X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=phylotree.cpp;fp=phylotree.cpp;h=0000000000000000000000000000000000000000;hb=4a877efa127e56e81a21f53cfdbbfd3bfbe8c4ff;hp=a9ef6cb0d85f44bde915606eb452db993ec40d8d;hpb=a6cf29fa4dac0909c7582cb1094151d34093ee76;p=mothur.git

diff --git a/phylotree.cpp b/phylotree.cpp
deleted file mode 100644
index a9ef6cb..0000000
--- a/phylotree.cpp
+++ /dev/null
@@ -1,656 +0,0 @@
-/*
- *  doTaxonomy.cpp
- *  
- *
- *  Created by Pat Schloss on 6/17/09.
- *  Copyright 2009 Patrick D. Schloss. All rights reserved.
- *
- */
-
-#include "phylotree.h"
-
-/**************************************************************************************************/
-
-PhyloTree::PhyloTree(){
-	try {
-		m = MothurOut::getInstance();
-		numNodes = 1;
-		numSeqs = 0;
-		tree.push_back(TaxNode("Root"));
-		tree[0].heirarchyID = "0";
-		maxLevel = 0;
-		calcTotals = true;
-		addSeqToTree("unknown", "unknown;");
-	}
-	catch(exception& e) {
-		m->errorOut(e, "PhyloTree", "PhyloTree");
-		exit(1);
-	}
-}
-/**************************************************************************************************/
-
-PhyloTree::PhyloTree(ifstream& in, string filename){
-	try {
-		m = MothurOut::getInstance();
-		calcTotals = false;
-		numNodes = 0;
-		numSeqs = 0;
-		
-		#ifdef USE_MPI
-			MPI_File inMPI;
-			MPI_Offset size;
-			MPI_Status status;
-
-			char inFileName[1024];
-			strcpy(inFileName, filename.c_str());
-
-			MPI_File_open(MPI_COMM_WORLD, inFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI);  
-			MPI_File_get_size(inMPI, &size);
-			
-			char* buffer = new char[size];
-			MPI_File_read(inMPI, buffer, size, MPI_CHAR, &status);
-
-			string tempBuf = buffer;
-			if (tempBuf.length() > size) { tempBuf = tempBuf.substr(0, size);  }
-			istringstream iss (tempBuf,istringstream::in);
-			delete buffer;
-			
-			//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; m->gobble(iss);
-			}
-			
-			//read genus nodes
-			int numGenus = 0;
-			iss >> numGenus; m->gobble(iss);
-			
-			int gnode, gsize;
-			totals.clear();
-			for (int i = 0; i < numGenus; i++) {
-				iss >> gnode >> gsize; m->gobble(iss);
-				
-				uniqueTaxonomies[gnode] = gnode;
-				totals.push_back(gsize);
-			}
-			
-			MPI_File_close(&inMPI);
-			
-		#else
-			//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; m->gobble(in);
-			}
-			
-			//read genus nodes
-			int numGenus = 0;
-			in >> numGenus; m->gobble(in);
-			
-			int gnode, gsize;
-			totals.clear();
-			for (int i = 0; i < numGenus; i++) {
-				in >> gnode >> gsize; m->gobble(in);
-				
-				uniqueTaxonomies[gnode] = gnode;
-				totals.push_back(gsize);
-			}
-			
-			in.close();
-			
-		#endif
-		
-	}
-	catch(exception& e) {
-		m->errorOut(e, "PhyloTree", "PhyloTree");
-		exit(1);
-	}
-}
-/**************************************************************************************************/
-
-PhyloTree::PhyloTree(string tfile){
-	try {
-		m = MothurOut::getInstance();
-		numNodes = 1;
-		numSeqs = 0;
-		tree.push_back(TaxNode("Root"));
-		tree[0].heirarchyID = "0";
-		maxLevel = 0;
-		calcTotals = true;
-		string name, tax;
-		
-		#ifdef USE_MPI
-			int pid, num, processors;
-			vector<unsigned long long> positions;
-			
-			MPI_Status status; 
-			MPI_File inMPI;
-			MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
-			MPI_Comm_size(MPI_COMM_WORLD, &processors);
-
-			char inFileName[1024];
