X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=removelineagecommand.cpp;fp=removelineagecommand.cpp;h=f55158fc259ace27c87d5a4fcca10e7c55539f13;hb=74dc92cf53df65fd8b14d8eaf35489bbecbccac6;hp=b72f4b669d43b4b44fa1c20df4812155aaff82fc;hpb=4c5e7a20a03ddc6feb49ff9d21fcb4c79bc5508d;p=mothur.git

diff --git a/removelineagecommand.cpp b/removelineagecommand.cpp
index b72f4b6..f55158f 100644
--- a/removelineagecommand.cpp
+++ b/removelineagecommand.cpp
@@ -555,7 +555,8 @@ int RemoveLineageCommand::readTax(){
 			if (hasConPos != string::npos) {  
 				taxonsHasConfidence[i] = true; 
 				searchTaxons[i] = getTaxons(listOfTaxons[i]); 
-				noConfidenceTaxons[i] = removeConfidences(listOfTaxons[i]);
+				noConfidenceTaxons[i] = listOfTaxons[i];
+				m->removeConfidences(noConfidenceTaxons[i]);
 			}
 		}
 		
@@ -577,7 +578,8 @@ int RemoveLineageCommand::readTax(){
 					
 					int hasConfidences = tax.find_first_of('(');
 					if (hasConfidences != string::npos) { 
-						newtax = removeConfidences(tax);
+						newtax = tax;
+						m->removeConfidences(newtax);
 					}
 					
 					int pos = newtax.find(noConfidenceTaxons[j]);
@@ -609,7 +611,8 @@ int RemoveLineageCommand::readTax(){
 						string noNewTax = tax;
 						int hasConfidences = tax.find_first_of('(');
 						if (hasConfidences != string::npos) { 
-							noNewTax = removeConfidences(tax);
+							noNewTax = tax;
+							m->removeConfidences(noNewTax);
 						}
 						
 						int pos = noNewTax.find(noConfidenceTaxons[j]);
@@ -726,29 +729,6 @@ vector< map<string, float> > RemoveLineageCommand::getTaxons(string tax) {
 		exit(1);
 	}
 }
-/**************************************************************************************************/
-string RemoveLineageCommand::removeConfidences(string tax) {
-	try {
-		
-		string taxon = "";
-		int taxLength = tax.length();
-		for(int i=0;i<taxLength;i++){
-			if(tax[i] == ';'){
-				taxon = taxon.substr(0, taxon.find_first_of('(')); //rip off confidence
-				taxon += ";";
-			}
-			else{
-				taxon += tax[i];
-			}
-		}
-				
-		return taxon;
-	}
-	catch(exception& e) {
-		m->errorOut(e, "RemoveLineageCommand", "removeConfidences");
-		exit(1);
-	}
-}
 //**********************************************************************************************************************
 //alignreport file has a column header line then all other lines contain 16 columns.  we just want the first column since that contains the name
 int RemoveLineageCommand::readAlign(){