added pipeline commands which involved change to command factory and command class...

[mothur.git] / readdistcommand.cpp

diff --git a/readdistcommand.cpp b/readdistcommand.cpp
index 0445eec63328e2cf7a646f1cc662bb36fdd3bb98..c600eb86c969303f608b6a440dedb77af3e50b1d 100644 (file)
--- a/readdistcommand.cpp
+++ b/readdistcommand.cpp
@@ -12,6 +12,42 @@
 #include "readcolumn.h"
 #include "readmatrix.hpp"
 
+//**********************************************************************************************************************
+vector<string> ReadDistCommand::getValidParameters(){  
+       try {
+               string Array[] =  {"phylip", "column", "name", "cutoff", "precision", "group","outputdir","inputdir","sim"};
+               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "ReadDistCommand", "getValidParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+vector<string> ReadDistCommand::getRequiredParameters(){       
+       try {
+               string Array[] =  {"phylip","column","or"};
+               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "ReadDistCommand", "getRequiredParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+vector<string> ReadDistCommand::getRequiredFiles(){    
+       try {
+               vector<string> myArray;
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "ReadDistCommand", "getRequiredFiles");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
 ReadDistCommand::ReadDistCommand(string option) {
        try {
                globaldata = GlobalData::getInstance();
@@ -208,8 +244,6 @@ int ReadDistCommand::execute(){
                time_t start = time(NULL);
                size_t numDists = 0;
                
-               vector<string> outputNames;
-               
                if (format == "matrix") {
                        ifstream in;
                        m->openInputFile(distFileName, in);