minor mods to seq.error

[mothur.git] / getsharedotucommand.cpp

diff --git a/getsharedotucommand.cpp b/getsharedotucommand.cpp
index f12b1cd19a4a6a1f5c0c61074d4dc22e68aac6dd..06e199f7a93c96e71ba5cb15f1cafd21c8ca2d8e 100644 (file)
--- a/getsharedotucommand.cpp
+++ b/getsharedotucommand.cpp
@@ -49,7 +49,7 @@ string GetSharedOTUCommand::getHelpString(){
                helpString += "Example get.sharedseqs(list=amazon.fn.list, label=unique-0.01, group=forest-pasture, fasta=amazon.fasta, output=accnos).\n";
                helpString += "The output to the screen is the distance and the number of otus at that distance for the groups you specified.\n";
                helpString += "The default value for label is all labels in your inputfile. The default for groups is all groups in your file.\n";
-               helpString += "Note: No spaces between parameter labels (i.e. label), '=' and parameters (i.e.yourLabel).\n\n";
+               helpString += "Note: No spaces between parameter labels (i.e. label), '=' and parameters (i.e.yourLabel).\n";
                return helpString;
        }
        catch(exception& e) {
@@ -82,6 +82,7 @@ GetSharedOTUCommand::GetSharedOTUCommand(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();
@@ -147,7 +148,7 @@ GetSharedOTUCommand::GetSharedOTUCommand(string option)  {
                                        m->mothurOut("No valid current list file. You must provide a list file."); m->mothurOutEndLine(); 
                                        abort = true;
                                }
-                       }else {  format = "list";       }
+                       }else {  format = "list";       m->setListFile(listfile); }
                        
                        groupfile = validParameter.validFile(parameters, "group", true);
                        if (groupfile == "not open") { abort = true; }  
@@ -158,7 +159,7 @@ GetSharedOTUCommand::GetSharedOTUCommand(string option)  {
                                        m->mothurOut("No valid current group file. You must provide a group file."); m->mothurOutEndLine(); 
                                        abort = true;
                                }
-                       }
+                       }else { m->setGroupFile(groupfile); }
                                                
                        if ((listfile == "") || (groupfile == "")) { m->mothurOut("The list and group parameters are required."); m->mothurOutEndLine(); abort = true; }
                        
@@ -196,7 +197,7 @@ GetSharedOTUCommand::GetSharedOTUCommand(string option)  {
                        fastafile = validParameter.validFile(parameters, "fasta", true);
                        if (fastafile == "not open") { abort = true; }
                        else if (fastafile == "not found") {  fastafile = "";  }        
-                               
+                       else { m->setFastaFile(fastafile); }
                }
 
        }