X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=weighted.cpp;h=a0d593c803f691821afdb680e79be80f179b0afa;hb=5334a314651228c55fd0f206dec0209bc3148b24;hp=1ce6230df933eab46bee132a76ec32c2c4e9a666;hpb=c53ef46b40b97c00e32bfd8c3924ce8c51b5cd7b;p=mothur.git

diff --git a/weighted.cpp b/weighted.cpp
index 1ce6230..a0d593c 100644
--- a/weighted.cpp
+++ b/weighted.cpp
@@ -73,7 +73,6 @@ EstOutput Weighted::createProcesses(Tree* t, vector< vector<string> > namesOfGro
 	try {
 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 		int process = 1;
-		int num = 0;
 		vector<int> processIDS;
 		
 		EstOutput results;
@@ -204,9 +203,7 @@ EstOutput Weighted::driver(Tree* t, vector< vector<string> > namesOfGroupCombos,
 		for (int h = start; h < (start+num); h++) {	
 			//report progress
 			m->mothurOut("Processing combo: " + toString(h)); m->mothurOutEndLine();
-			
-			int numLeaves = t->getNumLeaves();
-			
+						
 			string groupA = namesOfGroupCombos[h][0]; 
 			string groupB = namesOfGroupCombos[h][1];
 			
@@ -234,10 +231,13 @@ EstOutput Weighted::driver(Tree* t, vector< vector<string> > namesOfGroupCombos,
 				
 				//if this is not the root then add it
 				if (rootForGrouping[namesOfGroupCombos[h]].count(i) == 0) {
-					u = abs(u * t->tree[i].getBranchLength());
-					WScore[(groupA+groupB)] += u; 
+					if (t->tree[i].getBranchLength() != -1) {
+						u = abs(u * t->tree[i].getBranchLength());
+						WScore[(groupA+groupB)] += u; 
+					}
 				}
 				
+				
 			}
 		}
 		
@@ -247,7 +247,6 @@ EstOutput Weighted::driver(Tree* t, vector< vector<string> > namesOfGroupCombos,
 		count = 0;
 		for (int h = start; h < (start+num); h++) {
 			UN = (WScore[namesOfGroupCombos[h][0]+namesOfGroupCombos[h][1]] / D[count]);
-		
 			if (isnan(UN) || isinf(UN)) { UN = 0; } 
 			results.push_back(UN);
 			count++;
@@ -297,9 +296,7 @@ EstOutput Weighted::getValues(Tree* t, string groupA, string groupB) {
 		
 			D += weightedSum;
 		}
-		
-		int numLeaves = t->getNumLeaves();
-		
+				
 		//calculate u for the group comb 
 		for(int i=0;i<t->getNumNodes();i++){
 		 
@@ -324,12 +321,14 @@ EstOutput Weighted::getValues(Tree* t, string groupA, string groupB) {
 			
 			//if this is not the root then add it
 			if (rootForGrouping[groups].count(i) == 0) {
-				u = abs(u * t->tree[i].getBranchLength());
-				WScore[(groupA+groupB)] += u; 
+				if (t->tree[i].getBranchLength() != -1) {
+					u = abs(u * t->tree[i].getBranchLength());
+					WScore[(groupA+groupB)] += u;
+				}
 			}
 		}		
 		/********************************************************/
-		
+	 
 		//calculate weighted score for the group combination
 		double UN;	
 		UN = (WScore[(groupA+groupB)] / D);