mods for 1.16

[mothur.git] / pcacommand.cpp

diff --git a/pcacommand.cpp b/pcacommand.cpp
index 89e1cb71f282aa2f2606b84ae3aba03da5c74f6b..4ca977876e8fe9bf250338c799f3cd69d2a29062 100644 (file)
--- a/pcacommand.cpp
+++ b/pcacommand.cpp
@@ -111,7 +111,7 @@ 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);                 
@@ -130,7 +130,7 @@ 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 groups parameter allows you to specify which groups you would like analyzed. Groupnames are separated by dashes.\n");