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

[mothur.git] / removelineagecommand.cpp

diff --git a/removelineagecommand.cpp b/removelineagecommand.cpp
index d3160194fa5bea985ae0fd96e7cad8de3e73020a..557622db59b1f5480a87fda36050e98cfb9439a9 100644 (file)
--- a/removelineagecommand.cpp
+++ b/removelineagecommand.cpp
@@ -12,7 +12,58 @@
 #include "listvector.hpp"
 
 //**********************************************************************************************************************
-
+vector<string> RemoveLineageCommand::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, "RemoveLineageCommand", "getValidParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+RemoveLineageCommand::RemoveLineageCommand(){  
+       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, "RemoveLineageCommand", "RemoveLineageCommand");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+vector<string> RemoveLineageCommand::getRequiredParameters(){  
+       try {
+               string Array[] =  {"taxonomy"};
+               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "RemoveLineageCommand", "getRequiredParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+vector<string> RemoveLineageCommand::getRequiredFiles(){       
+       try {
+               vector<string> myArray;
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "RemoveLineageCommand", "getRequiredFiles");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
 RemoveLineageCommand::RemoveLineageCommand(string option)  {
        try {
                abort = false;
@@ -36,6 +87,15 @@ RemoveLineageCommand::RemoveLineageCommand(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 = "";         }
                        
@@ -237,7 +297,7 @@ int RemoveLineageCommand::readFasta(){
                out.close();
                
                if (wroteSomething == false) {  m->mothurOut("Your fasta file contains only sequences from " + taxons + "."); m->mothurOutEndLine();  }
-               outputNames.push_back(outputFileName); 
+               outputTypes["fasta"].push_back(outputFileName); 
                
                return 0;
                
@@ -308,7 +368,7 @@ int RemoveLineageCommand::readList(){
                out.close();
                
                if (wroteSomething == false) {  m->mothurOut("Your list file contains only sequences from " + taxons + "."); m->mothurOutEndLine();  }
-               outputNames.push_back(outputFileName); 
+               outputTypes["list"].push_back(outputFileName); 
                                
                return 0;
 
@@ -394,7 +454,7 @@ int RemoveLineageCommand::readName(){
                out.close();
 
                if (wroteSomething == false) {  m->mothurOut("Your name file contains only sequences from " + taxons + "."); m->mothurOutEndLine();  }
-               outputNames.push_back(outputFileName); 
+               outputTypes["name"].push_back(outputFileName);
                                
                return 0;
        }
@@ -438,7 +498,7 @@ int RemoveLineageCommand::readGroup(){
                out.close();
                
                if (wroteSomething == false) {  m->mothurOut("Your group file contains only sequences from " + taxons + "."); m->mothurOutEndLine();  }
-               outputNames.push_back(outputFileName); 
+               outputTypes["group"].push_back(outputFileName);
                
                return 0;
        }
@@ -492,7 +552,7 @@ int RemoveLineageCommand::readTax(){
                out.close();
                
                if (!wroteSomething) { m->mothurOut("Your taxonomy file contains only sequences from " + taxons + "."); m->mothurOutEndLine();  }
-               outputNames.push_back(outputFileName); 
+               outputTypes["taxonomy"].push_back(outputFileName);
                        
                return 0;
 
@@ -582,7 +642,7 @@ int RemoveLineageCommand::readAlign(){
                out.close();
                
                if (wroteSomething == false) {  m->mothurOut("Your align file contains only sequences from " + taxons + "."); m->mothurOutEndLine();  }
-               outputNames.push_back(outputFileName); 
+               outputTypes["alignreport"].push_back(outputFileName);
                
                return 0;