X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getrabundcommand.cpp;h=60f4ece3eb13de6fc68f6141c3e28ca283da694b;hb=5d6d303e481489e226fdf8d6c5385b99b50718bc;hp=6b68c32cad7673b950eeb8acfe6423b160630130;hpb=aa9238c0a9e6e7aa0ed8b8b606b08ad4fd7dcfe3;p=mothur.git

diff --git a/getrabundcommand.cpp b/getrabundcommand.cpp
index 6b68c32..60f4ece 100644
--- a/getrabundcommand.cpp
+++ b/getrabundcommand.cpp
@@ -10,7 +10,55 @@
 #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;
+		//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();
@@ -39,9 +87,13 @@ 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 +102,12 @@ 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 +118,8 @@ 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);
 			}
 		}
 
@@ -120,7 +172,7 @@ int GetRAbundCommand::execute(){
 		set<string> processedLabels;
 		set<string> userLabels = labels;
 		
-		if (m->control_pressed) {  out.close(); remove(filename.c_str()); delete read; delete input; 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 +181,7 @@ int GetRAbundCommand::execute(){
 					rabund = new RAbundVector();				
 					*rabund = (list->getRAbundVector());
 					
-					if (m->control_pressed) {  out.close(); remove(filename.c_str()); delete read; delete input; 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 +193,7 @@ 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 +203,7 @@ int GetRAbundCommand::execute(){
 					rabund = new RAbundVector();
 					*rabund = (list->getRAbundVector());
 					
-					if (m->control_pressed) {  out.close(); remove(filename.c_str()); delete read; delete input; 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 +245,7 @@ int GetRAbundCommand::execute(){
 			rabund = new RAbundVector();
 			*rabund = (list->getRAbundVector());
 			
-			if (m->control_pressed) {  out.close(); remove(filename.c_str()); delete read; delete input; 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 +256,12 @@ 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(); 
-		delete read; delete input;
-		globaldata->gListVector = NULL; 
+		
+		globaldata->gListVector = NULL;
 		
 		return 0;		
 	}