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

[mothur.git] / secondarystructurecommand.cpp

diff --git a/secondarystructurecommand.cpp b/secondarystructurecommand.cpp
index c08ee6ab2d512b56c6d39fa2a1290ab12da22bde..36e0f609ca67bd3cd37e7c0d33a98e88cee65e6f 100644 (file)
--- a/secondarystructurecommand.cpp
+++ b/secondarystructurecommand.cpp
@@ -10,6 +10,53 @@
 #include "secondarystructurecommand.h"
 #include "sequence.hpp"
 
+//**********************************************************************************************************************
+vector<string> AlignCheckCommand::getValidParameters(){        
+       try {
+               string Array[] =  {"fasta","map", "outputdir","inputdir"};
+               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "AlignCheckCommand", "getValidParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+AlignCheckCommand::AlignCheckCommand(){        
+       try {
+               //initialize outputTypes
+               vector<string> tempOutNames;
+               outputTypes["aligncheck"] = tempOutNames;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "AlignCheckCommand", "AlignCheckCommand");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+vector<string> AlignCheckCommand::getRequiredParameters(){     
+       try {
+               string Array[] =  {"fasta","map"};
+               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "AlignCheckCommand", "getRequiredParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+vector<string> AlignCheckCommand::getRequiredFiles(){  
+       try {
+               vector<string> myArray;
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "AlignCheckCommand", "getRequiredFiles");
+               exit(1);
+       }
+}
 //**********************************************************************************************************************
 
 AlignCheckCommand::AlignCheckCommand(string option)  {
@@ -36,6 +83,10 @@ AlignCheckCommand::AlignCheckCommand(string option)  {
                                if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
                        }
                        
+                       //initialize outputTypes
+                       vector<string> tempOutNames;
+                       outputTypes["aligncheck"] = tempOutNames;
+                       
                        //if the user changes the input directory command factory will send this info to us in the output parameter 
                        string inputDir = validParameter.validFile(parameters, "inputdir", false);              
                        if (inputDir == "not found"){   inputDir = "";          }
@@ -140,7 +191,7 @@ int AlignCheckCommand::execute(){
                
                m->mothurOutEndLine();
                m->mothurOut("Output File Name: "); m->mothurOutEndLine();
-               m->mothurOut(outfile); m->mothurOutEndLine();   
+               m->mothurOut(outfile); m->mothurOutEndLine();   outputNames.push_back(outfile); outputTypes["aligncheck"].push_back(outfile);
                m->mothurOutEndLine();
                
                return 0;