added name option to trim.seqs

[mothur.git] / matrixoutputcommand.cpp

diff --git a/matrixoutputcommand.cpp b/matrixoutputcommand.cpp
index effc368e0c7f932b719925a0afb349b5afee4bdf..7fbd83059dbc7ef882e889cbc7b9a7d8563d4b0c 100644 (file)
--- a/matrixoutputcommand.cpp
+++ b/matrixoutputcommand.cpp
@@ -74,6 +74,7 @@ vector<string> MatrixOutputCommand::setParameters(){
 string MatrixOutputCommand::getHelpString(){   
        try {
                string helpString = "";
+               ValidCalculators validCalculator;
                helpString += "The dist.shared command parameters are shared, groups, calc, output and label.  shared is a required, unless you have a valid current file.\n";
                helpString += "The groups parameter allows you to specify which of the groups in your groupfile you would like included used.\n";
                helpString += "The group names are separated by dashes. The label parameter allows you to select what distance levels you would like distance matrices created for, and is also separated by dashes.\n";
@@ -82,9 +83,9 @@ string MatrixOutputCommand::getHelpString(){
                helpString += "Example dist.shared(groups=A-B-C, calc=jabund-sorabund).\n";
                helpString += "The default value for groups is all the groups in your groupfile.\n";
                helpString += "The default value for calc is jclass and thetayc.\n";
-               helpString += validCalculator->printCalc("matrix");
+               helpString += validCalculator.printCalc("matrix");
                helpString += "The dist.shared command outputs a .dist file for each calculator you specify at each distance you choose.\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) {
@@ -113,7 +114,8 @@ MatrixOutputCommand::MatrixOutputCommand(string option)  {
                allLines = 1;
                                
                //allow user to run help
-               if(option == "help") { validCalculator = new ValidCalculators(); 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();
@@ -186,14 +188,19 @@ MatrixOutputCommand::MatrixOutputCommand(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; } }
+                       }
 
                        if (abort == false) {
                        
-                               validCalculator = new ValidCalculators();
+                               ValidCalculators validCalculator;
                                
                                int i;
                                for (i=0; i<Estimators.size(); i++) {
-                                       if (validCalculator->isValidCalculator("matrix", Estimators[i]) == true) { 
+                                       if (validCalculator.isValidCalculator("matrix", Estimators[i]) == true) { 
                                                if (Estimators[i] == "sharedsobs") { 
                                                        matrixCalculators.push_back(new SharedSobsCS());
                                                }else if (Estimators[i] == "sharedchao") { 
@@ -288,11 +295,7 @@ MatrixOutputCommand::MatrixOutputCommand(string option)  {
 
 //**********************************************************************************************************************
 
-MatrixOutputCommand::~MatrixOutputCommand(){
-       if (abort == false) {
-               delete validCalculator;
-       }
-}
+MatrixOutputCommand::~MatrixOutputCommand(){}
 
 //**********************************************************************************************************************