X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=normalizesharedcommand.cpp;h=37cfb5daa98b4eeb850b44d60e5e9d80fa268de5;hb=a4f05f09c250323132a4b9427f41a3ededaec634;hp=85265015a7e6ea4de35552bd7d27d7efdc688348;hpb=afeb767205e3e7efd11bb7a36a36ad79ad05a779;p=mothur.git

diff --git a/normalizesharedcommand.cpp b/normalizesharedcommand.cpp
index 8526501..37cfb5d 100644
--- a/normalizesharedcommand.cpp
+++ b/normalizesharedcommand.cpp
@@ -24,8 +24,7 @@ vector<string> NormalizeSharedCommand::getValidParameters(){
 //**********************************************************************************************************************
 NormalizeSharedCommand::NormalizeSharedCommand(){	
 	try {
-		abort = true;
-		//initialize outputTypes
+		abort = true; calledHelp = true; 
 		vector<string> tempOutNames;
 		outputTypes["shared"] = tempOutNames;
 	}
@@ -62,12 +61,12 @@ vector<string> NormalizeSharedCommand::getRequiredFiles(){
 NormalizeSharedCommand::NormalizeSharedCommand(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
@@ -185,7 +184,7 @@ NormalizeSharedCommand::~NormalizeSharedCommand(){}
 int NormalizeSharedCommand::execute(){
 	try {
 	
-		if (abort == true) { return 0; }
+		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
 		
 		string outputFileName = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + "norm.shared";
 		ofstream out;
@@ -382,6 +381,13 @@ int NormalizeSharedCommand::execute(){
 		m->mothurOut(outputFileName); m->mothurOutEndLine(); outputNames.push_back(outputFileName); outputTypes["shared"].push_back(outputFileName);
 		m->mothurOutEndLine();
 		
+		//set shared file as new current sharedfile
+		string current = "";
+		itTypes = outputTypes.find("shared");
+		if (itTypes != outputTypes.end()) {
+			if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setSharedFile(current); }
+		}
+		
 		return 0;
 	}
 	catch(exception& e) {
@@ -405,7 +411,7 @@ int NormalizeSharedCommand::normalize(vector<SharedRAbundVector*>& thisLookUp, o
 							
 						int abund = thisLookUp[i]->getAbundance(j);
 							
-						float relabund = relabund = abund / (float) thisLookUp[i]->getNumSeqs();
+						float relabund = abund / (float) thisLookUp[i]->getNumSeqs();
 						float newNorm = relabund * norm;
 						
 						//round to nearest int
@@ -479,7 +485,7 @@ int NormalizeSharedCommand::normalize(vector<SharedRAbundFloatVector*>& thisLook
 					
 					float abund = thisLookUp[i]->getAbundance(j);
 					
-					float relabund = relabund = abund / (float) thisLookUp[i]->getNumSeqs();
+					float relabund = abund / (float) thisLookUp[i]->getNumSeqs();
 					float newNorm = relabund * norm;
 					
 					thisLookUp[i]->set(j, newNorm, thisLookUp[i]->getGroup());