reworked amova / homova / anosim

[mothur.git] / getsabundcommand.cpp

diff --git a/getsabundcommand.cpp b/getsabundcommand.cpp
index ba05ea1e11d3e5e603ec84babe81ee172c68a440..2ae807c65c7d9f4ec814564fb5823ccd3f925471 100644 (file)
--- a/getsabundcommand.cpp
+++ b/getsabundcommand.cpp
@@ -10,16 +10,62 @@
 #include "getsabundcommand.h"
 
 //**********************************************************************************************************************
-
+vector<string> GetSAbundCommand::getValidParameters(){ 
+       try {
+               string Array[] =  {"label","outputdir","inputdir"};
+               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "GetSAbundCommand", "getValidParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+GetSAbundCommand::GetSAbundCommand(){  
+       try {
+               abort = true; calledHelp = true; 
+               vector<string> tempOutNames;
+               outputTypes["sabund"] = tempOutNames;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "GetSAbundCommand", "GetSAbundCommand");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+vector<string> GetSAbundCommand::getRequiredParameters(){      
+       try {
+               vector<string> myArray;
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "GetSAbundCommand", "getRequiredParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+vector<string> GetSAbundCommand::getRequiredFiles(){   
+       try {
+               string Array[] =  {"list","rabund"};
+               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "GetSAbundCommand", "getRequiredFiles");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
 GetSAbundCommand::GetSAbundCommand(string option)  {
        try {
                globaldata = GlobalData::getInstance();
-               abort = false;
+               abort = false; calledHelp = false;   
                allLines = 1;
                labels.clear();
                
                //allow user to run help
-               if(option == "help") { help(); abort = true; }
+               if(option == "help") { help(); abort = true; calledHelp = true; }
                
                else {
                        //valid paramters for this command
@@ -36,6 +82,10 @@ GetSAbundCommand::GetSAbundCommand(string option)  {
                                if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
                        }
                        
+                       //initialize outputTypes
+                       vector<string> tempOutNames;
+                       outputTypes["sabund"] = tempOutNames;
+               
                        //if the user changes the output directory command factory will send this info to us in the output parameter 
                        string outputDir = validParameter.validFile(parameters, "outputdir", false);            if (outputDir == "not found"){  
                                outputDir = ""; 
@@ -101,7 +151,7 @@ GetSAbundCommand::~GetSAbundCommand(){
 int GetSAbundCommand::execute(){
        try {
                
-               if (abort == true) { return 0; }
+               if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
        
                //using order vector so you don't have to distinguish between the list and rabund files
                read = new ReadOTUFile(globaldata->inputFileName);      
@@ -115,7 +165,7 @@ int GetSAbundCommand::execute(){
                set<string> processedLabels;
                set<string> userLabels = labels;
                
-               if (m->control_pressed) {  out.close(); remove(filename.c_str());  delete order; globaldata->gorder = NULL;  return 0; }
+               if (m->control_pressed) {  outputTypes.clear(); out.close(); remove(filename.c_str());  delete order; globaldata->gorder = NULL;  return 0; }
 
                
                while((order != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
@@ -127,7 +177,7 @@ int GetSAbundCommand::execute(){
                                        sabund->print(out);
                                        delete sabund;
                                        
-                                       if (m->control_pressed) {  out.close(); remove(filename.c_str());  delete order; globaldata->gorder = NULL;  return 0; }
+                                       if (m->control_pressed) { outputTypes.clear();  out.close(); remove(filename.c_str());  delete order; globaldata->gorder = NULL;  return 0; }
 
                                        processedLabels.insert(order->getLabel());
                                        userLabels.erase(order->getLabel());
@@ -145,7 +195,7 @@ int GetSAbundCommand::execute(){
                                        sabund->print(out);
                                        delete sabund;
                                        
-                                       if (m->control_pressed) {  out.close(); remove(filename.c_str());  delete order; globaldata->gorder = NULL;  return 0; }
+                                       if (m->control_pressed) {  outputTypes.clear(); out.close(); remove(filename.c_str());  delete order; globaldata->gorder = NULL;  return 0; }
 
                                        processedLabels.insert(order->getLabel());
                                        userLabels.erase(order->getLabel());
@@ -185,7 +235,7 @@ int GetSAbundCommand::execute(){
                        sabund->print(out);
                        delete sabund;
                        
-                       if (m->control_pressed) {  out.close(); remove(filename.c_str());  delete order; globaldata->gorder = NULL;  return 0; }
+                       if (m->control_pressed) {  outputTypes.clear(); out.close(); remove(filename.c_str());  delete order; globaldata->gorder = NULL;  return 0; }
                        
                        delete order;
                }
@@ -195,7 +245,7 @@ int GetSAbundCommand::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["sabund"].push_back(filename);
                m->mothurOutEndLine();
                
                return 0;