added sequence name to error string in fastq.info. Changed np_shannon to npshannon.

[mothur.git] / rarefactsharedcommand.cpp

diff --git a/rarefactsharedcommand.cpp b/rarefactsharedcommand.cpp
index 746b09e8df8f4719f7ded9504e4f732b49fb559b..64bdbb4ceebd18f5abeff63b26fbb4d4ac3dc924 100644 (file)
--- a/rarefactsharedcommand.cpp
+++ b/rarefactsharedcommand.cpp
@@ -49,7 +49,7 @@ string RareFactSharedCommand::getHelpString(){
                helpString += validCalculator.printCalc("sharedrarefaction");
                helpString += "The label parameter is used to analyze specific labels in your input.\n";
                helpString += "The groups parameter allows you to specify which of the groups in your groupfile you would like analyzed.  You must enter at least 2 valid groups.\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) {
@@ -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 
@@ -146,20 +147,25 @@ 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 = ""; }
                        else { 
                                m->splitAtDash(groups, Groups);
                        }
-                       m->Groups = Groups;
+                       m->setGroups(Groups);
                        
                        string temp;
                        temp = validParameter.validFile(parameters, "freq", false);                     if (temp == "not found") { temp = "100"; }
-                       convert(temp, freq); 
+                       m->mothurConvert(temp, freq); 
                        
                        temp = validParameter.validFile(parameters, "iters", false);                    if (temp == "not found") { temp = "1000"; }
-                       convert(temp, nIters); 
+                       m->mothurConvert(temp, nIters); 
                        
                        temp = validParameter.validFile(parameters, "jumble", false);                   if (temp == "not found") { temp = "T"; }
                        if (m->isTrue(temp)) { jumble = true; }
@@ -205,10 +211,10 @@ int RareFactSharedCommand::execute(){
                string lastLabel = lookup[0]->getLabel();
                
                if (m->control_pressed) { 
-                       m->Groups.clear(); 
+                       m->clearGroups(); 
                        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;
                }
@@ -227,10 +233,10 @@ int RareFactSharedCommand::execute(){
                //as long as you are not at the end of the file or done wih the lines you want
                while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
                        if (m->control_pressed) { 
-                               m->Groups.clear(); 
+                               m->clearGroups(); 
                                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;
                        }
@@ -272,10 +278,10 @@ int RareFactSharedCommand::execute(){
                }
                
                if (m->control_pressed) { 
-                       m->Groups.clear(); 
+                       m->clearGroups(); 
                        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;
                }
                
@@ -293,10 +299,10 @@ int RareFactSharedCommand::execute(){
                }
                
                if (m->control_pressed) { 
-                       m->Groups.clear(); 
+                       m->clearGroups(); 
                        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;
                }
                
@@ -313,10 +319,10 @@ int RareFactSharedCommand::execute(){
                }
                
                for(int i=0;i<rDisplays.size();i++){    delete rDisplays[i];    }       
-               m->Groups.clear(); 
+               m->clearGroups(); 
                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();