reworked amova / homova / anosim

[mothur.git] / getsabundcommand.cpp

diff --git a/getsabundcommand.cpp b/getsabundcommand.cpp
index d9197fe7724b32ca0f6789032a7ea98246bc69a5..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
@@ -36,10 +82,14 @@ 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 = ""; 
-                               outputDir += hasPath(globaldata->inputFileName); //if user entered a file with a path then preserve it  
+                               outputDir += m->hasPath(globaldata->inputFileName); //if user entered a file with a path then preserve it       
                        }
 
                        //make sure the user has already run the read.otu command
@@ -50,7 +100,7 @@ GetSAbundCommand::GetSAbundCommand(string option)  {
                        label = validParameter.validFile(parameters, "label", false);                   
                        if (label == "not found") { label = ""; }
                        else { 
-                               if(label != "all") {  splitAtDash(label, labels);  allLines = 0;  }
+                               if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
                                else { allLines = 1;  }
                        }
                        
@@ -61,8 +111,8 @@ GetSAbundCommand::GetSAbundCommand(string option)  {
                        }
                                
                        if (abort == false) {
-                               filename = outputDir + getRootName(getSimpleName(globaldata->inputFileName)) + "sabund";
-                               openOutputFile(filename, out);
+                               filename = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + "sabund";
+                               m->openOutputFile(filename, out);
                        }
                }
 
@@ -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);      
@@ -115,6 +165,9 @@ int GetSAbundCommand::execute(){
                set<string> processedLabels;
                set<string> userLabels = labels;
                
+               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))) {
                        
                        if(allLines == 1 || labels.count(order->getLabel()) == 1){
@@ -123,12 +176,14 @@ int GetSAbundCommand::execute(){
                                        *sabund = (order->getSAbundVector());
                                        sabund->print(out);
                                        delete sabund;
+                                       
+                                       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());
                        }
                        
-                       if ((anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+                       if ((m->anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
                                        string saveLabel = order->getLabel();
                                        
                                        delete order;           
@@ -139,6 +194,8 @@ int GetSAbundCommand::execute(){
                                        *sabund = (order->getSAbundVector());
                                        sabund->print(out);
                                        delete sabund;
+                                       
+                                       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());
@@ -177,6 +234,9 @@ int GetSAbundCommand::execute(){
                        *sabund = (order->getSAbundVector());
                        sabund->print(out);
                        delete sabund;
+                       
+                       if (m->control_pressed) {  outputTypes.clear(); out.close(); remove(filename.c_str());  delete order; globaldata->gorder = NULL;  return 0; }
+                       
                        delete order;
                }
                globaldata->gorder = NULL;
@@ -185,7 +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;