X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=phylotree.cpp;h=4ed3d8c1c02e1c5a1ee93b9dd6143309f5606f5c;hb=2009a1a1f47e7467094d844e7c07ab8ddf7bb447;hp=1fd4e5d238119bbcd6be5c54fbd7013fcdfc27bd;hpb=260ae19c36cb11a53ddc5a75b5e507f8dd8b31d6;p=mothur.git

diff --git a/phylotree.cpp b/phylotree.cpp
index 1fd4e5d..4ed3d8c 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");
@@ -127,11 +128,10 @@ PhyloTree::PhyloTree(string tfile){
 		maxLevel = 0;
 		calcTotals = true;
 		string name, tax;
-
 		
 		#ifdef USE_MPI
 			int pid, num, processors;
-			vector<unsigned long int> positions;
+			vector<unsigned long long> positions;
 			
 			MPI_Status status; 
 			MPI_File inMPI;
@@ -191,7 +191,16 @@ PhyloTree::PhyloTree(string tfile){
 		#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 +241,6 @@ string PhyloTree::getNextTaxon(string& heirarchy, string seqname){
 
 int PhyloTree::addSeqToTree(string seqName, string seqTaxonomy){
 	try {
-			
 		numSeqs++;
 		
 		map<string, int>::iterator childPointer;
@@ -241,6 +249,8 @@ int PhyloTree::addSeqToTree(string seqName, string seqTaxonomy){
 		int level = 1;
 		
 		tree[0].accessions.push_back(seqName);
+		m->removeConfidences(seqTaxonomy);
+		
 		string taxon;// = getNextTaxon(seqTaxonomy);
 	
 		while(seqTaxonomy != ""){
@@ -275,6 +285,8 @@ int PhyloTree::addSeqToTree(string seqName, string seqTaxonomy){
 	
 			if (seqTaxonomy == "") {   uniqueTaxonomies[currentNode] = currentNode;	}
 		}
+		
+		return 0;
 	}
 	catch(exception& e) {
 		m->errorOut(e, "PhyloTree", "addSeqToTree");
@@ -371,7 +383,7 @@ void PhyloTree::binUnclassified(string file){
 		map<string, int>::iterator childPointer;
 		
 		vector<TaxNode> copy = tree;
-			
+		
 		//fill out tree
 		fillOutTree(0, copy);
 	
@@ -480,16 +492,16 @@ 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;
@@ -602,23 +614,27 @@ 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;
 			}
 			
-			templateFileNames.erase(templateFileNames.begin()+i);
-			i--;
+			//templateFileNames.erase(templateFileNames.begin()+i);
+			//i--;
 		}
+		templateFileNames.clear();
 		
 		if (taxonomyFileNames.size() > 0) { //there are names in tax file that are not in template
 			okay = false;