added amova command

[mothur.git] / getlineagecommand.cpp

diff --git a/getlineagecommand.cpp b/getlineagecommand.cpp
index 8a825a1ca76c077cade0e6aecd078eb3fa72ea38..8a6f47c0998202943e398fce09a9ae52edfa5eda 100644 (file)
--- a/getlineagecommand.cpp
+++ b/getlineagecommand.cpp
@@ -542,7 +542,7 @@ int GetLineageCommand::readTax(){
                m->openInputFile(taxfile, in);
                string name, tax;
                
-               bool wroteSomething = false;
+               //bool wroteSomething = false;
                
                bool taxonsHasConfidence = false;
                vector< map<string, int> > searchTaxons;
@@ -677,8 +677,14 @@ vector< map<string, int> > GetLineageCommand::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);