X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=unifracweightedcommand.cpp;h=f9dc450444b242555710f91dc3567f96e69e6d3d;hb=8dd3c225255d7084e3aff8740aa4f1f1cabb367a;hp=994f09bcda36aa0bd5705b921cdc647387bd9500;hpb=c651c46022761aef61644f78462365d8f767ff0b;p=mothur.git

diff --git a/unifracweightedcommand.cpp b/unifracweightedcommand.cpp
index 994f09b..f9dc450 100644
--- a/unifracweightedcommand.cpp
+++ b/unifracweightedcommand.cpp
@@ -134,14 +134,14 @@ UnifracWeightedCommand::UnifracWeightedCommand(string option) {
 			}
 			
 			m->runParse = true;
-			m->Groups.clear();
-			m->namesOfGroups.clear();
+			m->clearGroups();
+			m->clearAllGroups();
 			m->Treenames.clear();
 			m->names.clear();
 			
 			//check for required parameters
 			treefile = validParameter.validFile(parameters, "tree", true);
-			if (treefile == "not open") { abort = true; }
+			if (treefile == "not open") { treefile = ""; abort = true; }
 			else if (treefile == "not found") { 				//if there is a current design file, use it
 				treefile = m->getTreeFile(); 
 				if (treefile != "") { m->mothurOut("Using " + treefile + " as input file for the tree parameter."); m->mothurOutEndLine(); }
@@ -155,7 +155,7 @@ UnifracWeightedCommand::UnifracWeightedCommand(string option) {
 			else { m->setGroupFile(groupfile); }
 			
 			namefile = validParameter.validFile(parameters, "name", true);
-			if (namefile == "not open") { abort = true; }
+			if (namefile == "not open") { namefile = ""; abort = true; }
 			else if (namefile == "not found") { namefile = ""; }
 			else { m->setNameFile(namefile); }
 			
@@ -168,11 +168,11 @@ UnifracWeightedCommand::UnifracWeightedCommand(string option) {
 			if (groups == "not found") { groups = ""; }
 			else { 
 				m->splitAtDash(groups, Groups);
-				m->Groups = Groups;
+				m->setGroups(Groups);
 			}
 				
 			itersString = validParameter.validFile(parameters, "iters", false);			if (itersString == "not found") { itersString = "1000"; }
-			convert(itersString, iters); 
+			m->mothurConvert(itersString, iters); 
 			
 			string temp = validParameter.validFile(parameters, "distance", false);			
 			if (temp == "not found") { phylip = false; outputForm = ""; }
@@ -189,9 +189,14 @@ UnifracWeightedCommand::UnifracWeightedCommand(string option) {
 			
 			temp = validParameter.validFile(parameters, "processors", false);	if (temp == "not found"){	temp = m->getProcessors();	}
 			m->setProcessors(temp);
-			convert(temp, processors);
+			m->mothurConvert(temp, processors);
 			
 			if (!random) {  iters = 0;  } //turn off random calcs
+			
+			if (namefile == "") {
+				vector<string> files; files.push_back(treefile);
+				parser.getNameFile(files);
+			}
 		}
 		
 		
@@ -253,7 +258,7 @@ int UnifracWeightedCommand::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++) {	m->mothurRemove(outputNames[i]); } outputTypes.clear();
-					m->Groups.clear();
+					m->clearGroups();
 					return 0;
 				}
 				
@@ -277,8 +282,11 @@ int UnifracWeightedCommand::execute() {
 			
 		util = new SharedUtil();
 		string s; //to make work with setgroups
-		util->setGroups(m->Groups, tmap->namesOfGroups, s, numGroups, "weighted");	//sets the groups the user wants to analyze
-		util->getCombos(groupComb, m->Groups, numComp);
+		Groups = m->getGroups();
+		vector<string> nameGroups = tmap->getNamesOfGroups();
+		util->setGroups(Groups, nameGroups, s, numGroups, "weighted");	//sets the groups the user wants to analyze
+		util->getCombos(groupComb, Groups, numComp);
+		m->setGroups(Groups);
 		delete util;
 		
 		weighted = new Weighted(tmap, includeRoot);
@@ -327,7 +335,7 @@ int UnifracWeightedCommand::execute() {
 				vector< vector<string> > namesOfGroupCombos;
 				for (int a=0; a<numGroups; a++) { 
 					for (int l = 0; l < a; l++) {	
-						vector<string> groups; groups.push_back(m->Groups[a]); groups.push_back(m->Groups[l]);
+						vector<string> groups; groups.push_back((m->getGroups())[a]); groups.push_back((m->getGroups())[l]);
 						namesOfGroupCombos.push_back(groups);
 					}
 				}
@@ -409,7 +417,7 @@ int UnifracWeightedCommand::execute() {
 		if (phylip) {	createPhylipFile();		}
 
 		//clear out users groups
-		m->Groups.clear();
+		m->clearGroups();
 		delete tmap; delete weighted;
 		for (int i = 0; i < T.size(); i++) { delete T[i]; }
 		
@@ -639,17 +647,17 @@ void UnifracWeightedCommand::createPhylipFile() {
 			
 			if ((outputForm == "lt") || (outputForm == "square")) {
 				//output numSeqs
-				out << m->Groups.size() << endl;
+				out << m->getNumGroups() << endl;
 			}
 
 			//make matrix with scores in it
-			vector< vector<float> > dists;	dists.resize(m->Groups.size());
-			for (int i = 0; i < m->Groups.size(); i++) {
-				dists[i].resize(m->Groups.size(), 0.0);
+			vector< vector<float> > dists;	dists.resize(m->getNumGroups());
+			for (int i = 0; i < m->getNumGroups(); i++) {
+				dists[i].resize(m->getNumGroups(), 0.0);
 			}
 			
 			//flip it so you can print it
-			for (int r=0; r<m->Groups.size(); r++) { 
+			for (int r=0; r<m->getNumGroups(); r++) { 
 				for (int l = 0; l < r; l++) {
 					dists[r][l] = utreeScores[count];
 					dists[l][r] = utreeScores[count];
@@ -658,9 +666,9 @@ void UnifracWeightedCommand::createPhylipFile() {
 			}
 
 			//output to file
-			for (int r=0; r<m->Groups.size(); r++) { 
+			for (int r=0; r<m->getNumGroups(); r++) { 
 				//output name
-				string name = m->Groups[r];
+				string name = (m->getGroups())[r];
 				if (name.length() < 10) { //pad with spaces to make compatible
 					while (name.length() < 10) {  name += " ";  }
 				}
@@ -675,12 +683,12 @@ void UnifracWeightedCommand::createPhylipFile() {
 					out << name << '\t';
 					
 					//output distances
-					for (int l = 0; l < m->Groups.size(); l++) {	out  << dists[r][l] << '\t';  }
+					for (int l = 0; l < m->getNumGroups(); l++) {	out  << dists[r][l] << '\t';  }
 					out << endl;
 				}else{
 					//output distances
 					for (int l = 0; l < r; l++) {	
-						string otherName = m->Groups[l];
+						string otherName = (m->getGroups())[l];
 						if (otherName.length() < 10) { //pad with spaces to make compatible
 							while (otherName.length() < 10) {  otherName += " ";  }
 						}