mods in testing 1.16.0

[mothur.git] / removelineagecommand.cpp

diff --git a/removelineagecommand.cpp b/removelineagecommand.cpp
index 9467ff60d50b3d72f3f016ed934ba828566f950f..0a5c5c7135941843452e2100977cfff9df3d4b19 100644 (file)
--- a/removelineagecommand.cpp
+++ b/removelineagecommand.cpp
@@ -551,6 +551,7 @@ 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 +569,7 @@ 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 +580,7 @@ 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) { 
@@ -671,8 +672,14 @@ 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));  
+                               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";
+                               }
                                int con = 0;
                                convert(confidence, con);