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

[mothur.git] / phylosummary.cpp

diff --git a/phylosummary.cpp b/phylosummary.cpp
index b645bac794777a1050de116407fa834370e7940e..22e8e75ce7047e00b135483f16b566eb506a71fb 100644 (file)
--- a/phylosummary.cpp
+++ b/phylosummary.cpp
@@ -131,7 +131,7 @@ int PhyloSummary::addSeqToTree(string seqName, string seqTaxonomy){
                int level = 0;
                
                //are there confidence scores, if so remove them
-               if (seqTaxonomy.find_first_of('(') != -1) {  removeConfidences(seqTaxonomy);    }
+               if (seqTaxonomy.find_first_of('(') != -1) {  m->removeConfidences(seqTaxonomy); }
                
                while (seqTaxonomy != "") {
                        
@@ -229,7 +229,7 @@ int PhyloSummary::addSeqToTree(string seqTaxonomy, vector<string> names){
                int level = 0;
                
                //are there confidence scores, if so remove them
-               if (seqTaxonomy.find_first_of('(') != -1) {  removeConfidences(seqTaxonomy);    }
+               if (seqTaxonomy.find_first_of('(') != -1) {  m->removeConfidences(seqTaxonomy); }
                
                while (seqTaxonomy != "") {
                        
@@ -496,35 +496,6 @@ void PhyloSummary::readTreeStruct(ifstream& in){
        }
 }
 /**************************************************************************************************/
-void PhyloSummary::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, "PhyloSummary", "removeConfidences");
-               exit(1);
-       }
-}
-/**************************************************************************************************/