X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;ds=sidebyside;f=pcoacommand.cpp;h=4be5ffb8c5b63c4202666aecd57ec58c2be05374;hb=662c0b60d65f79f672ab199300b7ee4975233465;hp=6777b5a56cb1182654c66bf6d065f9f973a10525;hpb=d04f948b1a2a1a2984fc4a45d04403b8c121c5bc;p=mothur.git

diff --git a/pcoacommand.cpp b/pcoacommand.cpp
index 6777b5a..4be5ffb 100644
--- a/pcoacommand.cpp
+++ b/pcoacommand.cpp
@@ -26,8 +26,7 @@ vector<string> PCOACommand::getValidParameters(){
 //**********************************************************************************************************************
 PCOACommand::PCOACommand(){	
 	try {
-		abort = true;
-		//initialize outputTypes
+		abort = true; calledHelp = true; 
 		vector<string> tempOutNames;
 		outputTypes["pcoa"] = tempOutNames;
 		outputTypes["loadings"] = tempOutNames;
@@ -64,10 +63,10 @@ vector<string> PCOACommand::getRequiredFiles(){
 
 PCOACommand::PCOACommand(string option)  {
 	try {
-		abort = false;
+		abort = false; calledHelp = false;   
 		
 		//allow user to run help
-		if(option == "help") { help(); abort = true; }
+		if(option == "help") { help(); abort = true; calledHelp = true; }
 		
 		else {
 			//valid paramters for this command
@@ -149,7 +148,7 @@ PCOACommand::~PCOACommand(){}
 int PCOACommand::execute(){
 	try {
 	
-		if (abort == true) { return 0; }
+		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
 		
 		cout.setf(ios::fixed, ios::floatfield);
 		cout.setf(ios::showpoint);
@@ -198,7 +197,7 @@ int PCOACommand::execute(){
 				
 				double corr = linearCalc.calcPearson(EuclidDists, D); //G is the pcoa file, D is the users distance matrix
 				
-				m->mothurOut("Pearson's coefficient using " + toString(i) + " axis: " + toString(corr)); m->mothurOutEndLine();
+				m->mothurOut("Rsq " + toString(i) + " axis: " + toString(corr * corr)); m->mothurOutEndLine();
 				
 				if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str());  } return 0; }
 			}
@@ -277,11 +276,11 @@ void PCOACommand::output(string fnameRoot, vector<string> name_list, vector<vect
 			}
 		}
 		
-		ofstream pcaData((fnameRoot+"pcoa").c_str(), ios::trunc);
+		ofstream pcaData((fnameRoot+"pcoa.axes").c_str(), ios::trunc);
 		pcaData.setf(ios::fixed, ios::floatfield);
 		pcaData.setf(ios::showpoint);	
-		outputNames.push_back(fnameRoot+"pcoa");
-		outputTypes["pcoa"].push_back(fnameRoot+"pcoa");
+		outputNames.push_back(fnameRoot+"pcoa.axes");
+		outputTypes["pcoa"].push_back(fnameRoot+"pcoa.axes");
 		
 		ofstream pcaLoadings((fnameRoot+"pcoa.loadings").c_str(), ios::trunc);
 		pcaLoadings.setf(ios::fixed, ios::floatfield);