added load.logfile command. changed summary.single output for subsample=t.

[mothur.git] / classify.cpp

diff --git a/classify.cpp b/classify.cpp
index 7726b3e00cca9de19971b70656f9581e43e97c8a..212e563f94c4ae7af3ba0916d1040afd9b0e11fa 100644 (file)
--- a/classify.cpp
+++ b/classify.cpp
@@ -306,28 +306,12 @@ int Classify::readTaxonomy(string file) {
                
                MPI_File_close(&inMPI);
                MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
-#else                          
-               ifstream inTax;
-               m->openInputFile(file, inTax);
-       
-               //read template seqs and save
-               while (!inTax.eof()) {
-                       inTax >> name; m->gobble(inTax);
-            inTax >> taxInfo;
-            
-            if (m->debug) {  m->mothurOut("[DEBUG]: name = '" + name + "' tax = '" + taxInfo + "'\n");  }
-
-                       taxonomy[name] = taxInfo;
-                       
-                       phyloTree->addSeqToTree(name, taxInfo);
-               
-                       m->gobble(inTax);
-               }
-               inTax.close();
-#endif 
-        
+#else  
         
-       
+        taxonomy.clear(); 
+        m->readTax(file, taxonomy);
+        for (map<string, string>::iterator itTax = taxonomy.begin(); itTax != taxonomy.end(); itTax++) {  phyloTree->addSeqToTree(itTax->first, itTax->second);  }
+#endif 
                phyloTree->assignHeirarchyIDs(0);
                
                phyloTree->setUp(file);