fixed clearcut version bug, added group count output to get.groups and remove.groups

[mothur.git] / getrabundcommand.cpp

diff --git a/getrabundcommand.cpp b/getrabundcommand.cpp
index b665c88cdede4273b1aadd5bf1d4ee21ddec6b85..3b03f3694967d6d480ba0dc00153454c7e8b074f 100644 (file)
--- a/getrabundcommand.cpp
+++ b/getrabundcommand.cpp
@@ -10,16 +10,63 @@
 #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 {
+               abort = true; calledHelp = true; 
+               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();
-               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
@@ -39,9 +86,13 @@ GetRAbundCommand::GetRAbundCommand(string option)  {
                        //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       
                        }
                        
+                       //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; }
                        
@@ -50,12 +101,12 @@ GetRAbundCommand::GetRAbundCommand(string option)  {
                        
                        string temp;
                        temp = validParameter.validFile(parameters, "sorted", false);                   if (temp == "not found") { temp = "T"; }
-                       sorted = isTrue(temp);
+                       sorted = m->isTrue(temp);
                        
                        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;  }
                        }
                        
@@ -66,8 +117,8 @@ GetRAbundCommand::GetRAbundCommand(string option)  {
                        }
                                
                        if (abort == false) {
-                               filename = outputDir + getRootName(getSimpleName(globaldata->inputFileName)) + "rabund";
-                               openOutputFile(filename, out);
+                               filename = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + "rabund";
+                               m->openOutputFile(filename, out);
                        }
                }
 
@@ -106,7 +157,7 @@ GetRAbundCommand::~GetRAbundCommand(){}
 int GetRAbundCommand::execute(){
        try {
        
-               if (abort == true) { return 0; }
+               if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
                
                //read first line
                read = new ReadOTUFile(globaldata->inputFileName);      
@@ -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);                         }
@@ -141,7 +192,7 @@ int GetRAbundCommand::execute(){
                                        userLabels.erase(list->getLabel());
                        }
                        
-                       if ((anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+                       if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
                                        string saveLabel = list->getLabel();
                                        
                                        delete list;
@@ -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);    }
@@ -204,13 +255,20 @@ 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(); 
                
                globaldata->gListVector = NULL;
                
+               //set rabund file as new current rabundfile
+               string current = "";
+               itTypes = outputTypes.find("rabund");
+               if (itTypes != outputTypes.end()) {
+                       if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setRabundFile(current); }
+               }
+               
                return 0;               
        }