X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=unifracweightedcommand.cpp;h=bc9d0c5048f198ac6e30309e4af0255c67dcf605;hb=4f2c7f477a1ef2d60a1c0c84ab1ba8243af67f87;hp=d6431a051b56f3144dcfc80d430e7d61351da30a;hpb=19fcbbdba99658f5eca244803280f9ee7f9f6607;p=mothur.git

diff --git a/unifracweightedcommand.cpp b/unifracweightedcommand.cpp
index d6431a0..bc9d0c5 100644
--- a/unifracweightedcommand.cpp
+++ b/unifracweightedcommand.cpp
@@ -134,8 +134,8 @@ UnifracWeightedCommand::UnifracWeightedCommand(string option) {
 			}
 			
 			m->runParse = true;
-			m->Groups.clear();
-			m->namesOfGroups.clear();
+			m->clearGroups();
+			m->clearAllGroups();
 			m->Treenames.clear();
 			m->names.clear();
 			
@@ -168,7 +168,7 @@ 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"; }
@@ -253,7 +253,7 @@ 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 +277,11 @@ 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 +330,7 @@ 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 +412,7 @@ 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]; }
 		
@@ -581,8 +584,10 @@ void UnifracWeightedCommand::printWeightedFile() {
 void UnifracWeightedCommand::printWSummaryFile() {
 	try {
 		//column headers
-		outSum << "Tree#" << '\t' << "Groups" << '\t' << "WScore" << '\t' << "WSig" <<  endl;
-		m->mothurOut("Tree#\tGroups\tWScore\tWSig"); m->mothurOutEndLine(); 
+		outSum << "Tree#" << '\t' << "Groups" << '\t' << "WScore" << '\t';
+		m->mothurOut("Tree#\tGroups\tWScore\t");
+		if (random) { outSum << "WSig"; m->mothurOut("WSig"); }
+		outSum << endl; m->mothurOutEndLine();
 		
 		//format output
 		outSum.setf(ios::fixed, ios::floatfield); outSum.setf(ios::showpoint);
@@ -602,9 +607,9 @@ void UnifracWeightedCommand::printWSummaryFile() {
 						m->mothurOutJustToLog(toString(i+1) +"\t" + groupComb[j] +"\t" + toString(utreeScores[count]) +"\t<" +  toString((1/float(iters))) + "\n");  
 					}
 				}else{
-					outSum << setprecision(6) << i+1 << '\t' << groupComb[j] << '\t' << utreeScores[count] << '\t' << "0.00" << endl; 
-					cout << setprecision(6) << i+1 << '\t' << groupComb[j] << '\t' << utreeScores[count] << '\t' << "0.00" << endl; 
-					m->mothurOutJustToLog(toString(i+1) +"\t" + groupComb[j] +"\t" + toString(utreeScores[count]) +"\t0.00\n"); 
+					outSum << setprecision(6) << i+1 << '\t' << groupComb[j] << '\t' << utreeScores[count] << endl; 
+					cout << setprecision(6) << i+1 << '\t' << groupComb[j] << '\t' << utreeScores[count]  << endl; 
+					m->mothurOutJustToLog(toString(i+1) +"\t" + groupComb[j] +"\t" + toString(utreeScores[count]) +"\n"); 
 				}
 				count++;
 			}
@@ -637,17 +642,17 @@ 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];
@@ -656,9 +661,9 @@ 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 += " ";  }
 				}
@@ -673,12 +678,12 @@ 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 += " ";  }
 						}