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

[mothur.git] / getlineagecommand.cpp

diff --git a/getlineagecommand.cpp b/getlineagecommand.cpp
index 5ace2a1077b4fe6984c470218c2aaee80113a041..a1d44857531ddea86b025ac1b6d0d888f21df702 100644 (file)
--- a/getlineagecommand.cpp
+++ b/getlineagecommand.cpp
@@ -11,8 +11,60 @@
 #include "sequence.hpp"
 #include "listvector.hpp"
 
-//**********************************************************************************************************************
 
+//**********************************************************************************************************************
+vector<string> GetLineageCommand::getValidParameters(){        
+       try {
+               string Array[] =  {"fasta","name", "group", "alignreport", "taxon", "dups", "list","taxonomy","outputdir","inputdir"};
+               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "GetLineageCommand", "getValidParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+GetLineageCommand::GetLineageCommand(){        
+       try {
+               //initialize outputTypes
+               vector<string> tempOutNames;
+               outputTypes["fasta"] = tempOutNames;
+               outputTypes["taxonomy"] = tempOutNames;
+               outputTypes["name"] = tempOutNames;
+               outputTypes["group"] = tempOutNames;
+               outputTypes["alignreport"] = tempOutNames;
+               outputTypes["list"] = tempOutNames;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "GetLineageCommand", "GetLineageCommand");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+vector<string> GetLineageCommand::getRequiredParameters(){     
+       try {
+               string Array[] =  {"taxonomy"};
+               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "GetLineageCommand", "getRequiredParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+vector<string> GetLineageCommand::getRequiredFiles(){  
+       try {
+               vector<string> myArray;
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "GetLineageCommand", "getRequiredFiles");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
 GetLineageCommand::GetLineageCommand(string option)  {
        try {
                abort = false;
@@ -36,6 +88,15 @@ GetLineageCommand::GetLineageCommand(string option)  {
                                if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
                        }
                        
+                       //initialize outputTypes
+                       vector<string> tempOutNames;
+                       outputTypes["fasta"] = tempOutNames;
+                       outputTypes["taxonomy"] = tempOutNames;
+                       outputTypes["name"] = tempOutNames;
+                       outputTypes["group"] = tempOutNames;
+                       outputTypes["alignreport"] = tempOutNames;
+                       outputTypes["list"] = tempOutNames;
+
                        //if the user changes the output directory command factory will send this info to us in the output parameter 
                        outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = "";         }
                        
@@ -183,7 +244,7 @@ int GetLineageCommand::execute(){
                if (listfile != "")                     {               readList();             }
                
                
-               if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str());  } return 0; }
+               if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) {   remove(outputNames[i].c_str());  } return 0; }
                
                if (outputNames.size() != 0) {
                        m->mothurOutEndLine();
@@ -238,7 +299,7 @@ int GetLineageCommand::readFasta(){
                out.close();
                
                if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();  }
-               outputNames.push_back(outputFileName); 
+               outputNames.push_back(outputFileName);  outputTypes["fasta"].push_back(outputFileName);
                
                return 0;
 
@@ -310,7 +371,7 @@ int GetLineageCommand::readList(){
                out.close();
                
                if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();  }
-               outputNames.push_back(outputFileName); 
+               outputNames.push_back(outputFileName); outputTypes["list"].push_back(outputFileName);
                
                return 0;
 
@@ -403,7 +464,7 @@ int GetLineageCommand::readName(){
                out.close();
                
                if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();  }
-               outputNames.push_back(outputFileName); 
+               outputNames.push_back(outputFileName);  outputTypes["name"].push_back(outputFileName);
                
                return 0;
                
@@ -451,7 +512,7 @@ int GetLineageCommand::readGroup(){
                out.close();
                
                if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();  }
-               outputNames.push_back(outputFileName); 
+               outputNames.push_back(outputFileName);  outputTypes["group"].push_back(outputFileName);
                
                return 0;
 
@@ -504,7 +565,7 @@ int GetLineageCommand::readTax(){
                out.close();
                
                if (names.size() == 0) { m->mothurOut("Your taxonomy file does not contain any sequences from " + taxons + "."); m->mothurOutEndLine();  }
-               outputNames.push_back(outputFileName); 
+               outputNames.push_back(outputFileName); outputTypes["taxonomy"].push_back(outputFileName);
                        
                return 0;
 
@@ -595,7 +656,7 @@ int GetLineageCommand::readAlign(){
                out.close();
                
                if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();  }
-               outputNames.push_back(outputFileName); 
+               outputNames.push_back(outputFileName); outputTypes["alignreport"].push_back(outputFileName);
                
                return 0;