X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=parsimony.cpp;h=0487822764bbf36e11da5bd8faada1bba34a63c4;hb=4745a956b3116a719f52f341d2a2db84df4817da;hp=7d08adf8ad3b0a0ad5a25bc98bbf74d1bacda3b9;hpb=f18d75f9c996cb619a5051a7664620c0c5ae05fb;p=mothur.git

diff --git a/parsimony.cpp b/parsimony.cpp
index 7d08adf..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++) {
@@ -89,13 +94,15 @@ EstOutput Parsimony::getValues(Tree* t) {
 		
 			//create pgroups that reflect the groups the user want to use
 			for(int i=copyTree->getNumLeaves();i<copyTree->getNumNodes();i++){
-//				cout << i << "..." << endl;
 				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();
 			
@@ -103,13 +110,6 @@ EstOutput Parsimony::getValues(Tree* t) {
 				int rcSize = copyTree->tree[rc].pGroups.size();
 				int lcSize = copyTree->tree[lc].pGroups.size();
 				
-//				cout << i+1 << '\t' << lc+1 << '\t' << rc+1 << ":\t";
-				
-//				for(it=copyTree->tree[i].pGroups.begin();it!=copyTree->tree[i].pGroups.end();it++){
-//					cout << it->first << '\t';
-//				}
-				
-//				cout << " : " << iSize << '\t' << rcSize << '\t' << lcSize << '\t';
 					
 				//if isize are 0 then that branch is to be ignored
 				if (iSize == 0) { }
@@ -118,12 +118,10 @@ EstOutput Parsimony::getValues(Tree* t) {
 				else if(iSize > rcSize || iSize > lcSize){
 					score++;
 				}
-//				cout << score << endl;
 			} 
 		
 			data[count] = score;
-			string hold;
-//			cin >> hold;
+
 		}
 		
 		delete copyTree;
@@ -131,14 +129,9 @@ EstOutput Parsimony::getValues(Tree* t) {
 		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);
-	}
-
 }
 
 /**************************************************************************************************/