1.21.0

[mothur.git] / rarefactsharedcommand.cpp

diff --git a/rarefactsharedcommand.cpp b/rarefactsharedcommand.cpp
index fb5527a03faa02c913e48a583e0a32705932ec45..02f434ae79f2d74c814aef0a6c4f7ecfa67f1ab4 100644 (file)
--- a/rarefactsharedcommand.cpp
+++ b/rarefactsharedcommand.cpp
@@ -81,6 +81,7 @@ RareFactSharedCommand::RareFactSharedCommand(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();
@@ -123,7 +124,7 @@ RareFactSharedCommand::RareFactSharedCommand(string option)  {
                                sharedfile = m->getSharedFile(); 
                                if (sharedfile != "") { m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
                                else {  m->mothurOut("You have no current sharedfile and the shared parameter is required."); m->mothurOutEndLine(); abort = true; }
-                       }
+                       }else { m->setSharedFile(sharedfile); }
                        
                        
                        //if the user changes the output directory command factory will send this info to us in the output parameter 
@@ -146,6 +147,11 @@ RareFactSharedCommand::RareFactSharedCommand(string option)  {
                                 if (calc == "default")  {  calc = "sharedobserved";  }
                        }
                        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; } }
+                       }
                        
                        groups = validParameter.validFile(parameters, "groups", false);                 
                        if (groups == "not found") { groups = ""; }
@@ -208,7 +214,7 @@ int RareFactSharedCommand::execute(){
                        m->Groups.clear(); 
                        delete input;
                        for(int i=0;i<rDisplays.size();i++){    delete rDisplays[i];    }
-                       for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());         }
+                       for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);        }
                        for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } 
                        return 0;
                }
@@ -230,7 +236,7 @@ int RareFactSharedCommand::execute(){
                                m->Groups.clear(); 
                                delete input;
                                for(int i=0;i<rDisplays.size();i++){    delete rDisplays[i];    }
-                               for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());         }
+                               for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);        }
                                for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } 
                                return 0;
                        }
@@ -275,7 +281,7 @@ int RareFactSharedCommand::execute(){
                        m->Groups.clear(); 
                        delete input;
                        for(int i=0;i<rDisplays.size();i++){    delete rDisplays[i];    }
-                       for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());         }
+                       for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);        }
                        return 0;
                }
                
@@ -296,7 +302,7 @@ int RareFactSharedCommand::execute(){
                        m->Groups.clear(); 
                        delete input; 
                        for(int i=0;i<rDisplays.size();i++){    delete rDisplays[i];    }
-                       for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());         }
+                       for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);        }
                        return 0;
                }
                
@@ -316,7 +322,7 @@ int RareFactSharedCommand::execute(){
                m->Groups.clear(); 
                delete input;
                
-               if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str()); } return 0; }
+               if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]); } return 0; }
                
                m->mothurOutEndLine();
                m->mothurOut("Output File Names: "); m->mothurOutEndLine();