X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=parsimony.cpp;h=49a73505c3df0c77b4ff3fe0b6e71f038eb5f13c;hb=8dd3c225255d7084e3aff8740aa4f1f1cabb367a;hp=4ec5e1ba7d31495ebef7b5efaf2b7e6bbc82ad7c;hpb=c53ef46b40b97c00e32bfd8c3924ce8c51b5cd7b;p=mothur.git

diff --git a/parsimony.cpp b/parsimony.cpp
index 4ec5e1b..49a7350 100644
--- a/parsimony.cpp
+++ b/parsimony.cpp
@@ -13,20 +13,20 @@
 
 EstOutput Parsimony::getValues(Tree* t, int p, string o) {
 	try {
-		globaldata = GlobalData::getInstance();
 		processors = p;
 		outputDir = o;
 		
 		//if the users enters no groups then give them the score of all groups
-		int numGroups = globaldata->Groups.size();
+		vector<string> mGroups = m->getGroups();
+		int numGroups = mGroups.size();
 		
 		//calculate number of comparsions
 		int numComp = 0;
 		vector< vector<string> > namesOfGroupCombos;
 		for (int r=0; r<numGroups; r++) { 
-			for (int l = r+1; l < numGroups; l++) {
+			for (int l = 0; l < r; l++) {
 				numComp++;
-				vector<string> groups; groups.push_back(globaldata->Groups[r]); groups.push_back(globaldata->Groups[l]);
+				vector<string> groups; groups.push_back(mGroups[r]); groups.push_back(mGroups[l]);
 				//cout << globaldata->Groups[r] << '\t' << globaldata->Groups[l] << endl;
 				namesOfGroupCombos.push_back(groups);
 			}
@@ -37,16 +37,17 @@ EstOutput Parsimony::getValues(Tree* t, int p, string o) {
 			vector<string> groups;
 			if (numGroups == 0) {
 				//get score for all users groups
-				for (int i = 0; i < tmap->namesOfGroups.size(); i++) {
-					if (tmap->namesOfGroups[i] != "xxx") {
-						groups.push_back(tmap->namesOfGroups[i]);
+				vector<string> tGroups = tmap->getNamesOfGroups();
+				for (int i = 0; i < tGroups.size(); i++) {
+					if (tGroups[i] != "xxx") {
+						groups.push_back(tGroups[i]);
 						//cout << tmap->namesOfGroups[i] << endl;
 					}
 				}
 				namesOfGroupCombos.push_back(groups);
 			}else {
-				for (int i = 0; i < globaldata->Groups.size(); i++) {
-					groups.push_back(globaldata->Groups[i]);
+				for (int i = 0; i < mGroups.size(); i++) {
+					groups.push_back(mGroups[i]);
 					//cout << globaldata->Groups[i] << endl;
 				}
 				namesOfGroupCombos.push_back(groups);
@@ -92,7 +93,6 @@ EstOutput Parsimony::createProcesses(Tree* t, vector< vector<string> > namesOfGr
 	try {
 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 		int process = 1;
-		int num = 0;
 		vector<int> processIDS;
 		
 		EstOutput results;
@@ -157,7 +157,7 @@ EstOutput Parsimony::createProcesses(Tree* t, vector< vector<string> > namesOfGr
 				m->gobble(in);
 			}
 			in.close();
-			remove(s.c_str());
+			m->mothurRemove(s);
 		}
 		
 		return results;
@@ -174,7 +174,7 @@ EstOutput Parsimony::driver(Tree* t, vector< vector<string> > namesOfGroupCombos
 		
 		EstOutput results; results.resize(num);
 		
-		Tree* copyTree = new Tree();
+		Tree* copyTree = new Tree(tmap);
 		int count = 0;
 		
 		for (int h = start; h < (start+num); h++) {