X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=pcacommand.cpp;h=2e8f132eefa8a491f1b5e23a2d9650da22ee1c84;hb=74d3aaf0f85080ea3cfb1f1871e706bab9f48392;hp=89e1cb71f282aa2f2606b84ae3aba03da5c74f6b;hpb=e6c4a7223199d800d496356604eb34dfe273673d;p=mothur.git

diff --git a/pcacommand.cpp b/pcacommand.cpp
index 89e1cb7..2e8f132 100644
--- a/pcacommand.cpp
+++ b/pcacommand.cpp
@@ -25,8 +25,7 @@ vector<string> PCACommand::getValidParameters(){
 //**********************************************************************************************************************
 PCACommand::PCACommand(){	
 	try {
-		abort = true;
-		//initialize outputTypes
+		abort = true; calledHelp = true; 
 		vector<string> tempOutNames;
 		outputTypes["pca"] = tempOutNames;
 		outputTypes["loadings"] = tempOutNames;
@@ -63,12 +62,12 @@ vector<string> PCACommand::getRequiredFiles(){
 
 PCACommand::PCACommand(string option)  {
 	try {
-		abort = false;
+		abort = false; calledHelp = false;   
 		
 		globaldata = GlobalData::getInstance();
 		
 		//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
@@ -111,7 +110,7 @@ PCACommand::PCACommand(string option)  {
 			metric = m->isTrue(temp); 
 			
 			label = validParameter.validFile(parameters, "label", false);			
-			if (label == "not found") { label = ""; m->mothurOut("You did not provide a label, I will use the first label in your inputfile."); m->mothurOutEndLine();  }	
+			if (label == "not found") { label = ""; labels = globaldata->labels; if(labels.size() == 0) {  m->mothurOut("You did not provide a label, I will use the first label in your inputfile."); m->mothurOutEndLine(); } }
 			else { m->splitAtDash(label, labels); }
 			
 			groups = validParameter.validFile(parameters, "groups", false);			
@@ -130,9 +129,9 @@ PCACommand::PCACommand(string option)  {
 //**********************************************************************************************************************
 void PCACommand::help(){
 	try {
-		m->mothurOut("The pca command can only be run after a successful read.otu command."); m->mothurOutEndLine();
+		m->mothurOut("The pca command can only be run after a successful read.otu command of a shared or relabund file."); m->mothurOutEndLine();
 		m->mothurOut("The pca command parameters are label, groups and metric. No parameters are required."); m->mothurOutEndLine();
-		m->mothurOut("The label parameter is used to analyze specific labels in your input. Default is the first label in your shared or relabund file. Multpile labels may be separated by dashes.\n");
+		m->mothurOut("The label parameter is used to analyze specific labels in your input. Default is the first label in your shared or relabund file. Multiple labels may be separated by dashes.\n");
 		m->mothurOut("The groups parameter allows you to specify which groups you would like analyzed. Groupnames are separated by dashes.\n");
 		m->mothurOut("The metric parameter allows indicate you if would like the pearson correlation coefficient calculated. Default=True"); m->mothurOutEndLine();
 		m->mothurOut("Example pca(groups=yourGroups).\n");
@@ -150,7 +149,7 @@ PCACommand::~PCACommand(){}
 int PCACommand::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);