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

[mothur.git] / getrabundcommand.cpp

diff --git a/getrabundcommand.cpp b/getrabundcommand.cpp
index b7dd7153609ada80c297d5d51cab70d3cae5ebc4..a38aeb30dea60a2fe67984fa05dc83b6fb9130e1 100644 (file)
--- a/getrabundcommand.cpp
+++ b/getrabundcommand.cpp
@@ -10,7 +10,54 @@
 #include "getrabundcommand.h"
 
 //**********************************************************************************************************************
-
+vector<string> GetRAbundCommand::getValidParameters(){ 
+       try {
+               string Array[] =  {"label","sorted","outputdir","inputdir"};
+               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "GetRAbundCommand", "getValidParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+GetRAbundCommand::GetRAbundCommand(){  
+       try {
+               //initialize outputTypes
+               vector<string> tempOutNames;
+               outputTypes["rabund"] = tempOutNames;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "GetRAbundCommand", "GetRAbundCommand");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+vector<string> GetRAbundCommand::getRequiredParameters(){      
+       try {
+               vector<string> myArray;
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "GetRAbundCommand", "getRequiredParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+vector<string> GetRAbundCommand::getRequiredFiles(){   
+       try {
+               string Array[] =  {"list"};
+               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+               
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "GetRAbundCommand", "getRequiredFiles");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
 GetRAbundCommand::GetRAbundCommand(string option)  {
        try {
                globaldata = GlobalData::getInstance();
@@ -42,6 +89,10 @@ GetRAbundCommand::GetRAbundCommand(string option)  {
                                outputDir += m->hasPath(globaldata->inputFileName); //if user entered a file with a path then preserve it       
                        }
                        
+                       //initialize outputTypes
+                       vector<string> tempOutNames;
+                       outputTypes["rabund"] = tempOutNames;
+                       
                        //make sure the user has already run the read.otu command
                        if (globaldata->getListFile() == "") { m->mothurOut("You must read a listfile before you can use the get.rabund command."); m->mothurOutEndLine(); abort = true; }
                        
@@ -120,7 +171,7 @@ int GetRAbundCommand::execute(){
                set<string> processedLabels;
                set<string> userLabels = labels;
                
-               if (m->control_pressed) {  out.close(); remove(filename.c_str());  delete list; globaldata->gListVector = NULL;  return 0; }
+               if (m->control_pressed) {  outputTypes.clear();  out.close(); remove(filename.c_str());  delete list; globaldata->gListVector = NULL;  return 0; }
                
                while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
                        
@@ -129,7 +180,7 @@ int GetRAbundCommand::execute(){
                                        rabund = new RAbundVector();                            
                                        *rabund = (list->getRAbundVector());
                                        
-                                       if (m->control_pressed) {  out.close(); remove(filename.c_str());  delete list; delete rabund; globaldata->gListVector = NULL;  return 0; }
+                                       if (m->control_pressed) {   outputTypes.clear(); out.close(); remove(filename.c_str());  delete list; delete rabund; globaldata->gListVector = NULL;  return 0; }
 
                                        
                                        if(sorted)      {   rabund->print(out);                         }
@@ -151,7 +202,7 @@ int GetRAbundCommand::execute(){
                                        rabund = new RAbundVector();
                                        *rabund = (list->getRAbundVector());
                                        
-                                       if (m->control_pressed) {  out.close(); remove(filename.c_str());  delete list; delete rabund; globaldata->gListVector = NULL;  return 0; }
+                                       if (m->control_pressed) {   outputTypes.clear(); out.close(); remove(filename.c_str());  delete list; delete rabund; globaldata->gListVector = NULL;  return 0; }
                                        
                                        if(sorted)      {   rabund->print(out);                         }
                                        else            {       rabund->nonSortedPrint(out);    }
@@ -193,7 +244,7 @@ int GetRAbundCommand::execute(){
                        rabund = new RAbundVector();
                        *rabund = (list->getRAbundVector());
                        
-                       if (m->control_pressed) {  out.close(); remove(filename.c_str());  delete list; delete rabund; globaldata->gListVector = NULL;  return 0; }
+                       if (m->control_pressed) {  outputTypes.clear(); out.close(); remove(filename.c_str());  delete list; delete rabund; globaldata->gListVector = NULL;  return 0; }
                        
                        if(sorted)      {   rabund->print(out);                         }
                        else            {       rabund->nonSortedPrint(out);    }
@@ -204,7 +255,7 @@ int GetRAbundCommand::execute(){
                
                m->mothurOutEndLine();
                m->mothurOut("Output File Name: "); m->mothurOutEndLine();
-               m->mothurOut(filename); m->mothurOutEndLine();  
+               m->mothurOut(filename); m->mothurOutEndLine();  outputNames.push_back(filename); outputTypes["rabund"].push_back(filename);
                m->mothurOutEndLine();
                
                out.close();