X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=unweighted.cpp;h=431323f066665bd07edce8da80c32dadb1600cf2;hb=2bb9267aa4b4ecdf8488b06605cc9f3f36fa4332;hp=a75ddc54058f878f63c579a4834754cb3890a374;hpb=f3edf14c46814ca437960f0e1070abfbea582c26;p=mothur.git

diff --git a/unweighted.cpp b/unweighted.cpp
index a75ddc5..431323f 100644
--- a/unweighted.cpp
+++ b/unweighted.cpp
@@ -13,12 +13,11 @@
 
 EstOutput Unweighted::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();
+		int numGroups = m->getNumGroups();
 		
 		//calculate number of comparsions
 		int numComp = 0;
@@ -26,7 +25,7 @@ EstOutput Unweighted::getValues(Tree* t, int p, string o) {
 		for (int r=0; r<numGroups; r++) { 
 			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((m->getGroups())[r]); groups.push_back((m->getGroups())[l]);
 				namesOfGroupCombos.push_back(groups);
 			}
 		}
@@ -35,15 +34,15 @@ EstOutput Unweighted::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]);
+				for (int i = 0; i < (tmap->getNamesOfGroups()).size(); i++) {
+					if ((tmap->getNamesOfGroups())[i] != "xxx") {
+						groups.push_back((tmap->getNamesOfGroups())[i]);
 					}
 				}
 				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 < m->getNumGroups(); i++) {
+					groups.push_back((m->getGroups())[i]);
 				}
 				namesOfGroupCombos.push_back(groups);
 			}
@@ -152,7 +151,7 @@ EstOutput Unweighted::createProcesses(Tree* t, vector< vector<string> > namesOfG
 				m->gobble(in);
 			}
 			in.close();
-			remove(s.c_str());
+			m->mothurRemove(s);
 		}
 		
 		m->mothurOut("DONE."); m->mothurOutEndLine(); m->mothurOutEndLine();
@@ -257,12 +256,11 @@ EstOutput Unweighted::driver(Tree* t, vector< vector<string> > namesOfGroupCombo
 
 EstOutput Unweighted::getValues(Tree* t, string groupA, string groupB, 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();
+		int numGroups = m->getNumGroups();
 		
 		//calculate number of comparsions
 		int numComp = 0;
@@ -270,7 +268,7 @@ EstOutput Unweighted::getValues(Tree* t, string groupA, string groupB, int p, st
 		for (int r=0; r<numGroups; r++) { 
 			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((m->getGroups())[r]); groups.push_back((m->getGroups())[l]);
 				namesOfGroupCombos.push_back(groups);
 			}
 		}
@@ -279,15 +277,15 @@ EstOutput Unweighted::getValues(Tree* t, string groupA, string groupB, int p, st
 			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]);
+				for (int i = 0; i < (tmap->getNamesOfGroups()).size(); i++) {
+					if ((tmap->getNamesOfGroups())[i] != "xxx") {
+						groups.push_back((tmap->getNamesOfGroups())[i]);
 					}
 				}
 				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 < m->getNumGroups(); i++) {
+					groups.push_back((m->getGroups())[i]);
 				}
 				namesOfGroupCombos.push_back(groups);
 			}
@@ -395,7 +393,7 @@ EstOutput Unweighted::createProcesses(Tree* t, vector< vector<string> > namesOfG
 				m->gobble(in);
 			}
 			in.close();
-			remove(s.c_str());
+			m->mothurRemove(s);
 		}
 		
 		return results;
@@ -414,7 +412,7 @@ EstOutput Unweighted::driver(Tree* t, vector< vector<string> > namesOfGroupCombo
 		
 		int count = 0;
 		
-		Tree* copyTree = new Tree;
+		Tree* copyTree = new Tree(tmap);
 		
 		for (int h = start; h < (start+num); h++) {