X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getrelabundcommand.cpp;fp=getrelabundcommand.cpp;h=5b9327b57bd928a5e456a7251a83be1a0664cd6c;hb=8bc3e5b38c2317a1715f53be22fa96455868c281;hp=4c79b21ab53e903fec94fa17296a7da30a9569bf;hpb=f663afa231c9bc1b5e18e0ea3bdd2b2ee784f5b2;p=mothur.git

diff --git a/getrelabundcommand.cpp b/getrelabundcommand.cpp
index 4c79b21..5b9327b 100644
--- a/getrelabundcommand.cpp
+++ b/getrelabundcommand.cpp
@@ -10,7 +10,53 @@
 #include "getrelabundcommand.h"
 
 //**********************************************************************************************************************
-
+vector<string> GetRelAbundCommand::getValidParameters(){	
+	try {
+		string Array[] =  {"groups","label","scale","outputdir","inputdir"};
+		vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+		return myArray;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "GetRelAbundCommand", "getValidParameters");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+GetRelAbundCommand::GetRelAbundCommand(){	
+	try {
+		//initialize outputTypes
+		vector<string> tempOutNames;
+		outputTypes["relabund"] = tempOutNames;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "GetRelAbundCommand", "GetRelAbundCommand");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+vector<string> GetRelAbundCommand::getRequiredParameters(){	
+	try {
+		vector<string> myArray;
+		return myArray;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "GetRelAbundCommand", "getRequiredParameters");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+vector<string> GetRelAbundCommand::getRequiredFiles(){	
+	try {
+		string Array[] =  {"shared"};
+		vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+		return myArray;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "GetRelAbundCommand", "getRequiredFiles");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
 GetRelAbundCommand::GetRelAbundCommand(string option) {
 	try {
 		globaldata = GlobalData::getInstance();
@@ -36,6 +82,10 @@ GetRelAbundCommand::GetRelAbundCommand(string option) {
 				if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 			}
 			
+			//initialize outputTypes
+			vector<string> tempOutNames;
+			outputTypes["relabund"] = tempOutNames;
+		
 			//if the user changes the output directory command factory will send this info to us in the output parameter 
 			outputDir = validParameter.validFile(parameters, "outputdir", false);		if (outputDir == "not found"){	
 				outputDir = "";	
@@ -136,7 +186,7 @@ int GetRelAbundCommand::execute(){
 		//as long as you are not at the end of the file or done wih the lines you want
 		while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 			
-			if (m->control_pressed) {  for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } globaldata->Groups.clear(); delete read;  out.close(); remove(outputFileName.c_str()); return 0; }
+			if (m->control_pressed) {  outputTypes.clear();  for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } globaldata->Groups.clear(); delete read;  out.close(); remove(outputFileName.c_str()); return 0; }
 	
 			if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){			
 
@@ -167,13 +217,13 @@ int GetRelAbundCommand::execute(){
 			//prevent memory leak
 			for (int i = 0; i < lookup.size(); i++) {  delete lookup[i]; lookup[i] = NULL; }
 			
-			if (m->control_pressed) {  globaldata->Groups.clear(); delete read;  out.close(); remove(outputFileName.c_str()); return 0; }
+			if (m->control_pressed) {  outputTypes.clear();  globaldata->Groups.clear(); delete read;  out.close(); remove(outputFileName.c_str()); return 0; }
 
 			//get next line to process
 			lookup = input->getSharedRAbundVectors();				
 		}
 		
-		if (m->control_pressed) { globaldata->Groups.clear(); delete read;  out.close(); remove(outputFileName.c_str());  return 0; }
+		if (m->control_pressed) { outputTypes.clear(); globaldata->Groups.clear(); delete read;  out.close(); remove(outputFileName.c_str());  return 0; }
 
 		//output error messages about any remaining user labels
 		set<string>::iterator it;
@@ -206,11 +256,11 @@ int GetRelAbundCommand::execute(){
 		delete read;
 		out.close();
 		
-		if (m->control_pressed) { remove(outputFileName.c_str()); return 0;}
+		if (m->control_pressed) { outputTypes.clear(); remove(outputFileName.c_str()); return 0;}
 		
 		m->mothurOutEndLine();
 		m->mothurOut("Output File Names: "); m->mothurOutEndLine();
-		m->mothurOut(outputFileName); m->mothurOutEndLine();
+		m->mothurOut(outputFileName); m->mothurOutEndLine(); outputNames.push_back(outputFileName); outputTypes["relabund"].push_back(outputFileName);
 		m->mothurOutEndLine();
 		
 		return 0;