From dbba2779042727476e41d2cdfa7346780ca00cbd Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Wed, 13 Apr 2005 16:42:21 +0000
Subject: [PATCH] Gap characters are now properly detected in the conservation
 and PID calculation. They are always counted in the '-'
 element of the residue count hash.

---
 src/jalview/analysis/AAFrequency.java |   39 +++++++++++++++++++--------------
 1 file changed, 23 insertions(+), 16 deletions(-)

diff --git a/src/jalview/analysis/AAFrequency.java b/src/jalview/analysis/AAFrequency.java
index c61e7ef..edcc50f 100755
--- a/src/jalview/analysis/AAFrequency.java
+++ b/src/jalview/analysis/AAFrequency.java
@@ -20,6 +20,7 @@ public class AAFrequency {
     // This class is used extensively in calculating alignment colourschemes
     // that depend on the amount of conservation in each alignment column.
 
+
     public static Vector calculate(Vector sequences,int start,int end) {
 
     Vector result = new Vector();
@@ -45,6 +46,8 @@ public class AAFrequency {
 
             if (!jalview.util.Comparison.isGap(res.charAt(0)))
               nongap++;
+            else
+              res = "-"; // we always use this for gaps in the property vectors
 
             if (residueHash.containsKey(res))
             {
@@ -133,26 +136,28 @@ public class AAFrequency {
 
 	    for (int k = winstart; k <= winend; k++) {
 		String refchar = refseq.getSequence().substring(k,k+1);
+                if (jalview.util.Comparison.isGap(refchar.charAt(0)))
+                  refchar="-";
+                else {
+                  for (int j = 0; j < sequences.size(); j++) {
 
-		for (int j = 0; j < sequences.size(); j++) {
+                    Sequence s = (Sequence)sequences.elementAt(j);
 
-		    if (refchar.equals("-") == false) {
+                    if (s.getSequence().length() > k) {
 
-			Sequence s = (Sequence)sequences.elementAt(j);
+                      String res = s.getSequence().substring(k,k+1); // no gapchar test needed
 
-			if (s.getSequence().length() > k) {
+                      if (res.equals(refchar)) {
+                        int val = ((Integer)values.elementAt(j)).intValue();
+                        val++;
+                        values.setElementAt(new Integer(val),j);
+                      }
+                    }
+                  }
+                }
 
-			    String res = s.getSequence().substring(k,k+1);
+              }
 
-			    if (res.equals(refchar)) {
-				int val = ((Integer)values.elementAt(j)).intValue();
-				val++;
-				values.setElementAt(new Integer(val),j);
-			    }
-			}
-		    }
-		}
-	    }
 	    prev = values;
 	} else {
 	    int winstart = i-window/2;
@@ -189,11 +194,13 @@ public class AAFrequency {
 
 		// Now substract 1 if the chars at winstart-1 match
 
-		if (pre_refchar.equals("-") == false && pre_char.equals(pre_refchar)) {
+                if (jalview.util.Comparison.isGap(pre_refchar.charAt(0)) == false
+                    && pre_char.equals(pre_refchar)) {
 		    val--;
 		}
 
-		if (pos_refchar.equals("-") == false && pos_char.equals(pos_refchar)) {
+                if (jalview.util.Comparison.isGap(pos_refchar.charAt(0)) == false
+                    && pos_char.equals(pos_refchar)) {
 		    val++;
 		}
 
-- 
1.7.10.2