X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=treegroupscommand.cpp;h=8c5aa4bbdc926515c6e3796a3a7969aa9abffca9;hb=2bb9267aa4b4ecdf8488b06605cc9f3f36fa4332;hp=582a3233ae847f64bc74209e14c918d2b6ebdc45;hpb=8f7f4fc08b8c70d9ef0f79607813dba4e926e102;p=mothur.git

diff --git a/treegroupscommand.cpp b/treegroupscommand.cpp
index 582a323..8c5aa4b 100644
--- a/treegroupscommand.cpp
+++ b/treegroupscommand.cpp
@@ -179,21 +179,22 @@ TreeGroupCommand::TreeGroupCommand(string option)  {
 			phylipfile = validParameter.validFile(parameters, "phylip", true);
 			if (phylipfile == "not open") { phylipfile = ""; abort = true; }
 			else if (phylipfile == "not found") { phylipfile = ""; }	
-			else {  inputfile = phylipfile;  format = "phylip"; 	}
+			else {  inputfile = phylipfile;  format = "phylip"; m->setPhylipFile(phylipfile);	}
 			
 			columnfile = validParameter.validFile(parameters, "column", true);
 			if (columnfile == "not open") { columnfile = ""; abort = true; }	
 			else if (columnfile == "not found") { columnfile = ""; }
-			else {  inputfile = columnfile; format = "column";	}
+			else {  inputfile = columnfile; format = "column";	m->setColumnFile(columnfile); }
 			
 			sharedfile = validParameter.validFile(parameters, "shared", true);
 			if (sharedfile == "not open") { sharedfile = ""; abort = true; }	
 			else if (sharedfile == "not found") { sharedfile = ""; }
-			else {  inputfile = sharedfile; format = "sharedfile";	}
+			else {  inputfile = sharedfile; format = "sharedfile";	m->setSharedFile(sharedfile); }
 			
 			namefile = validParameter.validFile(parameters, "name", true);
 			if (namefile == "not open") { abort = true; }	
 			else if (namefile == "not found") { namefile = ""; }
+			else { m->setNameFile(namefile); }
 			
 			if ((phylipfile == "") && (columnfile == "") && (sharedfile == "")) { 
 				//is there are current file available for either of these?
@@ -239,7 +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);			
@@ -256,10 +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 
@@ -395,20 +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;
@@ -437,13 +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;
@@ -467,7 +469,7 @@ int TreeGroupCommand::execute(){
 		}
 				
 		//reset groups parameter
-		m->Groups.clear(); 
+		m->clearGroups(); 
 		
 		//set tree file as new current treefile
 		string current = "";
@@ -563,7 +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;
 	
@@ -758,8 +760,8 @@ int TreeGroupCommand::process(vector<SharedRAbundVector*> thisLookup) {
 								if (m->control_pressed) { return 1; }
 								
 								//save values in similarity matrix
-								simMatrix[k][l] = data[0];
-								simMatrix[l][k] = data[0];
+								simMatrix[k][l] = -(data[0]-1.0);
+								simMatrix[l][k] = -(data[0]-1.0);
 							}
 						}
 					}