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

[mothur.git] / sharedcommand.cpp

diff --git a/sharedcommand.cpp b/sharedcommand.cpp
index fb3691e662a7ee2b378d8e1dd13e4221b698106d..454bb0558cce6080cdd1859fc0382ed3d47360e3 100644 (file)
--- a/sharedcommand.cpp
+++ b/sharedcommand.cpp
@@ -14,17 +14,69 @@ inline bool compareSharedRabunds(SharedRAbundVector* left, SharedRAbundVector* r
        return (left->getGroup() < right->getGroup());  
 } 
 //**********************************************************************************************************************
+vector<string> SharedCommand::getValidParameters(){    
+       try {
+               vector<string> myArray; 
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "SharedCommand", "getValidParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+SharedCommand::SharedCommand(){        
+       try {
+               //initialize outputTypes
+               vector<string> tempOutNames;
+               outputTypes["rabund"] = tempOutNames;
+               outputTypes["shared"] = tempOutNames;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "SharedCommand", "SharedCommand");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+vector<string> SharedCommand::getRequiredParameters(){ 
+       try {
+               vector<string> myArray;
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "SharedCommand", "getRequiredParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+vector<string> SharedCommand::getRequiredFiles(){      
+       try {
+               vector<string> myArray;
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "SharedCommand", "getRequiredFiles");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
 
 SharedCommand::SharedCommand(string o) : outputDir(o) {
        try {
                globaldata = GlobalData::getInstance();
                
+               //initialize outputTypes
+               vector<string> tempOutNames;
+               outputTypes["rabund"] = tempOutNames;
+               outputTypes["shared"] = tempOutNames;
+               
                //getting output filename
                filename = globaldata->inputFileName;
                if (outputDir == "") { outputDir += m->hasPath(filename); }
                
                filename = outputDir + m->getRootName(m->getSimpleName(filename));
                filename = filename + "shared";
+               outputTypes["shared"].push_back(filename);
                
                m->openOutputFile(filename, out);
                pickedGroups = false;
@@ -54,6 +106,7 @@ SharedCommand::SharedCommand(string o) : outputDir(o) {
                for (int i=0; i<groups.size(); i++) {
                        remove((fileroot + groups[i] + ".rabund").c_str());
                        outputNames.push_back((fileroot + groups[i] + ".rabund"));
+                       outputTypes["rabund"].push_back((fileroot + groups[i] + ".rabund"));
                }
 
        }