changes to beta diversity calculators

[mothur.git] / rarefactcommand.cpp

diff --git a/rarefactcommand.cpp b/rarefactcommand.cpp
index b6ad295e819a0bef866270c79cea6c61ae7e567c..82251c4a8fad67ea36fea2d7232b2f9171d5e3f5 100644 (file)
--- a/rarefactcommand.cpp
+++ b/rarefactcommand.cpp
@@ -64,7 +64,7 @@ string RareFactCommand::getHelpString(){
                helpString += "The default values for iters is 1000, freq is 100, and calc is rarefaction which calculates the rarefaction curve for the observed richness.\n";
                validCalculator.printCalc("rarefaction");
                helpString += "The label parameter is used to analyze specific labels in your input.\n";
-               helpString += "Note: No spaces between parameter labels (i.e. freq), '=' and parameters (i.e.yourFreq).\n\n";
+               helpString += "Note: No spaces between parameter labels (i.e. freq), '=' and parameters (i.e.yourFreq).\n";
                return helpString;
        }
        catch(exception& e) {
@@ -107,7 +107,8 @@ RareFactCommand::RareFactCommand(string option)  {
                allLines = 1;
                                                
                //allow user to run help
-               if(option == "help") { abort = true; calledHelp = true; }
+               if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();
@@ -242,6 +243,11 @@ RareFactCommand::RareFactCommand(string option)  {
                                 if (calc == "default")  {  calc = "sobs";  }
                        }
                        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, "freq", false);                     if (temp == "not found") { temp = "100"; }