X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=phylotree.cpp;h=dba1e3b56951f8ae1c484ace22187a9b65053d35;hb=8dd3c225255d7084e3aff8740aa4f1f1cabb367a;hp=2ea219350c1f8bf8099b7cfc40d28ddcdfc9d872;hpb=050220fe7822cc660615972a0054cf4a83eefbe4;p=mothur.git

diff --git a/phylotree.cpp b/phylotree.cpp
index 2ea2193..dba1e3b 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");
@@ -55,24 +56,24 @@ PhyloTree::PhyloTree(ifstream& in, string filename){
 			delete buffer;
 			
 			//read version
-			getline(iss); gobble(iss);
+			m->getline(iss); m->gobble(iss);
 			
-			iss >> numNodes; gobble(iss);
+			iss >> numNodes; m->gobble(iss);
 			
 			tree.resize(numNodes);
 			
 			for (int i = 0; i < tree.size(); i++) {
-				iss >> tree[i].name >> tree[i].level >> tree[i].parent; gobble(iss);
+				iss >> tree[i].name >> tree[i].level >> tree[i].parent; m->gobble(iss);
 			}
 			
 			//read genus nodes
 			int numGenus = 0;
-			iss >> numGenus; gobble(iss);
+			iss >> numGenus; m->gobble(iss);
 			
 			int gnode, gsize;
 			totals.clear();
 			for (int i = 0; i < numGenus; i++) {
-				iss >> gnode >> gsize; gobble(iss);
+				iss >> gnode >> gsize; m->gobble(iss);
 				
 				uniqueTaxonomies[gnode] = gnode;
 				totals.push_back(gsize);
@@ -82,24 +83,24 @@ PhyloTree::PhyloTree(ifstream& in, string filename){
 			
 		#else
 			//read version
-			string line = getline(in); gobble(in);
+			string line = m->getline(in); m->gobble(in);
 			
-			in >> numNodes; gobble(in);
+			in >> numNodes; m->gobble(in);
 			
 			tree.resize(numNodes);
 			
 			for (int i = 0; i < tree.size(); i++) {
-				in >> tree[i].name >> tree[i].level >> tree[i].parent; gobble(in);
+				in >> tree[i].name >> tree[i].level >> tree[i].parent; m->gobble(in);
 			}
 			
 			//read genus nodes
 			int numGenus = 0;
-			in >> numGenus; gobble(in);
+			in >> numGenus; m->gobble(in);
 			
 			int gnode, gsize;
 			totals.clear();
 			for (int i = 0; i < numGenus; i++) {
-				in >> gnode >> gsize; gobble(in);
+				in >> gnode >> gsize; m->gobble(in);
 				
 				uniqueTaxonomies[gnode] = gnode;
 				totals.push_back(gsize);
@@ -127,11 +128,12 @@ PhyloTree::PhyloTree(string tfile){
 		maxLevel = 0;
 		calcTotals = true;
 		string name, tax;
+		addSeqToTree("unknown", "unknown;");
 
 		
 		#ifdef USE_MPI
 			int pid, num, processors;
-			vector<unsigned long int> positions;
+			vector<unsigned long long> positions;
 			
 			MPI_Status status; 
 			MPI_File inMPI;
@@ -144,7 +146,7 @@ PhyloTree::PhyloTree(string tfile){
 			MPI_File_open(MPI_COMM_WORLD, inFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
 
 			if (pid == 0) {
-				positions = setFilePosEachLine(tfile, num);
+				positions = m->setFilePosEachLine(tfile, num);
 				
 				//send file positions to all processes
 				for(int i = 1; i < processors; i++) { 
@@ -179,11 +181,11 @@ PhyloTree::PhyloTree(string tfile){
 		
 		#else
 			ifstream in;
-			openInputFile(tfile, in);
+			m->openInputFile(tfile, in);
 			
 			//read in users taxonomy file and add sequences to tree
 			while(!in.eof()){
-				in >> name >> tax; gobble(in);
+				in >> name >> tax; m->gobble(in);
 			
 				addSeqToTree(name, tax);
 			}
@@ -232,7 +234,6 @@ string PhyloTree::getNextTaxon(string& heirarchy, string seqname){
 
 int PhyloTree::addSeqToTree(string seqName, string seqTaxonomy){
 	try {
-			
 		numSeqs++;
 		
 		map<string, int>::iterator childPointer;
@@ -241,6 +242,8 @@ 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 +278,8 @@ int PhyloTree::addSeqToTree(string seqName, string seqTaxonomy){
 	
 			if (seqTaxonomy == "") {   uniqueTaxonomies[currentNode] = currentNode;	}
 		}
+		
+		return 0;
 	}
 	catch(exception& e) {
 		m->errorOut(e, "PhyloTree", "addSeqToTree");
@@ -365,13 +370,13 @@ void PhyloTree::binUnclassified(string file){
 	try {
 	
 		ofstream out;
-		openOutputFile(file, out);
+		m->openOutputFile(file, out);
 		
 		map<string, int>::iterator itBin;
 		map<string, int>::iterator childPointer;
 		
 		vector<TaxNode> copy = tree;
-			
+		
 		//fill out tree
 		fillOutTree(0, copy);
 	
@@ -480,16 +485,16 @@ 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;
@@ -519,7 +524,7 @@ void PhyloTree::printTreeNodes(string treefilename) {
 		#endif
 
 			ofstream outTree;
-			openOutputFile(treefilename, outTree);
+			m->openOutputFile(treefilename, outTree);
 			
 			//output mothur version
 			outTree << "#" << m->getVersion() << endl;
@@ -602,6 +607,7 @@ bool PhyloTree::ErrorCheck(vector<string> templateFileNames){
 	try {
 	
 		bool okay = true;
+		templateFileNames.push_back("unknown");
 		
 		map<string, int>::iterator itFind;
 		map<string, int> taxonomyFileNames = name2Taxonomy;
@@ -616,9 +622,10 @@ bool PhyloTree::ErrorCheck(vector<string> templateFileNames){
 				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;