X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=treegroupscommand.cpp;h=8c5aa4bbdc926515c6e3796a3a7969aa9abffca9;hb=8dd3c225255d7084e3aff8740aa4f1f1cabb367a;hp=902b9a253b0aa7e5515b74adf464b7fe17a65e2c;hpb=7bf9a81bba76538ecaf351ae208de3da4bf1b6dd;p=mothur.git

diff --git a/treegroupscommand.cpp b/treegroupscommand.cpp
index 902b9a2..8c5aa4b 100644
--- a/treegroupscommand.cpp
+++ b/treegroupscommand.cpp
@@ -240,7 +240,7 @@ TreeGroupCommand::TreeGroupCommand(string option)  {
 			if (groups == "not found") { groups = ""; }
 			else { 
 				m->splitAtDash(groups, Groups);
-				m->Groups = Groups;
+				m->setGroups(Groups);
 			}
 				
 			calc = validParameter.validFile(parameters, "calc", false);			
@@ -257,10 +257,10 @@ TreeGroupCommand::TreeGroupCommand(string option)  {
 
 			string temp;
 			temp = validParameter.validFile(parameters, "precision", false);			if (temp == "not found") { temp = "100"; }
-			convert(temp, precision); 
+			m->mothurConvert(temp, precision); 
 			
 			temp = validParameter.validFile(parameters, "cutoff", false);			if (temp == "not found") { temp = "10"; }
-			convert(temp, cutoff); 
+			m->mothurConvert(temp, cutoff); 
 			cutoff += (5 / (precision * 10.0));
 			
 			//if the user changes the output directory command factory will send this info to us in the output parameter 
@@ -396,20 +396,20 @@ int TreeGroupCommand::execute(){
 			
 			//create treemap class from groupmap for tree class to use
 			tmap = new TreeMap();
-			tmap->makeSim(m->namesOfGroups);
+			tmap->makeSim(m->getAllGroups());
 			
 			//clear globaldatas old tree names if any
 			m->Treenames.clear();
 			
 			//fills globaldatas tree names
-			m->Treenames = m->Groups;
+			m->Treenames = m->getGroups();
 		
 			if (m->control_pressed) { return 0; }
 			
 			//create tree file
 			makeSimsShared();
 			
-			if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str());  } return 0; }
+			if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]);  } return 0; }
 		}else{
 			//read in dist file
 			filename = inputfile;
@@ -438,13 +438,14 @@ int TreeGroupCommand::execute(){
 			
 			tmap->makeSim(list);
 			
-			m->Groups = tmap->namesOfGroups;
+			vector<string> namesGroups = tmap->getNamesOfGroups();
+			m->setGroups(namesGroups);
 		
 			//clear globaldatas old tree names if any
 			m->Treenames.clear();
 		
 			//fills globaldatas tree names
-			m->Treenames = m->Groups;
+			m->Treenames = m->getGroups();
 			
 			//used in tree constructor 
 			m->runParse = false;
@@ -468,7 +469,7 @@ int TreeGroupCommand::execute(){
 		}
 				
 		//reset groups parameter
-		m->Groups.clear(); 
+		m->clearGroups(); 
 		
 		//set tree file as new current treefile
 		string current = "";
@@ -564,7 +565,7 @@ int TreeGroupCommand::createTree(){
 		//delete tree
 		delete t;
 		
-		if (m->control_pressed) { remove(outputFile.c_str()); outputNames.pop_back(); return 1; }
+		if (m->control_pressed) { m->mothurRemove(outputFile); outputNames.pop_back(); return 1; }
 		
 		return 0;