added cutoff change to mgcluster

[mothur.git] / corraxescommand.cpp

diff --git a/corraxescommand.cpp b/corraxescommand.cpp
index 82cfa3683cbd0801da4a9805a567c84f67d3c427..cd188b8a921a33aaac255852b5ab22d6008f605e 100644 (file)
--- a/corraxescommand.cpp
+++ b/corraxescommand.cpp
@@ -46,7 +46,7 @@ string CorrAxesCommand::getHelpString(){
                helpString += "The corr.axes command should be in the following format: corr.axes(axes=yourPcoaFile, shared=yourSharedFile, method=yourMethod).\n";
                helpString += "Example corr.axes(axes=genus.pool.thetayc.genus.lt.pcoa, shared=genus.pool.shared, method=kendall).\n";
                helpString += "The corr.axes command outputs a .corr.axes file.\n";
-               helpString += "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n\n";
+               helpString += "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n";
                return helpString;
        }
        catch(exception& e) {
@@ -74,6 +74,7 @@ CorrAxesCommand::CorrAxesCommand(string option)  {
                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();
@@ -139,12 +140,12 @@ CorrAxesCommand::CorrAxesCommand(string option)  {
                        sharedfile = validParameter.validFile(parameters, "shared", true);
                        if (sharedfile == "not open") { abort = true; }
                        else if (sharedfile == "not found") { sharedfile = ""; }
-                       else { inputFileName = sharedfile; }
+                       else { inputFileName = sharedfile; m->setSharedFile(sharedfile); }
                        
                        relabundfile = validParameter.validFile(parameters, "relabund", true);
                        if (relabundfile == "not open") { abort = true; }
                        else if (relabundfile == "not found") { relabundfile = ""; }
-                       else { inputFileName = relabundfile; }
+                       else { inputFileName = relabundfile; m->setRelAbundFile(relabundfile); }
                        
                        metadatafile = validParameter.validFile(parameters, "metadata", true);
                        if (metadatafile == "not open") { abort = true; }