From: westcott <westcott>
Date: Thu, 5 Aug 2010 10:52:19 +0000 (+0000)
Subject: fixed bug with creation of .tree.sum file
X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=commitdiff_plain;h=2df35fdeea85f574630d75b11fb5b08c39aec31a

fixed bug with creation of .tree.sum file
---

diff --git a/bayesian.cpp b/bayesian.cpp
index e5ab89e..ae96a22 100644
--- a/bayesian.cpp
+++ b/bayesian.cpp
@@ -20,6 +20,7 @@ Classify(), kmerSize(ksize), confidenceThreshold(cutoff), iters(i)  {
 		string tfileroot = tfile.substr(0,tfile.find_last_of(".")+1);
 		string tempfileroot = getRootName(getSimpleName(tempFile));
 		string phyloTreeName = tfileroot + "tree.train";
+		string phyloTreeSumName = tfileroot + "tree.sum";
 		string probFileName = tfileroot + tempfileroot + char('0'+ kmerSize) + "mer.prob";
 		string probFileName2 = tfileroot + tempfileroot + char('0'+ kmerSize) + "mer.numNonZero";
 		
@@ -29,10 +30,11 @@ Classify(), kmerSize(ksize), confidenceThreshold(cutoff), iters(i)  {
 		ifstream phyloTreeTest(phyloTreeName.c_str());
 		ifstream probFileTest2(probFileName2.c_str());
 		ifstream probFileTest(probFileName.c_str());
+		ifstream probFileTest3(phyloTreeSumName.c_str());
 		
 		int start = time(NULL);
 		
-		if(probFileTest && probFileTest2 && phyloTreeTest){	
+		if(probFileTest && probFileTest2 && phyloTreeTest && probFileTest3){	
 			m->mothurOut("Reading template taxonomy...     "); cout.flush();
 			
 			phyloTree = new PhyloTree(phyloTreeTest, phyloTreeName);
diff --git a/classify.cpp b/classify.cpp
index 9a2de1f..6bf2cb5 100644
--- a/classify.cpp
+++ b/classify.cpp
@@ -254,7 +254,7 @@ int Classify::readTaxonomy(string file) {
 		phyloTree->assignHeirarchyIDs(0);
 		
 		phyloTree->setUp(file);
-		
+	
 		m->mothurOut("DONE.");
 		m->mothurOutEndLine();	cout.flush();
 		
diff --git a/phylosummary.cpp b/phylosummary.cpp
index 3339697..08cedeb 100644
--- a/phylosummary.cpp
+++ b/phylosummary.cpp
@@ -255,6 +255,8 @@ void PhyloSummary::readTreeStruct(ifstream& in){
 		in >> num; gobble(in);
 		
 		tree.resize(num);
+		
+		in >> maxLevel; gobble(in);
 	
 		//read the tree file
 		for (int i = 0; i < tree.size(); i++) {
@@ -280,7 +282,7 @@ void PhyloSummary::readTreeStruct(ifstream& in){
 			
 			gobble(in);
 			
-			if (tree[i].level > maxLevel) {  maxLevel = tree[i].level;  }
+			//if (tree[i].level > maxLevel) {  maxLevel = tree[i].level;  }
 		}
 
 	}
diff --git a/phylotree.cpp b/phylotree.cpp
index 6b32e27..e2b0805 100644
--- a/phylotree.cpp
+++ b/phylotree.cpp
@@ -178,14 +178,14 @@ PhyloTree::PhyloTree(string tfile){
 			//read in users taxonomy file and add sequences to tree
 			while(!in.eof()){
 				in >> name >> tax; gobble(in);
-				
+			
 				addSeqToTree(name, tax);
 			}
 			in.close();
 		#endif
-		
+	
 		assignHeirarchyIDs(0);
-		
+	
 		//create file for summary if needed
 		setUp(tfile);
 	}
@@ -346,12 +346,7 @@ void PhyloTree::setUp(string tfile){
 			if (pid == 0) {  binUnclassified(taxFileNameTest);  }
 		
 		#else
-			//create file needed for summary if it doesn't exist
-			ifstream FileTest(taxFileNameTest.c_str());
-			
-			if (!FileTest) { 
-				binUnclassified(taxFileNameTest); 
-			}
+			binUnclassified(taxFileNameTest); 
 		#endif
 	}
 	catch(exception& e) {
@@ -381,9 +376,9 @@ void PhyloTree::binUnclassified(string file){
 				leafNodes[i] = i;
 			}
 		}
-	//cout << "maxLevel = " << maxLevel << endl;	
-		int copyNodes = copy.size();
 		
+		int copyNodes = copy.size();
+	
 		//go through the seqs and if a sequence finest taxon is not the same level as the most finely defined taxon then classify it as unclassified where necessary
 		map<int, int>::iterator itLeaf;
 		for (itLeaf = leafNodes.begin(); itLeaf != leafNodes.end(); itLeaf++) {
@@ -432,25 +427,24 @@ void PhyloTree::binUnclassified(string file){
 /**************************************************************************************************/
 void PhyloTree::fillOutTree(int index, vector<TaxNode>& copy) {
 	try {
+	
 		map<string,int>::iterator it;
 		
-		if (copy[index].level < maxLevel) {
-			it = copy[index].children.find("unclassified");
-			if (it == copy[index].children.end()) { //no unclassified at this level
-				string taxon = "unclassified";
-				copy.push_back(TaxNode(taxon));
-				copy[index].children[taxon] = copy.size()-1;
-				copy[copy.size()-1].parent = index;
-				copy[copy.size()-1].level = copy[index].level + 1;
-			}
+		it = copy[index].children.find("unclassified");
+		if (it == copy[index].children.end()) { //no unclassified at this level
+			string taxon = "unclassified";
+			copy.push_back(TaxNode(taxon));
+			copy[index].children[taxon] = copy.size()-1;
+			copy[copy.size()-1].parent = index;
+			copy[copy.size()-1].level = copy[index].level + 1;
+		}
 		
-			
-			for(it=copy[index].children.begin();it!=copy[index].children.end();it++){ //check your children
+		if (tree[index].level < maxLevel) {
+			for(it=tree[index].children.begin();it!=tree[index].children.end();it++){ //check your children
 				fillOutTree(it->second, copy);
 			}
-			
 		}
-		
+
 	}
 	catch(exception& e) {
 		m->errorOut(e, "PhyloTree", "fillOutTree");
@@ -482,6 +476,8 @@ void PhyloTree::print(ofstream& out, vector<TaxNode>& copy){
 	try {
 		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';