Adds tax spaces to get/remove.lineage

#265

source/commands/getlineagecommand.cpp

@@ -350,7 +350,7 @@ int GetLineageCommand::execute(){
                 m->mothurOut("\n[NOTE]: The count file should contain only unique names, so mothur assumes your fasta, list and taxonomy files also contain only uniques.\n\n");
             }
         }
-		
+        
 		//read through the correct file and output lines you want to keep
 		if (taxfile != "")			{
             readTax(); //fills the set of names to get
@@ -1081,8 +1081,8 @@ int GetLineageCommand::readTax(){
 
 			if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName);  return 0; }
 
-			in >> name;				//read from first column
-			in >> tax;			//read from second column
+            in >> name; m->gobble(in);
+            tax = m->getline(in); m->gobble(in);
 			
             string noQuotesTax = m->removeQuotes(tax);
             
@@ -1178,8 +1178,6 @@ int GetLineageCommand::readTax(){
 				}
 			
 			}
-			
-			m->gobble(in);
 		}
 		in.close();
 		out.close();
@@ -1239,7 +1237,7 @@ int GetLineageCommand::readConsTax(){
             
 			in >> otuLabel;	 		m->gobble(in);
             in >> numReps;          m->gobble(in);
-			in >> tax;              m->gobble(in);
+            tax = m->getline(in);   m->gobble(in);
 			
             string noQuotesTax = m->removeQuotes(tax);
             

source/commands/removelineagecommand.cpp

@@ -1070,9 +1070,9 @@ int RemoveLineageCommand::readTax(){
 
 			if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName);  return 0; }
 
-			in >> name;				//read from first column
-			in >> tax;			//read from second column
-			
+            in >> name; m->gobble(in);
+            tax = m->getline(in); m->gobble(in);
+            
 			bool remove = false;
 			
             string noQuotesTax = m->removeQuotes(tax);
@@ -1176,7 +1176,6 @@ int RemoveLineageCommand::readTax(){
 			}
 			
 			if (!remove) {  wroteSomething = true; out << name << '\t' << tax << endl; }
-			m->gobble(in);
 		}
 		in.close();
 		out.close();
@@ -1237,7 +1236,7 @@ int RemoveLineageCommand::readConsTax(){
             
 			in >> otuLabel;	 		m->gobble(in);
             in >> numReps;          m->gobble(in);
-			in >> tax;              m->gobble(in);
+			tax = m->getline(in);   m->gobble(in);
 			
             bool remove = false;
 			

source/optionparser.cpp

@@ -24,7 +24,11 @@ OptionParser::OptionParser(string option) {
 				if ((key == "candidate") || (key == "query")) { key = "fasta"; }
 				if (key == "template") { key = "reference"; }
 				key = m->splitWhiteSpace(key).front();
-			    value = m->splitWhiteSpace(value).front();
+                //if value is wrapped in '' preserve spaces
+                if ((value[0] == '\'') && (value[(value.length()-1)] == '\'')) {  value = value.substr(1); value = value.substr(0, (value.length()-1)); }
+                else {
+                    value = m->splitWhiteSpace(value).front();
+                }
 				parameters[key] = value;
 			}
 			
@@ -33,7 +37,11 @@ OptionParser::OptionParser(string option) {
 			if ((key == "candidate") || (key == "query")) { key = "fasta"; }
 			if (key == "template") { key = "reference"; }
             key = m->splitWhiteSpace(key).front();
-			option = m->splitWhiteSpace(option).front();
+            //if value is wrapped in '' preserve spaces
+            if ((option[0] == '\'') && (option[(option.length()-1)] == '\'')) {  option = option.substr(1); option = option.substr(0, (option.length()-1)); }
+            else {
+                option = m->splitWhiteSpace(option).front();
+            }
 			parameters[key] = option;
 		}
 	}
@@ -57,7 +65,11 @@ OptionParser::OptionParser(string option, map<string, string>& copy) {
 				if ((key == "candidate") || (key == "query")) { key = "fasta"; }
 				if (key == "template") { key = "reference"; }
 				key = m->splitWhiteSpace(key).front();
-			    value = m->splitWhiteSpace(value).front();
+                //if value is wrapped in '' preserve spaces
+                if ((value[0] == '\'') && (value[(value.length()-1)] == '\'')) {  value = value.substr(1); value = value.substr(0, (value.length()-1)); }
+                else {
+                    value = m->splitWhiteSpace(value).front();
+                }
 				parameters[key] = value;
 			}
 			
@@ -66,7 +78,11 @@ OptionParser::OptionParser(string option, map<string, string>& copy) {
 			if ((key == "candidate") || (key == "query")) { key = "fasta"; }
 			if (key == "template") { key = "reference"; }
 			key = m->splitWhiteSpace(key).front();
-			option = m->splitWhiteSpace(option).front();
+            //if value is wrapped in '' preserve spaces
+            if ((option[0] == '\'') && (option[(option.length()-1)] == '\'')) {  option = option.substr(1); option = option.substr(0, (option.length()-1)); }
+            else {
+                option = m->splitWhiteSpace(option).front();
+            }
 			parameters[key] = option;
 		}