X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=summarysharedcommand.cpp;h=b5214448cd2a5e8f8af0b70bfc700ee05465d4af;hb=4169642e8a8d45f71a4a7241ee02f1b1aae29520;hp=029ca26638830f456179f5595b3fd8300f631c70;hpb=5694c92fbf646fe01abc87bde2af59e14a9a56b6;p=mothur.git

diff --git a/summarysharedcommand.cpp b/summarysharedcommand.cpp
index 029ca26..b521444 100644
--- a/summarysharedcommand.cpp
+++ b/summarysharedcommand.cpp
@@ -65,8 +65,7 @@ vector<string> SummarySharedCommand::getValidParameters(){
 //**********************************************************************************************************************
 SummarySharedCommand::SummarySharedCommand(){	
 	try {
-		abort = true;
-		//initialize outputTypes
+		abort = true; calledHelp = true; 
 		vector<string> tempOutNames;
 		outputTypes["summary"] = tempOutNames;
 	}
@@ -103,13 +102,13 @@ vector<string> SummarySharedCommand::getRequiredFiles(){
 SummarySharedCommand::SummarySharedCommand(string option)  {
 	try {
 		globaldata = GlobalData::getInstance();
-		abort = false;
+		abort = false; calledHelp = false;   
 		allLines = 1;
 		labels.clear();
 		Estimators.clear();
 		
 		//allow user to run help
-		if(option == "help") { validCalculator = new ValidCalculators(); help(); abort = true; }
+		if(option == "help") { validCalculator = new ValidCalculators(); help(); abort = true; calledHelp = true; }
 		
 		else {
 			//valid paramters for this command
@@ -317,7 +316,7 @@ SummarySharedCommand::~SummarySharedCommand(){
 int SummarySharedCommand::execute(){
 	try {
 	
-		if (abort == true) { return 0; }
+		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
 		
 		ofstream outputFileHandle, outAll;
 		string outputFileName = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + "shared.summary";
@@ -744,7 +743,7 @@ int SummarySharedCommand::driver(vector<SharedRAbundVector*> thisLookup, int sta
 					outputFileHandle << '\t';
 					sumCalculators[i]->print(outputFileHandle);
 					
-					seqDist temp(l, k, tempdata[0]);
+					seqDist temp(l, k, (1.0 - tempdata[0]));
 					calcDists[i].push_back(temp);
 				}
 				outputFileHandle << endl;