X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=phylotree.cpp;h=3dde18680c625eb816230a8d13774ccfc47032cf;hb=fdfbfe59134dd7dd3e49d90609d129128ba2d370;hp=e430fb9e85622dcd1d425534857fe37dff600da9;hpb=d0051dc9939d3477bd92b42c86bcd3eda743b955;p=mothur.git

diff --git a/phylotree.cpp b/phylotree.cpp
index e430fb9..3dde186 100644
--- a/phylotree.cpp
+++ b/phylotree.cpp
@@ -20,6 +20,7 @@ PhyloTree::PhyloTree(){
 		tree[0].heirarchyID = "0";
 		maxLevel = 0;
 		calcTotals = true;
+		addSeqToTree("unknown", "unknown;");
 	}
 	catch(exception& e) {
 		m->errorOut(e, "PhyloTree", "PhyloTree");
@@ -127,7 +128,6 @@ PhyloTree::PhyloTree(string tfile){
 		maxLevel = 0;
 		calcTotals = true;
 		string name, tax;
-
 		
 		#ifdef USE_MPI
 			int pid, num, processors;
@@ -178,20 +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);
 	}
@@ -232,7 +238,6 @@ string PhyloTree::getNextTaxon(string& heirarchy, string seqname){
 
 int PhyloTree::addSeqToTree(string seqName, string seqTaxonomy){
 	try {
-			
 		numSeqs++;
 		
 		map<string, int>::iterator childPointer;
@@ -375,7 +380,7 @@ void PhyloTree::binUnclassified(string file){
 		map<string, int>::iterator childPointer;
 		
 		vector<TaxNode> copy = tree;
-			
+		
 		//fill out tree
 		fillOutTree(0, copy);
 	
@@ -484,16 +489,16 @@ string PhyloTree::getFullTaxonomy(string seqName) {
 
 void PhyloTree::print(ofstream& out, vector<TaxNode>& copy){
 	try {
-	
+		
 		//output mothur version
 		out << "#" << m->getVersion() << endl;
 		
 		out << copy.size() << endl;
 		
 		out << maxLevel << endl;
-		
+				
 		for (int i = 0; i < copy.size(); i++) {
-	
+				
 			out << copy[i].level << '\t'<< copy[i].name << '\t' << copy[i].children.size() << '\t';
 			
 			map<string,int>::iterator it;
@@ -606,17 +611,20 @@ bool PhyloTree::ErrorCheck(vector<string> templateFileNames){
 	try {
 	
 		bool okay = true;
+		templateFileNames.push_back("unknown");
 		
 		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;
 			}