X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=phylotree.cpp;h=2e3136e1f42e1a93d15fcab921b2e612f55f3997;hp=d6c740ae791b494ea64951a03405b38535593152;hb=b206f634aae1b4ce13978d203247fb64757d5482;hpb=762b3e4c83e1e8e8392c1199b6482d36ee89e50f

diff --git a/phylotree.cpp b/phylotree.cpp
index d6c740a..2e3136e 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");
@@ -54,48 +55,54 @@ PhyloTree::PhyloTree(ifstream& in, string filename){
 			istringstream iss (tempBuf,istringstream::in);
 			delete buffer;
 			
-			iss >> numNodes; gobble(iss);
+			//read version
+			m->getline(iss); m->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;
+				uniqueTaxonomies.insert(gnode);
 				totals.push_back(gsize);
 			}
 			
 			MPI_File_close(&inMPI);
 			
 		#else
-			in >> numNodes; gobble(in);
+			//read version
+			string line = m->getline(in); m->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;
+				uniqueTaxonomies.insert(gnode);
 				totals.push_back(gsize);
 			}
 			
@@ -121,11 +128,10 @@ PhyloTree::PhyloTree(string tfile){
 		maxLevel = 0;
 		calcTotals = true;
 		string name, tax;
-
 		
 		#ifdef USE_MPI
 			int pid, num, processors;
-			vector<long> positions;
+			vector<unsigned long long> positions;
 			
 			MPI_Status status; 
 			MPI_File inMPI;
@@ -138,7 +144,7 @@ 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++) { 
@@ -172,20 +178,26 @@ PhyloTree::PhyloTree(string tfile){
 			MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 		
 		#else
-			ifstream in;
-			openInputFile(tfile, in);
-			
-			//read in users taxonomy file and add sequences to tree
-			while(!in.eof()){
-				in >> name >> tax; 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);
 	}
@@ -221,12 +233,53 @@ string PhyloTree::getNextTaxon(string& heirarchy, string seqname){
 		exit(1);
 	}
 }
+/**************************************************************************************************/
+
+vector<string> PhyloTree::getSeqs(string seqTaxonomy){
+	try {
+        string taxCopy = seqTaxonomy;
+        vector<string> names;
+        map<string, int>::iterator childPointer;
+		
+		int currentNode = 0;
+
+        m->removeConfidences(seqTaxonomy);
+        
+        string taxon;
+        while(seqTaxonomy != ""){
+			
+			if (m->control_pressed) { return names; }
+			
+			taxon = getNextTaxon(seqTaxonomy, "");
+            
+            if (m->debug) { m->mothurOut(taxon +'\n'); }
+			
+			if (taxon == "") {  m->mothurOut(taxCopy + " has an error in the taxonomy.  This may be due to a ;;"); m->mothurOutEndLine(); break;  }
+			
+			childPointer = tree[currentNode].children.find(taxon);
+			
+			if(childPointer != tree[currentNode].children.end()){	//if the node already exists, move on
+				currentNode = childPointer->second;
+			}
+			else{											//otherwise, error this taxonomy is not in tree
+				m->mothurOut("[ERROR]: " + taxCopy + " is not in taxonomy tree, please correct."); m->mothurOutEndLine(); m->control_pressed = true; return names;
+			}
+            
+			if (seqTaxonomy == "") {   names = tree[currentNode].accessions;	}
+		}
+        
+        return names;
+    }
+	catch(exception& e) {
+		m->errorOut(e, "PhyloTree", "getSeqs");
+		exit(1);
+	}
+}
 
 /**************************************************************************************************/
 
 int PhyloTree::addSeqToTree(string seqName, string seqTaxonomy){
 	try {
-			
 		numSeqs++;
 		
 		map<string, int>::iterator childPointer;
@@ -235,6 +288,8 @@ 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 != ""){
@@ -246,8 +301,10 @@ int PhyloTree::addSeqToTree(string seqName, string seqTaxonomy){
 			//somehow the parent is getting one too many accnos
 			//use print to reassign the taxa id
 			taxon = getNextTaxon(seqTaxonomy, seqName);
+            
+            if (m->debug) { m->mothurOut(seqName +'\t' + taxon +'\n'); }
 			
-			if (taxon == "") {  m->mothurOut(seqName + " has an error in the taxonomy.  This may be due to a ;;"); m->mothurOutEndLine(); if (currentNode != 0) {  uniqueTaxonomies[currentNode] = currentNode; } break;  }
+			if (taxon == "") {  m->mothurOut(seqName + " has an error in the taxonomy.  This may be due to a ;;"); m->mothurOutEndLine(); if (currentNode != 0) {  uniqueTaxonomies.insert(currentNode); } break;  }
 			
 			childPointer = tree[currentNode].children.find(taxon);
 			
@@ -267,8 +324,10 @@ int PhyloTree::addSeqToTree(string seqName, string seqTaxonomy){
 				name2Taxonomy[seqName] = currentNode;
 			}
 	
