X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=metastatscommand.cpp;h=e13e37c92c3103a3aabd1a4a6a7c68db443592ef;hb=03acfa01ede71b107817966fcf27cd728038b3c9;hp=866bc94e07553d417b38036bca46184fad973261;hpb=191ae1be0679d5cf4eda950b3b1bf26fb7dd503d;p=mothur.git

diff --git a/metastatscommand.cpp b/metastatscommand.cpp
index 866bc94..e13e37c 100644
--- a/metastatscommand.cpp
+++ b/metastatscommand.cpp
@@ -26,8 +26,7 @@ vector<string> MetaStatsCommand::getValidParameters(){
 //**********************************************************************************************************************
 MetaStatsCommand::MetaStatsCommand(){	
 	try {
-		abort = true;
-		//initialize outputTypes
+		abort = true; calledHelp = true; 
 		vector<string> tempOutNames;
 		outputTypes["metastats"] = tempOutNames;
 	}
@@ -65,12 +64,12 @@ vector<string> MetaStatsCommand::getRequiredFiles(){
 MetaStatsCommand::MetaStatsCommand(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
@@ -206,7 +205,7 @@ MetaStatsCommand::~MetaStatsCommand(){}
 int MetaStatsCommand::execute(){
 	try {
 	
-		if (abort == true) { return 0; }
+		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
 		
 		designMap = new GroupMap(designfile);
 		designMap->readDesignMap();
@@ -347,7 +346,6 @@ int MetaStatsCommand::execute(){
 
 int MetaStatsCommand::process(vector<SharedRAbundVector*>& thisLookUp){
 	try {
-		if (pickedGroups) { eliminateZeroOTUS(thisLookUp); }
 		
 		#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 				if(processors == 1){
@@ -366,7 +364,11 @@ int MetaStatsCommand::process(vector<SharedRAbundVector*>& thisLookUp){
 						}else if (pid == 0){
 							driver(lines[process].start, lines[process].num, thisLookUp);
 							exit(0);
-						}else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
+						}else { 
+							m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine(); 
+							for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
+							exit(0);
+						}
 					}
 					
 					//do my part
@@ -442,7 +444,6 @@ int MetaStatsCommand::driver(int start, int num, vector<SharedRAbundVector*>& th
 				}
 				
 				m->mothurOut("Comparing " + setA + " and " + setB + "..."); m->mothurOutEndLine(); 
-				
 				metastat_main(output, thisLookUp[0]->getNumBins(), subset.size(), threshold, iters, data, setACount);
 				
 				m->mothurOutEndLine(); 
@@ -463,45 +464,3 @@ int MetaStatsCommand::driver(int start, int num, vector<SharedRAbundVector*>& th
 	}
 }
 //**********************************************************************************************************************
-int MetaStatsCommand::eliminateZeroOTUS(vector<SharedRAbundVector*>& thislookup) {
-	try {
-		
-		vector<SharedRAbundVector*> newLookup;
-		for (int i = 0; i < thislookup.size(); i++) {
-			SharedRAbundVector* temp = new SharedRAbundVector();
-			temp->setLabel(thislookup[i]->getLabel());
-			temp->setGroup(thislookup[i]->getGroup());
-			newLookup.push_back(temp);
-		}
-		
-		//for each bin
-		for (int i = 0; i < thislookup[0]->getNumBins(); i++) {
-			if (m->control_pressed) { for (int j = 0; j < newLookup.size(); j++) {  delete newLookup[j];  } return 0; }
-		
-			//look at each sharedRabund and make sure they are not all zero
-			bool allZero = true;
-			for (int j = 0; j < thislookup.size(); j++) {
-				if (thislookup[j]->getAbundance(i) != 0) { allZero = false;  break;  }
-			}
-			
-			//if they are not all zero add this bin
-			if (!allZero) {
-				for (int j = 0; j < thislookup.size(); j++) {
-					newLookup[j]->push_back(thislookup[j]->getAbundance(i), thislookup[j]->getGroup());
-				}
-			}
-		}
-
-		for (int j = 0; j < thislookup.size(); j++) {  delete thislookup[j];  }
-
-		thislookup = newLookup;
-		
-		return 0;
- 
-	}
-	catch(exception& e) {
-		m->errorOut(e, "MetaStatsCommand", "eliminateZeroOTUS");
-		exit(1);
-	}
-}
-//**********************************************************************************************************************