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

[mothur.git] / catchallcommand.cpp

diff --git a/catchallcommand.cpp b/catchallcommand.cpp
index b185b9f49baf98e96a78fc836c4668a5d0a14972..d6264db3309bd867696ee0b89041b9e34d3b6556 100644 (file)
--- a/catchallcommand.cpp
+++ b/catchallcommand.cpp
@@ -10,6 +10,53 @@
 #include "catchallcommand.h"
 #include "globaldata.hpp"
 
+//**********************************************************************************************************************
+vector<string> CatchAllCommand::getValidParameters(){  
+       try {
+               string AlignArray[] =  {"sabund","label","inputdir","outputdir"};
+               vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "CatchAllCommand", "getValidParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+CatchAllCommand::CatchAllCommand(){    
+       try {
+               //initialize outputTypes
+               
+               //need to determine outputFIles and types
+       }
+       catch(exception& e) {
+               m->errorOut(e, "CatchAllCommand", "CatchAllCommand");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+vector<string> CatchAllCommand::getRequiredParameters(){       
+       try {
+               string AlignArray[] =  {"sabund"};
+               vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "CatchAllCommand", "getRequiredParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+vector<string> CatchAllCommand::getRequiredFiles(){    
+       try {
+               vector<string> myArray;
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "CatchAllCommand", "getRequiredFiles");
+               exit(1);
+       }
+}
 /**************************************************************************************/
 CatchAllCommand::CatchAllCommand(string option)  {     
        try {
@@ -36,6 +83,11 @@ CatchAllCommand::CatchAllCommand(string option)  {
                                if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
                        }
                        
+                       
+                       //initialize outputTypes
+                       //need to determine outputFIles and types
+                       
+                       
                        //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 = "";          }
@@ -53,7 +105,7 @@ CatchAllCommand::CatchAllCommand(string option)  {
                        //check for required parameters
                        sabundfile = validParameter.validFile(parameters, "sabund", true);
                        if (sabundfile == "not open") { sabundfile = ""; abort = true; }
-                       else if (sabundfile == "not found") { sabundfile = "";  m->mothurOut("You must provide either a sabund file for the catchall command."); m->mothurOutEndLine(); abort=true; }
+                       else if (sabundfile == "not found") { sabundfile = "";  m->mothurOut("You must provide a sabund file for the catchall command."); m->mothurOutEndLine(); abort=true; }
                        else { globaldata->setSabundFile(sabundfile); globaldata->setFormat("sabund"); }
                        
                        string label = validParameter.validFile(parameters, "label", false);                    
@@ -99,8 +151,6 @@ int CatchAllCommand::execute() {
                
                if (abort == true) { return 0; }
                
-               vector<string> outputNames;
-               
                //prepare full output directory
                outputDir = m->getFullPathName(outputDir);