X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=classify.cpp;h=212e563f94c4ae7af3ba0916d1040afd9b0e11fa;hb=6ede3bf5c0a9eedb23f24577a97da81ab3e1f7df;hp=3bf0d572f88d0ad7ffd76989d71f10807e8cc659;hpb=16abd6271c455bd01b34ff89a2e3641bef0fa128;p=mothur.git

diff --git a/classify.cpp b/classify.cpp
index 3bf0d57..212e563 100644
--- a/classify.cpp
+++ b/classify.cpp
@@ -249,7 +249,8 @@ int Classify::readTaxonomy(string file) {
 		
 		m->mothurOutEndLine();
 		m->mothurOut("Reading in the " + file + " taxonomy...\t");	cout.flush();
-
+        if (m->debug) { m->mothurOut("[DEBUG]: Taxonomies read in...\n"); }
+        
 #ifdef USE_MPI	
 		int pid, num, processors;
 		vector<unsigned long long> positions;
@@ -296,30 +297,21 @@ int Classify::readTaxonomy(string file) {
 			delete buf4;
 
 			istringstream iss (tempBuf,istringstream::in);
-			iss >> name >> taxInfo;
+			iss >> name; m->gobble(iss);
+            iss >> taxInfo;
+            if (m->debug) { m->mothurOut("[DEBUG]: name = " + name + " tax = " + taxInfo + "\n"); }
 			taxonomy[name] = taxInfo;
 			phyloTree->addSeqToTree(name, taxInfo);
 		}
 		
 		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 >> taxInfo;
-			
-			taxonomy[name] = taxInfo;
-			
-			phyloTree->addSeqToTree(name, taxInfo);
-		
-			m->gobble(inTax);
-		}
-		inTax.close();
+#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);