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

[mothur.git] / deconvolutecommand.cpp

diff --git a/deconvolutecommand.cpp b/deconvolutecommand.cpp
index b3fa7ddd397e973b7ac3895acfb8c0ebf0505f1f..3129ea0ad368cb8c08a5ca2e9f036c38e4b1a441 100644 (file)
--- a/deconvolutecommand.cpp
+++ b/deconvolutecommand.cpp
@@ -9,6 +9,54 @@
 
 #include "deconvolutecommand.h"
 
+//**********************************************************************************************************************
+vector<string> DeconvoluteCommand::getValidParameters(){       
+       try {
+               string Array[] =  {"fasta", "name","outputdir","inputdir"};
+               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "DeconvoluteCommand", "getValidParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+DeconvoluteCommand::DeconvoluteCommand(){      
+       try {
+               //initialize outputTypes
+               vector<string> tempOutNames;
+               outputTypes["fasta"] = tempOutNames;
+               outputTypes["name"] = tempOutNames;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "DeconvoluteCommand", "DeconvoluteCommand");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+vector<string> DeconvoluteCommand::getRequiredParameters(){    
+       try {
+               string Array[] =  {"fasta"};
+               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "DeconvoluteCommand", "getRequiredParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+vector<string> DeconvoluteCommand::getRequiredFiles(){ 
+       try {
+               vector<string> myArray;
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "DeconvoluteCommand", "getRequiredFiles");
+               exit(1);
+       }
+}
 /**************************************************************************************/
 DeconvoluteCommand::DeconvoluteCommand(string option)  {       
        try {
@@ -33,6 +81,11 @@ DeconvoluteCommand::DeconvoluteCommand(string option)  {
                                if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
                        }
                        
+                       //initialize outputTypes
+                       vector<string> tempOutNames;
+                       outputTypes["fasta"] = tempOutNames;
+                       outputTypes["name"] = tempOutNames;
+               
                        //if the user changes the input directory command factory will send this info to us in the output parameter 
                        string inputDir = validParameter.validFile(parameters, "inputdir", false);              
                        if (inputDir == "not found"){   inputDir = "";          }
@@ -115,12 +168,13 @@ int DeconvoluteCommand::execute() {
                fastamap.printCondensedFasta(outFastaFile);
                fastamap.printNamesFile(outNameFile);
                
-               if (m->control_pressed) { remove(outFastaFile.c_str()); remove(outNameFile.c_str()); return 0; }
+               if (m->control_pressed) { outputTypes.clear(); remove(outFastaFile.c_str()); remove(outNameFile.c_str()); return 0; }
                
                m->mothurOutEndLine();
                m->mothurOut("Output File Names: "); m->mothurOutEndLine();
                m->mothurOut(outFastaFile); m->mothurOutEndLine();      
                m->mothurOut(outNameFile); m->mothurOutEndLine();
+               outputNames.push_back(outFastaFile);  outputNames.push_back(outNameFile); outputTypes["fasta"].push_back(outFastaFile);  outputTypes["name"].push_back(outNameFile); 
                m->mothurOutEndLine();