X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=classify.cpp;h=7726b3e00cca9de19971b70656f9581e43e97c8a;hb=ee8403d4eb5760187d62b42a9cf4272de8fc0ec4;hp=25aa2dd7b9f2f8a4f36030eebf0d3284f7d28b08;hpb=ba2b95b22ab8947d5583ca2c2da74557870b6861;p=mothur.git

diff --git a/classify.cpp b/classify.cpp
index 25aa2dd..7726b3e 100644
--- a/classify.cpp
+++ b/classify.cpp
@@ -238,7 +238,7 @@ void Classify::generateDatabaseAndNames(string tfile, string tempFile, string me
 	}
 }
 /**************************************************************************************************/
-Classify::Classify() {		m = MothurOut::getInstance();	database = NULL;	}
+Classify::Classify() {		m = MothurOut::getInstance();	database = NULL;	flipped=false; }
 /**************************************************************************************************/
 
 int Classify::readTaxonomy(string file) {
@@ -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;
@@ -296,7 +297,9 @@ 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);
 		}
@@ -309,8 +312,11 @@ int Classify::readTaxonomy(string file) {
 	
 		//read template seqs and save
 		while (!inTax.eof()) {
-			inTax >> name >> taxInfo;
-			
+			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);
@@ -319,6 +325,8 @@ int Classify::readTaxonomy(string file) {
 		}
 		inTax.close();
 #endif	
+        
+        
 	
 		phyloTree->assignHeirarchyIDs(0);