X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getlineagecommand.cpp;fp=getlineagecommand.cpp;h=99359bd882e1e2b668cd6bef2b2ec7cfc32fc0bf;hb=9b53f130ac9af5e95444ce2e817fce25ed19ff03;hp=645655d03f72bbebac45cfa108c499cc1daf8e3b;hpb=5c5c0428f6d548c28a8b903ac80efed4f92d59db;p=mothur.git

diff --git a/getlineagecommand.cpp b/getlineagecommand.cpp
index 645655d..99359bd 100644
--- a/getlineagecommand.cpp
+++ b/getlineagecommand.cpp
@@ -814,20 +814,27 @@ int GetLineageCommand::readTax(){
 /**************************************************************************************************/
 vector< map<string, float> > GetLineageCommand::getTaxons(string tax) {
 	try {
-		
+        
 		vector< map<string, float> > t;
 		string taxon = "";
 		int taxLength = tax.length();
+        
 		for(int i=0;i<taxLength;i++){
 			if(tax[i] == ';'){
-		
-				int openParen = taxon.find_first_of('(');
+                
+				int openParen = taxon.find_last_of('(');
 				int closeParen = taxon.find_last_of(')');
 				
 				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));  
+                    string confidenceScore = taxon.substr(openParen+1, (closeParen-(openParen+1)));
+                    if (m->isNumeric1(confidenceScore)) {  //its a confidence
+                        newtaxon = taxon.substr(0, openParen); //rip off confidence
+                        confidence = taxon.substr((openParen+1), (closeParen-openParen-1));  
+                    }else { //its part of the taxon
+                        newtaxon = taxon;
+                        confidence = "0";
+                    }
 				}else{
 					newtaxon = taxon;
 					confidence = "0";
@@ -837,12 +844,13 @@ vector< map<string, float> > GetLineageCommand::getTaxons(string tax) {
 				
 				map<string, float> temp;
 				temp[newtaxon] = con;
+                
 				t.push_back(temp);
-				
 				taxon = "";
 			}
 			else{
 				taxon += tax[i];
+                
 			}
 		}