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

[mothur.git] / getseqscommand.cpp

diff --git a/getseqscommand.cpp b/getseqscommand.cpp
index 1926ae0b017abc926c2256e2c3b0396de1dbae40..34788b8897cca88fa06ba46a5b37f88b70df70c0 100644 (file)
--- a/getseqscommand.cpp
+++ b/getseqscommand.cpp
@@ -12,7 +12,58 @@
 #include "listvector.hpp"
 
 //**********************************************************************************************************************
-
+vector<string> GetSeqsCommand::getValidParameters(){   
+       try {
+               string Array[] =  {"fasta","name", "group", "alignreport", "accnos", "dups", "list","taxonomy","outputdir","inputdir"};
+               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "GetSeqsCommand", "getValidParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+GetSeqsCommand::GetSeqsCommand(){      
+       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, "GetSeqsCommand", "GetSeqsCommand");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+vector<string> GetSeqsCommand::getRequiredParameters(){        
+       try {
+               string Array[] =  {"accnos"};
+               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "GetSeqsCommand", "getRequiredParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+vector<string> GetSeqsCommand::getRequiredFiles(){     
+       try {
+               vector<string> myArray;
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "GetSeqsCommand", "getRequiredFiles");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
 GetSeqsCommand::GetSeqsCommand(string option)  {
        try {
                abort = false;
@@ -36,6 +87,15 @@ GetSeqsCommand::GetSeqsCommand(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 = "";         }
                        
@@ -185,7 +245,7 @@ int GetSeqsCommand::execute(){
                if (listfile != "")                     {               readList();             }
                if (taxfile != "")                      {               readTax();              }
                
-               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();
@@ -240,7 +300,7 @@ int GetSeqsCommand::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;
 
@@ -312,7 +372,7 @@ int GetSeqsCommand::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;
 
@@ -405,7 +465,7 @@ int GetSeqsCommand::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;
                
@@ -453,7 +513,7 @@ int GetSeqsCommand::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;
 
@@ -498,7 +558,7 @@ int GetSeqsCommand::readTax(){
                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["taxonomy"].push_back(outputFileName);
                        
                return 0;
 
@@ -566,7 +626,7 @@ int GetSeqsCommand::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;