added getCommandInfoCommand for gui

[mothur.git] / collectcommand.cpp

diff --git a/collectcommand.cpp b/collectcommand.cpp
index adaff9b1bc7b17d979b30106de2ee88c0d03631d..5549fd121dfca80e5cd4a406084f68803875dc58 100644 (file)
--- a/collectcommand.cpp
+++ b/collectcommand.cpp
@@ -63,15 +63,16 @@ vector<string> CollectCommand::setParameters(){
 string CollectCommand::getHelpString(){        
        try {
                string helpString = "";
+               ValidCalculators validCalculator;
                helpString += "The collect.single command parameters are list, sabund, rabund, shared, label, freq, calc and abund.  list, sabund, rabund or shared is required unless you have a valid current file. \n";
                helpString += "The collect.single command should be in the following format: \n";
                helpString += "The freq parameter is used indicate when to output your data, by default it is set to 100. But you can set it to a percentage of the number of sequence. For example freq=0.10, means 10%. \n";
                helpString += "collect.single(label=yourLabel, iters=yourIters, freq=yourFreq, calc=yourEstimators).\n";
                helpString += "Example collect(label=unique-.01-.03, iters=10000, freq=10, calc=sobs-chao-ace-jack).\n";
                helpString += "The default values for freq is 100, and calc are sobs-chao-ace-jack-shannon-npshannon-simpson.\n";
-               helpString += validCalculator->printCalc("single");
+               helpString += validCalculator.printCalc("single");
                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) {
@@ -123,7 +124,7 @@ CollectCommand::CollectCommand(string option)  {
                allLines = 1;
                
                //allow user to run help
-               if(option == "help") { validCalculator = new ValidCalculators(); help(); delete validCalculator; abort = true; }
+               if(option == "help") { help(); abort = true; }
                
                else {
                        vector<string> myArray = setParameters();
@@ -310,10 +311,10 @@ int CollectCommand::execute(){
                                m->mothurOutEndLine(); m->mothurOut("Processing group " + groups[p]); m->mothurOutEndLine(); m->mothurOutEndLine();
                        }
                
-                       validCalculator = new ValidCalculators();
+                       ValidCalculators validCalculator;
                        
                        for (int i=0; i<Estimators.size(); i++) {
-                               if (validCalculator->isValidCalculator("single", Estimators[i]) == true) { 
+                               if (validCalculator.isValidCalculator("single", Estimators[i]) == true) { 
                                        if (Estimators[i] == "sobs") { 
                                                cDisplays.push_back(new CollectDisplay(new Sobs(), new OneColumnFile(fileNameRoot+"sobs")));
                                                outputNames.push_back(fileNameRoot+"sobs"); outputTypes["sobs"].push_back(fileNameRoot+"sobs");
@@ -409,7 +410,6 @@ int CollectCommand::execute(){
                                for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());         } outputTypes.clear(); 
                                delete input;  
                                delete order; 
-                               delete validCalculator;
                                m->Groups.clear();
                                return 0;
                        }
@@ -422,7 +422,6 @@ int CollectCommand::execute(){
                                        for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());         } outputTypes.clear(); 
                                        delete input;  
                                        delete order; 
-                                       delete validCalculator;
                                        m->Groups.clear();
                                        return 0;
                                }
@@ -471,7 +470,6 @@ int CollectCommand::execute(){
                                        for(int i=0;i<cDisplays.size();i++){    delete cDisplays[i];    }
                                        for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());         } outputTypes.clear(); 
                                        delete input;  
-                                       delete validCalculator;
                                        m->Groups.clear();
                                        return 0;
                        }
@@ -504,8 +502,7 @@ int CollectCommand::execute(){
                                        for(int i=0;i<cDisplays.size();i++){    delete cDisplays[i];    }
                                        for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());         } outputTypes.clear(); 
                                        delete input;  
-                                       delete order; 
-                                       delete validCalculator;
+                                       delete order;
                                        m->Groups.clear();
                                        return 0;
                                }
@@ -515,7 +512,6 @@ int CollectCommand::execute(){
                        for(int i=0;i<cDisplays.size();i++){    delete cDisplays[i];    }
                        cDisplays.clear();
                        delete input;  
-                       delete validCalculator;
                }
                
                if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str());         } return 0; }