paralellized seq.error and dist.shared added some error checks to libshuff and dist...

[mothur.git] / treegroupscommand.cpp

diff --git a/treegroupscommand.cpp b/treegroupscommand.cpp
index e5b7e74a7d71343af56fcb0dc6c54a18b61afd73..582a3233ae847f64bc74209e14c918d2b6ebdc45 100644 (file)
--- a/treegroupscommand.cpp
+++ b/treegroupscommand.cpp
@@ -94,7 +94,7 @@ string TreeGroupCommand::getHelpString(){
                helpString += validCalculator.printCalc("treegroup");
                helpString += "Or the tree.shared command can be in the following format: tree.shared(phylip=yourPhylipFile).\n";
                helpString += "Example tree.shared(phylip=abrecovery.dist).\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) {
@@ -125,6 +125,7 @@ TreeGroupCommand::TreeGroupCommand(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();
@@ -247,6 +248,11 @@ TreeGroupCommand::TreeGroupCommand(string option)  {
                                 if (calc == "default")  {  calc = "jclass-thetayc";  }
                        }
                        m->splitAtDash(calc, Estimators);
+                       if (m->inUsersGroups("citation", Estimators)) { 
+                               ValidCalculators validCalc; validCalc.printCitations(Estimators); 
+                               //remove citation from list of calcs
+                               for (int i = 0; i < Estimators.size(); i++) { if (Estimators[i] == "citation") {  Estimators.erase(Estimators.begin()+i); break; } }
+                       }
 
                        string temp;
                        temp = validParameter.validFile(parameters, "precision", false);                        if (temp == "not found") { temp = "100"; }