X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=parsimonycommand.cpp;h=3752935aac5ad0211c5f9bf5b66ca00dce2b366b;hb=55386dddad84cc1140d736cabaf4dd0ae16f2e01;hp=6e69cad4f8dbde50541a8daad71dbcce712b8953;hpb=7bf9a81bba76538ecaf351ae208de3da4bf1b6dd;p=mothur.git

diff --git a/parsimonycommand.cpp b/parsimonycommand.cpp
index 6e69cad..3752935 100644
--- a/parsimonycommand.cpp
+++ b/parsimonycommand.cpp
@@ -126,8 +126,8 @@ ParsimonyCommand::ParsimonyCommand(string option)  {
 			}
 			
 			m->runParse = true;
-			m->Groups.clear();
-			m->namesOfGroups.clear();
+			m->clearGroups();
+			m->clearAllGroups();
 			m->Treenames.clear();
 			m->names.clear();
 			
@@ -164,10 +164,10 @@ ParsimonyCommand::ParsimonyCommand(string option)  {
 			//check for optional parameter and set defaults
 			// ...at some point should added some additional type checking...
 			groups = validParameter.validFile(parameters, "groups", false);			
-			if (groups == "not found") { groups = ""; m->Groups.clear(); }
+			if (groups == "not found") { groups = ""; m->clearGroups(); }
 			else { 
 				m->splitAtDash(groups, Groups);
-				m->Groups = Groups;
+				m->setGroups(Groups);
 			}
 				
 			itersString = validParameter.validFile(parameters, "iters", false);			if (itersString == "not found") { itersString = "1000"; }
@@ -219,7 +219,7 @@ int ParsimonyCommand::execute() {
 			read->AssembleTrees();
 			T = read->getTrees();
 			delete read;
-			
+
 			//make sure all files match
 			//if you provide a namefile we will use the numNames in the namefile as long as the number of unique match the tree names size.
 			int numNamesInTree;
@@ -241,8 +241,8 @@ int ParsimonyCommand::execute() {
 					
 					if (m->control_pressed) { 
 						delete tmap; for (int i = 0; i < T.size(); i++) { delete T[i]; }
-						for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str()); } outputTypes.clear();
-						m->Groups.clear();
+						for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); } outputTypes.clear();
+						m->clearGroups();
 						return 0;
 					}
 					
@@ -280,8 +280,11 @@ int ParsimonyCommand::execute() {
 			
 		//set users groups to analyze
 		util = new SharedUtil();
-		util->setGroups(m->Groups, tmap->namesOfGroups, allGroups, numGroups, "parsimony");	//sets the groups the user wants to analyze
-		util->getCombos(groupComb, m->Groups, numComp);
+		vector<string> mGroups = m->getGroups();
+		vector<string> tGroups = tmap->getNamesOfGroups();
+		util->setGroups(mGroups, tGroups, allGroups, numGroups, "parsimony");	//sets the groups the user wants to analyze
+		util->getCombos(groupComb, mGroups, numComp);
+		m->setGroups(mGroups);
 		delete util;
 			
 		if (numGroups == 1) { numComp++; groupComb.push_back(allGroups); }
@@ -296,8 +299,8 @@ int ParsimonyCommand::execute() {
 			delete reading; delete pars; delete output;
 			delete tmap; for (int i = 0; i < T.size(); i++) { delete T[i]; }
 			if (randomtree == "") {  outSum.close();  }
-			for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str()); } outputTypes.clear();
-			m->Groups.clear();
+			for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); } outputTypes.clear();
+			m->clearGroups();
 			return 0;
 		}
 			
@@ -321,8 +324,8 @@ int ParsimonyCommand::execute() {
 					delete reading; delete pars; delete output;
 					delete tmap; for (int i = 0; i < T.size(); i++) { delete T[i]; }
 					if (randomtree == "") {  outSum.close();  }
-					for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str()); } outputTypes.clear();
-					m->Groups.clear();
+					for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); } outputTypes.clear();
+					m->clearGroups();
 					return 0;
 				}
 
@@ -359,9 +362,9 @@ int ParsimonyCommand::execute() {
 				if (m->control_pressed) { 
 					delete reading; delete pars; delete output; delete randT;
 					if (randomtree == "") {  outSum.close();  }
-					for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str()); } outputTypes.clear();
+					for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); } outputTypes.clear();
 					delete tmap; for (int i = 0; i < T.size(); i++) { delete T[i]; }
-					m->Groups.clear();
+					m->clearGroups();
 					return 0;
 				}
 					
@@ -397,8 +400,8 @@ int ParsimonyCommand::execute() {
 				if (m->control_pressed) { 
 					delete reading; delete pars; delete output; delete randT;
 					delete tmap; 
-					for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str()); } outputTypes.clear();
-					m->Groups.clear();
+					for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); } outputTypes.clear();
+					m->clearGroups();
 					return 0;
 				}
 
@@ -409,8 +412,8 @@ int ParsimonyCommand::execute() {
 				if (m->control_pressed) { 
 					delete reading; delete pars;  delete output; delete randT;
 					delete tmap; 
-					for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str()); } outputTypes.clear();
-					m->Groups.clear();
+					for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); } outputTypes.clear();
+					m->clearGroups();
 					return 0;
 				}
 			
@@ -466,8 +469,8 @@ int ParsimonyCommand::execute() {
 				delete reading; delete pars; delete output;
 				delete tmap; for (int i = 0; i < T.size(); i++) { delete T[i]; }
 				if (randomtree == "") {  outSum.close();  }
-				for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str()); } outputTypes.clear();
-				m->Groups.clear();
+				for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); } outputTypes.clear();
+				m->clearGroups();
 				return 0;
 		}
 		
@@ -480,12 +483,12 @@ int ParsimonyCommand::execute() {
 		if (randomtree == "") { printUSummaryFile(); }
 		
 		//reset groups parameter
-		m->Groups.clear(); 
+		m->clearGroups(); 
 		
 		delete pars; delete output; 
 		delete tmap; for (int i = 0; i < T.size(); i++) { delete T[i]; }
 		
-		if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str()); } outputTypes.clear(); return 0;}
+		if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); } outputTypes.clear(); return 0;}
 		
 		m->mothurOutEndLine();
 		m->mothurOut("Output File Names: "); m->mothurOutEndLine();
@@ -585,6 +588,7 @@ void ParsimonyCommand::getUserInput() {
 		count = 1;
 		numEachGroup.resize(numGroups, 0);  
 		
+		
 		for (int i = 1; i <= numGroups; i++) {
 			m->mothurOut("Please enter the number of sequences in group " + toString(i) +  ": ");
 			cin >> num;
@@ -592,7 +596,7 @@ void ParsimonyCommand::getUserInput() {
 				
 			//set tmaps seqsPerGroup
 			tmap->seqsPerGroup[toString(i)] = num;
-			tmap->namesOfGroups.push_back(toString(i));
+			tmap->addGroup(toString(i));
 			
 			//set tmaps namesOfSeqs
 			for (int j = 0; j < num; j++) {