X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=removelineagecommand.cpp;h=ef1e77e01755f57acbaa4581c36a3e66d376c198;hb=a4f05f09c250323132a4b9427f41a3ededaec634;hp=9467ff60d50b3d72f3f016ed934ba828566f950f;hpb=8f89a92f4ada82a2b3bf51b23b6a977770f2b9e2;p=mothur.git

diff --git a/removelineagecommand.cpp b/removelineagecommand.cpp
index 9467ff6..ef1e77e 100644
--- a/removelineagecommand.cpp
+++ b/removelineagecommand.cpp
@@ -26,8 +26,7 @@ vector<string> RemoveLineageCommand::getValidParameters(){
 //**********************************************************************************************************************
 RemoveLineageCommand::RemoveLineageCommand(){	
 	try {
-		abort = true;
-		//initialize outputTypes
+		abort = true; calledHelp = true; 
 		vector<string> tempOutNames;
 		outputTypes["fasta"] = tempOutNames;
 		outputTypes["taxonomy"] = tempOutNames;
@@ -67,10 +66,10 @@ vector<string> RemoveLineageCommand::getRequiredFiles(){
 //**********************************************************************************************************************
 RemoveLineageCommand::RemoveLineageCommand(string option)  {
 	try {
-		abort = false;
+		abort = false; calledHelp = false;   
 				
 		//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
@@ -237,7 +236,7 @@ void RemoveLineageCommand::help(){
 int RemoveLineageCommand::execute(){
 	try {
 		
-		if (abort == true) { return 0; }
+		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
 		
 		if (m->control_pressed) { return 0; }
 		
@@ -257,6 +256,33 @@ int RemoveLineageCommand::execute(){
 			m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 			for (int i = 0; i < outputNames.size(); i++) {	m->mothurOut(outputNames[i]); m->mothurOutEndLine();	}
 			m->mothurOutEndLine();
+			
+			//set fasta file as new current fastafile
+			string current = "";
+			itTypes = outputTypes.find("fasta");
+			if (itTypes != outputTypes.end()) {
+				if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
+			}
+			
+			itTypes = outputTypes.find("name");
+			if (itTypes != outputTypes.end()) {
+				if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setNameFile(current); }
+			}
+			
+			itTypes = outputTypes.find("group");
+			if (itTypes != outputTypes.end()) {
+				if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setGroupFile(current); }
+			}
+			
+			itTypes = outputTypes.find("list");
+			if (itTypes != outputTypes.end()) {
+				if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setListFile(current); }
+			}
+			
+			itTypes = outputTypes.find("taxonomy");
+			if (itTypes != outputTypes.end()) {
+				if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setTaxonomyFile(current); }
+			}
 		}
 		
 		return 0;		
@@ -530,7 +556,7 @@ int RemoveLineageCommand::readTax(){
 		bool wroteSomething = false;
 		
 		bool taxonsHasConfidence = false;
-		vector< map<string, int> > searchTaxons;
+		vector< map<string, float> > searchTaxons;
 		string noConfidenceTaxons = taxons;
 		int hasConPos = taxons.find_first_of('(');
 		if (hasConPos != string::npos) {  
@@ -551,6 +577,7 @@ int RemoveLineageCommand::readTax(){
 			
 			//if the users file contains confidence scores we want to ignore them when searching for the taxons, unless the taxon has them
 			if (!taxonsHasConfidence) {
+				
 				int hasConfidences = tax.find_first_of('(');
 				if (hasConfidences != string::npos) { 
 					newtax = removeConfidences(tax);
@@ -568,7 +595,7 @@ int RemoveLineageCommand::readTax(){
 			}else{//if taxons has them and you don't them remove taxons
 				int hasConfidences = tax.find_first_of('(');
 				if (hasConfidences == string::npos) { 
-					
+				
 					int pos = newtax.find(noConfidenceTaxons);
 					
 					if (pos == string::npos) { 
@@ -579,7 +606,7 @@ int RemoveLineageCommand::readTax(){
 					}
 				}else { //both have confidences so we want to make sure the users confidences are greater then or equal to the taxons
 					//first remove confidences from both and see if the taxonomy exists
-					
+				
 					string noNewTax = tax;
 					int hasConfidences = tax.find_first_of('(');
 					if (hasConfidences != string::npos) { 
@@ -591,7 +618,7 @@ int RemoveLineageCommand::readTax(){
 					if (pos != string::npos) { //if yes, then are the confidences okay
 						
 						bool remove = false;
-						vector< map<string, int> > usersTaxon = getTaxons(newtax);
+						vector< map<string, float> > usersTaxon = getTaxons(newtax);
 						
 						//the usersTaxon is most likely longer than the searchTaxons, and searchTaxon[0] may relate to userTaxon[4]
 						//we want to "line them up", so we will find the the index where the searchstring starts
@@ -659,10 +686,10 @@ int RemoveLineageCommand::readTax(){
 	}
 }
 /**************************************************************************************************/
-vector< map<string, int> > RemoveLineageCommand::getTaxons(string tax) {
+vector< map<string, float> > RemoveLineageCommand::getTaxons(string tax) {
 	try {
 		
-		vector< map<string, int> > t;
+		vector< map<string, float> > t;
 		string taxon = "";
 		int taxLength = tax.length();
 		for(int i=0;i<taxLength;i++){
@@ -671,12 +698,18 @@ vector< map<string, int> > RemoveLineageCommand::getTaxons(string tax) {
 				int openParen = taxon.find_first_of('(');
 				int closeParen = taxon.find_last_of(')');
 				
-				string newtaxon = taxon.substr(0, openParen); //rip off confidence
-				string confidence = taxon.substr((openParen+1), (closeParen-openParen-1));  
-				int con = 0;
+				string newtaxon, confidence;
+				if ((openParen != string::npos) && (closeParen != string::npos)) {
+					newtaxon = taxon.substr(0, openParen); //rip off confidence
+					confidence = taxon.substr((openParen+1), (closeParen-openParen-1));  
+				}else{
+					newtaxon = taxon;
+					confidence = "0";
+				}
+				float con = 0;
 				convert(confidence, con);
 				
-				map<string, int> temp;
+				map<string, float> temp;
 				temp[newtaxon] = con;
 				t.push_back(temp);