-			if (seqTaxonomy == "") {   uniqueTaxonomies[currentNode] = currentNode;	}
+			if (seqTaxonomy == "") {   uniqueTaxonomies.insert(currentNode);	}
 		}
+		
+		return 0;
 	}
 	catch(exception& e) {
 		m->errorOut(e, "PhyloTree", "addSeqToTree");
@@ -280,9 +339,16 @@ vector<int> PhyloTree::getGenusNodes()	{
 	try {
 		genusIndex.clear();
 		//generate genusIndexes
-		map<int, int>::iterator it2;
-		for (it2=uniqueTaxonomies.begin(); it2!=uniqueTaxonomies.end(); it2++) {  genusIndex.push_back(it2->first);	}
-		
+		set<int>::iterator it2;
+        map<int, int> temp;
+		for (it2=uniqueTaxonomies.begin(); it2!=uniqueTaxonomies.end(); it2++) {  genusIndex.push_back(*it2); 	temp[*it2] = genusIndex.size()-1; }
+		
+        for (map<string, int>::iterator itName = name2Taxonomy.begin(); itName != name2Taxonomy.end(); itName++) {
+            map<int, int>::iterator itTemp = temp.find(itName->second);
+            if (itTemp != temp.end()) { name2GenusNodeIndex[itName->first] = itTemp->second; }
+            else {  m->mothurOut("[ERROR]: trouble making name2GenusNodeIndex, aborting.\n"); m->control_pressed = true; }
+        }
+        
 		return genusIndex;
 	}
 	catch(exception& e) {
@@ -319,6 +385,9 @@ void PhyloTree::assignHeirarchyIDs(int index){
 		int counter = 1;
 		
 		for(it=tree[index].children.begin();it!=tree[index].children.end();it++){
+            
+            if (m->debug) { m->mothurOut(toString(index) +'\t' + tree[it->second].name +'\n'); }
+                
 			tree[it->second].heirarchyID = tree[index].heirarchyID + '.' + toString(counter);
 			counter++;
 			tree[it->second].level = tree[index].level + 1;
@@ -346,12 +415,7 @@ 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) {
@@ -364,17 +428,17 @@ 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);
-		
-		//get leaf nodes that may need externsion
+	
+		//get leaf nodes that may need extension
 		for (int i = 0; i < copy.size(); i++) {  
 
 			if (copy[i].children.size() == 0) {
@@ -382,8 +446,10 @@ void PhyloTree::binUnclassified(string file){
 			}
 		}
 		
+        if (m->debug) { m->mothurOut("maxLevel = " + toString(maxLevel) +'\n'); }
+        
 		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++) {
@@ -392,11 +458,14 @@ void PhyloTree::binUnclassified(string file){
 			
 			int level = copy[itLeaf->second].level;
 			int currentNode = itLeaf->second;
+            
+            if (m->debug) { m->mothurOut(copy[currentNode].name +'\n'); }
 			
 			//this sequence is unclassified at some levels
-			while(level <= maxLevel){
+			while(level < maxLevel){
 		
 				level++;
+                if (m->debug) { m->mothurOut("level = " + toString(level) +'\n'); }
 			
 				string taxon = "unclassified";	
 				
@@ -432,6 +501,7 @@ void PhyloTree::binUnclassified(string file){
 /**************************************************************************************************/
 void PhyloTree::fillOutTree(int index, vector<TaxNode>& copy) {
 	try {
+	
 		map<string,int>::iterator it;
 		
 		it = copy[index].children.find("unclassified");
@@ -443,12 +513,12 @@ void PhyloTree::fillOutTree(int index, vector<TaxNode>& copy) {
 			copy[copy.size()-1].level = copy[index].level + 1;
 		}
 		
-		if (tree[index].level <= maxLevel) {
+		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");
@@ -478,10 +548,16 @@ 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;
@@ -511,7 +587,10 @@ void PhyloTree::printTreeNodes(string treefilename) {
 		#endif
 
 			ofstream outTree;
-			openOutputFile(treefilename, outTree);
+			m->openOutputFile(treefilename, outTree);
+			
+			//output mothur version
+			outTree << "#" << m->getVersion() << endl;
 			
 			//print treenodes
 			outTree << tree.size() << endl;
@@ -521,8 +600,8 @@ void PhyloTree::printTreeNodes(string treefilename) {
 			
 			//print genus nodes
 			outTree << endl << uniqueTaxonomies.size() << endl;
-			map<int, int>::iterator it2;
-			for (it2=uniqueTaxonomies.begin(); it2!=uniqueTaxonomies.end(); it2++) {  outTree << it2->first << '\t' << tree[it2->first].accessions.size() << endl;	}
+			set<int>::iterator it2;
+			for (it2=uniqueTaxonomies.begin(); it2!=uniqueTaxonomies.end(); it2++) {  outTree << *it2 << '\t' << tree[*it2].accessions.size() << endl;	}
 			outTree << endl;
 			
 			outTree.close();
@@ -574,12 +653,12 @@ string PhyloTree::getName(int i ){
 	}
 }
 /**************************************************************************************************/
-int PhyloTree::getIndex(string seqName){
+int PhyloTree::getGenusIndex(string seqName){
 	try {
-		map<string, int>::iterator itFind = name2Taxonomy.find(seqName);
+		map<string, int>::iterator itFind = name2GenusNodeIndex.find(seqName);
 	
-		if (itFind != name2Taxonomy.end()) {  return name2Taxonomy[seqName];  }
-		else { m->mothurOut("Cannot find " + seqName + ". Mismatch with taxonomy and template files. Cannot continue."); m->mothurOutEndLine(); exit(1);}
+		if (itFind != name2GenusNodeIndex.end()) {  return itFind->second;  }
+		else { m->mothurOut("Cannot find " + seqName + ". Could be a mismatch with taxonomy and template files. Cannot continue."); m->mothurOutEndLine(); exit(1);}
 	}
 	catch(exception& e) {
 		m->errorOut(e, "PhyloTree", "get");
@@ -591,23 +670,27 @@ 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;