X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=parsimony.cpp;h=0487822764bbf36e11da5bd8faada1bba34a63c4;hb=c27e902ede71ea4d20af65752ef04459c101611b;hp=0dea64e99a5f7bbe3adfe3dbd648ab8fb5365acf;hpb=fc7cf3aac8fd6106fd725b43baa8ab5ca6f836f8;p=mothur.git

diff --git a/parsimony.cpp b/parsimony.cpp
index 0dea64e..0487822 100644
--- a/parsimony.cpp
+++ b/parsimony.cpp
@@ -49,6 +49,9 @@ EstOutput Parsimony::getValues(Tree* t) {
 				}
 		
 				for(int i=copyTree->getNumLeaves();i<copyTree->getNumNodes();i++){
+				
+					if (m->control_pressed) { return data; }
+					
 					int lc = copyTree->tree[i].getLChild();
 					int rc = copyTree->tree[i].getRChild();
 			
@@ -75,7 +78,9 @@ EstOutput Parsimony::getValues(Tree* t) {
 			if (numGroups == 0) {
 				//get score for all users groups
 				for (int i = 0; i < tmap->namesOfGroups.size(); i++) {
-					groups.push_back(tmap->namesOfGroups[i]);
+					if (tmap->namesOfGroups[i] != "xxx") {
+						groups.push_back(tmap->namesOfGroups[i]);
+					}
 				}
 			}else {
 				for (int i = 0; i < globaldata->Groups.size(); i++) {
@@ -92,14 +97,20 @@ EstOutput Parsimony::getValues(Tree* t) {
 				copyTree->tree[i].pGroups = (copyTree->mergeUserGroups(i, groups));
 			}
 		
+//			map<string,int>::iterator it;
+			
 			for(int i=copyTree->getNumLeaves();i<copyTree->getNumNodes();i++){
+			
+				if (m->control_pressed) { return data; }
+				
 				int lc = copyTree->tree[i].getLChild();
 				int rc = copyTree->tree[i].getRChild();
 			
 				int iSize = copyTree->tree[i].pGroups.size();
 				int rcSize = copyTree->tree[rc].pGroups.size();
 				int lcSize = copyTree->tree[lc].pGroups.size();
-		
+				
+					
 				//if isize are 0 then that branch is to be ignored
 				if (iSize == 0) { }
 				else if ((rcSize == 0) || (lcSize == 0)) { }
@@ -110,19 +121,17 @@ EstOutput Parsimony::getValues(Tree* t) {
 			} 
 		
 			data[count] = score;
+
 		}
 		
+		delete copyTree;
+		
 		return data;
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the Parsimony class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "Parsimony", "getValues");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the Parsimony class function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-
 }
 
 /**************************************************************************************************/