minor mods to seq.error

[mothur.git] / classifyotucommand.cpp

diff --git a/classifyotucommand.cpp b/classifyotucommand.cpp
index 5ac7e2c4bd618dac3ce498a0a883ca6722980311..d065b3a37c5ac41f9c6c3b59eb9ca3832f8697a9 100644 (file)
--- a/classifyotucommand.cpp
+++ b/classifyotucommand.cpp
@@ -87,7 +87,8 @@ ClassifyOtuCommand::ClassifyOtuCommand(string option)  {
                //allow user to run help
                if (option == "help") { 
                        help(); abort = true; calledHelp = true;
-               } else {
+               }else if(option == "citation") { citation(); abort = true; calledHelp = true;} 
+               else {
                        vector<string> myArray = setParameters();
                        
                        OptionParser parser(option);
@@ -165,6 +166,7 @@ ClassifyOtuCommand::ClassifyOtuCommand(string option)  {
                                else {  m->mothurOut("You have no current listfile and the list parameter is required."); m->mothurOutEndLine(); abort = true; }
                        }
                        else if (listfile == "not open") { abort = true; }      
+                       else { m->setListFile(listfile); }
                        
                        taxfile = validParameter.validFile(parameters, "taxonomy", true);
                        if (taxfile == "not found") {  //if there is a current list file, use it
@@ -173,6 +175,7 @@ ClassifyOtuCommand::ClassifyOtuCommand(string option)  {
                                else {  m->mothurOut("You have no current taxonomy file and the taxonomy parameter is required."); m->mothurOutEndLine(); abort = true; }
                        }
                        else if (taxfile == "not open") { abort = true; }
+                       else { m->setTaxonomyFile(taxfile); }
                        
                        refTaxonomy = validParameter.validFile(parameters, "reftaxonomy", true);
                        if (refTaxonomy == "not found") { refTaxonomy = ""; m->mothurOut("reftaxonomy is not required, but if given will keep the rankIDs in the summary file static."); m->mothurOutEndLine(); }
@@ -181,10 +184,12 @@ ClassifyOtuCommand::ClassifyOtuCommand(string option)  {
                        namefile = validParameter.validFile(parameters, "name", true);
                        if (namefile == "not open") { abort = true; }   
                        else if (namefile == "not found") { namefile = ""; }
+                       else { m->setNameFile(namefile); }
                        
                        groupfile = validParameter.validFile(parameters, "group", true);
                        if (groupfile == "not open") { abort = true; }  
                        else if (groupfile == "not found") { groupfile = ""; }
+                       else { m->setGroupFile(groupfile); }
                        
                        //check for optional parameter and set defaults
                        // ...at some point should added some additional type checking...