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

[mothur.git] / removeseqscommand.cpp

diff --git a/removeseqscommand.cpp b/removeseqscommand.cpp
index 0ab181b411738d38b769a0255baeaf5968308d35..afba6514e0ea1360ef78f65d9470f89e63e18d53 100644 (file)
--- a/removeseqscommand.cpp
+++ b/removeseqscommand.cpp
@@ -12,7 +12,58 @@
 #include "listvector.hpp"
 
 //**********************************************************************************************************************
-
+vector<string> RemoveSeqsCommand::getValidParameters(){        
+       try {
+               string Array[] =  {"fasta","name", "group", "alignreport", "accnos", "list","taxonomy","outputdir","inputdir", "dups" };
+               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "RemoveSeqsCommand", "getValidParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+RemoveSeqsCommand::RemoveSeqsCommand(){        
+       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, "RemoveSeqsCommand", "RemoveSeqsCommand");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+vector<string> RemoveSeqsCommand::getRequiredParameters(){     
+       try {
+               string Array[] =  {"accnos"};
+               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "RemoveSeqsCommand", "getRequiredParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+vector<string> RemoveSeqsCommand::getRequiredFiles(){  
+       try {
+               vector<string> myArray;
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "RemoveSeqsCommand", "getRequiredFiles");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
 RemoveSeqsCommand::RemoveSeqsCommand(string option)  {
        try {
                abort = false;
@@ -36,6 +87,15 @@ RemoveSeqsCommand::RemoveSeqsCommand(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 = "";         }
                        
@@ -243,7 +303,7 @@ int RemoveSeqsCommand::readFasta(){
                out.close();
                
                if (wroteSomething == false) {  m->mothurOut("Your file contains only sequences from the .accnos file."); m->mothurOutEndLine();  }
-               outputNames.push_back(outputFileName); 
+               outputTypes["fasta"].push_back(outputFileName); 
                
                return 0;
                
@@ -314,7 +374,7 @@ int RemoveSeqsCommand::readList(){
                out.close();
                
                if (wroteSomething == false) {  m->mothurOut("Your file contains only sequences from the .accnos file."); m->mothurOutEndLine();  }
-               outputNames.push_back(outputFileName); 
+               outputTypes["list"].push_back(outputFileName); 
                                
                return 0;
 
@@ -400,7 +460,7 @@ int RemoveSeqsCommand::readName(){
                out.close();
 
                if (wroteSomething == false) {  m->mothurOut("Your file contains only sequences from the .accnos file."); m->mothurOutEndLine();  }
-               outputNames.push_back(outputFileName); 
+               outputTypes["name"].push_back(outputFileName);
                                
                return 0;
        }
@@ -444,7 +504,7 @@ int RemoveSeqsCommand::readGroup(){
                out.close();
                
                if (wroteSomething == false) {  m->mothurOut("Your file contains only sequences from the .accnos file."); m->mothurOutEndLine();  }
-               outputNames.push_back(outputFileName); 
+               outputTypes["group"].push_back(outputFileName); 
                
                return 0;
        }
@@ -486,7 +546,7 @@ int RemoveSeqsCommand::readTax(){
                out.close();
                
                if (wroteSomething == false) {  m->mothurOut("Your file contains only sequences from the .accnos file."); m->mothurOutEndLine();  }
-               outputNames.push_back(outputFileName); 
+               outputTypes["taxonomy"].push_back(outputFileName);
                
                return 0;
        }
@@ -552,7 +612,7 @@ int RemoveSeqsCommand::readAlign(){
                out.close();
                
                if (wroteSomething == false) {  m->mothurOut("Your file contains only sequences from the .accnos file."); m->mothurOutEndLine();  }
-               outputNames.push_back(outputFileName); 
+               outputTypes["alignreport"].push_back(outputFileName);
                
                return 0;