X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=phylotree.cpp;h=3dde18680c625eb816230a8d13774ccfc47032cf;hb=0cefb55a2616975bd4a144fc345693695ffc9bb6;hp=dba1e3b56951f8ae1c484ace22187a9b65053d35;hpb=16abd6271c455bd01b34ff89a2e3641bef0fa128;p=mothur.git

diff --git a/phylotree.cpp b/phylotree.cpp
index dba1e3b..3dde186 100644
--- a/phylotree.cpp
+++ b/phylotree.cpp
@@ -128,8 +128,6 @@ PhyloTree::PhyloTree(string tfile){
 		maxLevel = 0;
 		calcTotals = true;
 		string name, tax;
-		addSeqToTree("unknown", "unknown;");
-
 		
 		#ifdef USE_MPI
 			int pid, num, processors;
@@ -180,20 +178,26 @@ PhyloTree::PhyloTree(string tfile){
 			MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 		
 		#else
-			ifstream in;
-			m->openInputFile(tfile, in);
-			
-			//read in users taxonomy file and add sequences to tree
-			while(!in.eof()){
-				in >> name >> tax; m->gobble(in);
-			
-				addSeqToTree(name, tax);
-			}
-			in.close();
+            map<string, string> temp;
+            m->readTax(tfile, temp);
+        
+            for (map<string, string>::iterator itTemp = temp.begin(); itTemp != temp.end();) {
+                addSeqToTree(itTemp->first, itTemp->second);
+                temp.erase(itTemp++);
+            }
 		#endif
 	
 		assignHeirarchyIDs(0);
-	
+        
+        
+        string unknownTax = "unknown;";
+        //added last taxon until you get desired level
+		for (int i = 1; i < maxLevel; i++) {
+			unknownTax += "unclassfied;";
+		}
+        
+        addSeqToTree("unknown", unknownTax);
+        
 		//create file for summary if needed
 		setUp(tfile);
 	}
@@ -612,13 +616,15 @@ bool PhyloTree::ErrorCheck(vector<string> templateFileNames){
 		map<string, int>::iterator itFind;
 		map<string, int> taxonomyFileNames = name2Taxonomy;
 		
+        if (m->debug) { m->mothurOut("[DEBUG]: in error check. Numseqs in template = " + toString(templateFileNames.size()) + ". Numseqs in taxonomy = " + toString(taxonomyFileNames.size()) + ".\n"); }
+        
 		for (int i = 0; i < templateFileNames.size(); i++) {
 			itFind = taxonomyFileNames.find(templateFileNames[i]);
 			
 			if (itFind != taxonomyFileNames.end()) { //found it so erase it
 				taxonomyFileNames.erase(itFind);
 			}else {
-				m->mothurOut(templateFileNames[i] + " is in your template file and is not in your taxonomy file. Please correct."); m->mothurOutEndLine();
+				m->mothurOut("'" +templateFileNames[i] + "' is in your template file and is not in your taxonomy file. Please correct."); m->mothurOutEndLine();
 				okay = false;
 			}