fixed an mpi bug in shhh.seqs

[mothur.git] / pcacommand.cpp

diff --git a/pcacommand.cpp b/pcacommand.cpp
index 0842c53163a51da38800598281cde5c30d3e6778..2e8f132eefa8a491f1b5e23a2d9650da22ee1c84 100644 (file)
--- 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);
@@ -364,11 +363,11 @@ void PCACommand::output(string fnameRoot, vector<string> name_list, vector<vecto
                        }
                }
                
-               ofstream pcaData((fnameRoot+".pca").c_str(), ios::trunc);
+               ofstream pcaData((fnameRoot+".pca.axes").c_str(), ios::trunc);
                pcaData.setf(ios::fixed, ios::floatfield);
                pcaData.setf(ios::showpoint);   
-               outputNames.push_back(fnameRoot+".pca");
-               outputTypes["pca"].push_back(fnameRoot+".pca");
+               outputNames.push_back(fnameRoot+".pca.axes");
+               outputTypes["pca"].push_back(fnameRoot+".pca.axes");
                
                ofstream pcaLoadings((fnameRoot+".pca.loadings").c_str(), ios::trunc);
                pcaLoadings.setf(ios::fixed, ios::floatfield);