working on chimera.perseus. made removeConfidences function smarter. Fixed bug in...

[mothur.git] / classifyotucommand.cpp

diff --git a/classifyotucommand.cpp b/classifyotucommand.cpp
index 7b1a04f3658bcb0a3e919fefe34a30dedcfaa882..f36631a0590725867dffc402f74fd73af6168e20 100644 (file)
--- a/classifyotucommand.cpp
+++ b/classifyotucommand.cpp
@@ -368,7 +368,7 @@ int ClassifyOtuCommand::readTaxonomyFile() {
                        m->gobble(in);
                        
                        //are there confidence scores, if so remove them
-                       if (tax.find_first_of('(') != -1) {  removeConfidences(tax);    }
+                       if (tax.find_first_of('(') != -1) {  m->removeConfidences(tax); }
                        
                        taxMap[name] = tax;
                        
@@ -550,7 +550,7 @@ int ClassifyOtuCommand::process(ListVector* processList) {
                        out << (i+1) << '\t' << size << '\t' << conTax << endl;
                        
                        string noConfidenceConTax = conTax;
-                       removeConfidences(noConfidenceConTax);
+                       m->removeConfidences(noConfidenceConTax);
                        
                        //add this bins taxonomy to summary
                        if (basis == "sequence") {
@@ -604,36 +604,6 @@ string ClassifyOtuCommand::addUnclassifieds(string tax, int maxlevel) {
                exit(1);
        }
 }
-
-/**************************************************************************************************/
-void ClassifyOtuCommand::removeConfidences(string& tax) {
-       try {
-               
-               string taxon;
-               string newTax = "";
-               
-               while (tax.find_first_of(';') != -1) {
-                       //get taxon
-                       taxon = tax.substr(0,tax.find_first_of(';'));
-                       
-                       int pos = taxon.find_first_of('(');
-                       if (pos != -1) {
-                               taxon = taxon.substr(0, pos); //rip off confidence 
-                       }
-                       
-                       taxon += ";";
-                       
-                       tax = tax.substr(tax.find_first_of(';')+1, tax.length());
-                       newTax += taxon;
-               }
-               
-               tax = newTax;
-       }
-       catch(exception& e) {
-               m->errorOut(e, "ClassifyOtuCommand", "removeConfidences");
-               exit(1);
-       }
-}
 //**********************************************************************************************************************