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

[mothur.git] / splitgroupscommand.cpp

diff --git a/splitgroupscommand.cpp b/splitgroupscommand.cpp
index 6f8788a28daed38deeed9b419b28b699cffb6b55..4be7a0ec8a82133a9eb4def8ee78bd47e0ecbe44 100644 (file)
--- a/splitgroupscommand.cpp
+++ b/splitgroupscommand.cpp
@@ -10,6 +10,54 @@
 #include "splitgroupscommand.h"
 #include "sharedutilities.h"
 
+//**********************************************************************************************************************
+vector<string> SplitGroupCommand::getValidParameters(){        
+       try {
+               string Array[] =  {"name","group","groups","fasta","outputdir","inputdir"}; 
+               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "SplitGroupCommand", "getValidParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+vector<string> SplitGroupCommand::getRequiredParameters(){     
+       try {
+               string Array[] =  {"fasta","group"};
+               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "SplitGroupCommand", "getRequiredParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+vector<string> SplitGroupCommand::getRequiredFiles(){  
+       try {
+               vector<string> myArray;
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "SplitGroupCommand", "getRequiredFiles");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+SplitGroupCommand::SplitGroupCommand(){        
+       try {
+               //initialize outputTypes
+               vector<string> tempOutNames;
+               outputTypes["fasta"] = tempOutNames;
+               outputTypes["name"] = tempOutNames;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "SplitGroupCommand", "SplitGroupCommand");
+               exit(1);
+       }
+}
 //**********************************************************************************************************************
 SplitGroupCommand::SplitGroupCommand(string option)  {
        try {
@@ -33,7 +81,12 @@ SplitGroupCommand::SplitGroupCommand(string option)  {
                        for (it = parameters.begin(); it != parameters.end(); it++) { 
                                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 = "";          }
@@ -187,13 +240,13 @@ int SplitGroupCommand::splitFasta() {
                        temp = new ofstream;
                        filehandles[Groups[i]+"fasta"] = temp;
                        m->openOutputFile(filerootFasta + Groups[i] + ".fasta", *(filehandles[Groups[i]+"fasta"]));
-                       outputNames.push_back(filerootFasta + Groups[i] + ".fasta");
+                       outputNames.push_back(filerootFasta + Groups[i] + ".fasta"); outputTypes["fasta"].push_back(filerootFasta + Groups[i] + ".fasta");
                        
                        if (namefile != "") {
                                temp2 = new ofstream;
                                filehandles[Groups[i]+"name"] = temp2;
                                m->openOutputFile(filerootName + Groups[i] + ".names", *(filehandles[Groups[i]+"name"]));
-                               outputNames.push_back(filerootName + Groups[i] + ".names");
+                               outputNames.push_back(filerootName + Groups[i] + ".names"); outputTypes["name"].push_back(filerootFasta + Groups[i] + ".names");
                        }
                }