X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=onegapignore.h;h=fdbc196e9f2f7ff539a9b61bf35a8120483ac66b;hp=6421741c0d4c153794ab40efc9318af6d64349a4;hb=cf9987b67aa49777a4c91c2d21f96e58bf17aa82;hpb=cdcf99b7760701e6869ca8e4e6e91c8e8c4ae186

diff --git a/onegapignore.h b/onegapignore.h
index 6421741..fdbc196 100644
--- a/onegapignore.h
+++ b/onegapignore.h
@@ -9,6 +9,7 @@
  *
  */
 
+
 #include "dist.h"
 
 /**************************************************************************************************/
@@ -16,6 +17,9 @@
 class oneGapIgnoreTermGapDist : public Dist {
 	
 public:
+	
+	oneGapIgnoreTermGapDist() {}
+	
 	void calcDist(Sequence A, Sequence B){
 		
 		int difference = 0;
@@ -24,21 +28,26 @@ public:
 		int minLength = 0;
 		int start = 0;
 		int end = 0;
+		bool overlap = false;
 		
 		string seqA = A.getAligned();
 		string seqB = B.getAligned();
 		int alignLength = seqA.length();
-		
+
 		// this assumes that sequences start and end with '.'s instead of'-'s.
 		for(int i=0;i<alignLength;i++){
-			if(seqA[i] != '.' && seqB[i] != '.'){
+			if(seqA[i] != '.' && seqB[i] != '.' && seqA[i] != '-' && seqB[i] != '-' ){
 				start = i;
+//				cout << "start: " << start << endl;
+				overlap = true;
 				break;
 			}
 		}
 		for(int i=alignLength-1;i>=0;i--){
-			if(seqA[i] != '.' && seqB[i] != '.'){
+			if(seqA[i] != '.' && seqB[i] != '.' && seqA[i] != '-' && seqB[i] != '-' ){
 				end = i;
+//				cout << "end: " << end << endl;
+				overlap = true;
 				break;
 			}
 		}
@@ -70,7 +79,10 @@ public:
 				openGapB = 0;
 			}
 		}
-
+		
+		//non-overlapping sequences
+		if (!overlap) { minLength = 0; }
+		
 		if(minLength == 0)	{	dist = 1.0000;							}
 		else				{	dist = (double)difference / minLength;	}
 	}