:00 2001
From: jprocter <jprocter@compbio.dundee.ac.uk>
Date: Mon, 30 May 2011 07:34:28 +0100
Subject: [PATCH] first patch for JAL-838 - allow new typed of PID calcs

---
 src/jalview/util/Comparison.java |   42 ++++++++++++++++++++++++++++++--------
 1 file changed, 33 insertions(+), 9 deletions(-)
 mode change 100755 => 100644 src/jalview/util/Comparison.java

diff --git a/src/jalview/util/Comparison.java b/src/jalview/util/Comparison.java
old mode 100755
new mode 100644
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;
   }
 
   /**
-- 
1.7.10.2