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

[mothur.git] / getrelabundcommand.cpp

diff --git a/getrelabundcommand.cpp b/getrelabundcommand.cpp
index 4c79b21ab53e903fec94fa17296a7da30a9569bf..5b9327b57bd928a5e456a7251a83be1a0664cd6c 100644 (file)
--- a/getrelabundcommand.cpp
+++ b/getrelabundcommand.cpp
@@ -10,7 +10,53 @@
 #include "getrelabundcommand.h"
 
 //**********************************************************************************************************************
-
+vector<string> GetRelAbundCommand::getValidParameters(){       
+       try {
+               string Array[] =  {"groups","label","scale","outputdir","inputdir"};
+               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "GetRelAbundCommand", "getValidParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+GetRelAbundCommand::GetRelAbundCommand(){      
+       try {
+               //initialize outputTypes
+               vector<string> tempOutNames;
+               outputTypes["relabund"] = tempOutNames;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "GetRelAbundCommand", "GetRelAbundCommand");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+vector<string> GetRelAbundCommand::getRequiredParameters(){    
+       try {
+               vector<string> myArray;
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "GetRelAbundCommand", "getRequiredParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+vector<string> GetRelAbundCommand::getRequiredFiles(){ 
+       try {
+               string Array[] =  {"shared"};
+               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "GetRelAbundCommand", "getRequiredFiles");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
 GetRelAbundCommand::GetRelAbundCommand(string option) {
        try {
                globaldata = GlobalData::getInstance();
@@ -36,6 +82,10 @@ GetRelAbundCommand::GetRelAbundCommand(string option) {
                                if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
                        }
                        
+                       //initialize outputTypes
+                       vector<string> tempOutNames;
+                       outputTypes["relabund"] = 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 = ""; 
@@ -136,7 +186,7 @@ int GetRelAbundCommand::execute(){
                //as long as you are not at the end of the file or done wih the lines you want
                while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
                        
-                       if (m->control_pressed) {  for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } globaldata->Groups.clear(); delete read;  out.close(); remove(outputFileName.c_str()); return 0; }
+                       if (m->control_pressed) {  outputTypes.clear();  for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } globaldata->Groups.clear(); delete read;  out.close(); remove(outputFileName.c_str()); return 0; }
        
                        if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){                  
 
@@ -167,13 +217,13 @@ int GetRelAbundCommand::execute(){
                        //prevent memory leak
                        for (int i = 0; i < lookup.size(); i++) {  delete lookup[i]; lookup[i] = NULL; }
                        
-                       if (m->control_pressed) {  globaldata->Groups.clear(); delete read;  out.close(); remove(outputFileName.c_str()); return 0; }
+                       if (m->control_pressed) {  outputTypes.clear();  globaldata->Groups.clear(); delete read;  out.close(); remove(outputFileName.c_str()); return 0; }
 
                        //get next line to process
                        lookup = input->getSharedRAbundVectors();                               
                }
                
-               if (m->control_pressed) { globaldata->Groups.clear(); delete read;  out.close(); remove(outputFileName.c_str());  return 0; }
+               if (m->control_pressed) { outputTypes.clear(); globaldata->Groups.clear(); delete read;  out.close(); remove(outputFileName.c_str());  return 0; }
 
                //output error messages about any remaining user labels
                set<string>::iterator it;
@@ -206,11 +256,11 @@ int GetRelAbundCommand::execute(){
                delete read;
                out.close();
                
-               if (m->control_pressed) { remove(outputFileName.c_str()); return 0;}
+               if (m->control_pressed) { outputTypes.clear(); remove(outputFileName.c_str()); return 0;}
                
                m->mothurOutEndLine();
                m->mothurOut("Output File Names: "); m->mothurOutEndLine();
-               m->mothurOut(outputFileName); m->mothurOutEndLine();
+               m->mothurOut(outputFileName); m->mothurOutEndLine(); outputNames.push_back(outputFileName); outputTypes["relabund"].push_back(outputFileName);
                m->mothurOutEndLine();
                
                return 0;