-			strcpy(inFileName, tfile.c_str());
-
-			MPI_File_open(MPI_COMM_WORLD, inFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
-
-			if (pid == 0) {
-				positions = m->setFilePosEachLine(tfile, num);
-				
-				//send file positions to all processes
-				for(int i = 1; i < processors; i++) { 
-					MPI_Send(&num, 1, MPI_INT, i, 2001, MPI_COMM_WORLD);
-					MPI_Send(&positions[0], (num+1), MPI_LONG, i, 2001, MPI_COMM_WORLD);
-				}
-			}else{
-				MPI_Recv(&num, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status);
-				positions.resize(num+1);
-				MPI_Recv(&positions[0], (num+1), MPI_LONG, 0, 2001, MPI_COMM_WORLD, &status);
-			}
-		
-			//read file 
-			for(int i=0;i<num;i++){
-				//read next sequence
-				int length = positions[i+1] - positions[i];
-				char* buf4 = new char[length];
-
-				MPI_File_read_at(inMPI, positions[i], buf4, length, MPI_CHAR, &status);
-
-				string tempBuf = buf4;
-				if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length); }
-				delete buf4;
-
-				istringstream iss (tempBuf,istringstream::in);
-				iss >> name >> tax;
-				addSeqToTree(name, tax);
-			}
-			
-			MPI_File_close(&inMPI);
-			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();
-		#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);
-	}
-	catch(exception& e) {
-		m->errorOut(e, "PhyloTree", "PhyloTree");
-		exit(1);
-	}
-}
-
-/**************************************************************************************************/
-
-string PhyloTree::getNextTaxon(string& heirarchy, string seqname){
-	try {
-		string currentLevel = "";
-		if(heirarchy != ""){
-			int pos = heirarchy.find_first_of(';');
-			
-			if (pos == -1) { //you can't find another ;
-				currentLevel = heirarchy;
-				heirarchy = "";
-				m->mothurOut(seqname + " is missing a ;, please check for other errors."); m->mothurOutEndLine();
-			}else{
-				currentLevel=heirarchy.substr(0,pos);
-				if (pos != (heirarchy.length()-1)) {  heirarchy=heirarchy.substr(pos+1);  }
-				else { heirarchy = ""; }
-			}
-			
-		}
-		return currentLevel;
-	}
-	catch(exception& e) {
-		m->errorOut(e, "PhyloTree", "getNextTaxon");
-		exit(1);
-	}
-}
-
-/**************************************************************************************************/
-
-int PhyloTree::addSeqToTree(string seqName, string seqTaxonomy){
-	try {
-		numSeqs++;
-		
-		map<string, int>::iterator childPointer;
-		
-		int currentNode = 0;
-		int level = 1;
-		
-		tree[0].accessions.push_back(seqName);
-		m->removeConfidences(seqTaxonomy);
-		
-		string taxon;// = getNextTaxon(seqTaxonomy);
-	
-		while(seqTaxonomy != ""){
-			
-			level++;
-		
-			if (m->control_pressed) { return 0; }
-			
-			//somehow the parent is getting one too many accnos
-			//use print to reassign the taxa id
-			taxon = getNextTaxon(seqTaxonomy, seqName);
-			
-			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;  }
-			
-			childPointer = tree[currentNode].children.find(taxon);
-			
-			if(childPointer != tree[currentNode].children.end()){	//if the node already exists, move on
-				currentNode = childPointer->second;
-				tree[currentNode].accessions.push_back(seqName);
-				name2Taxonomy[seqName] = currentNode;
-			}
-			else{											//otherwise, create it
-				tree.push_back(TaxNode(taxon));
-				numNodes++;
-				tree[currentNode].children[taxon] = numNodes-1;
-				tree[numNodes-1].parent = currentNode;
-				
-				currentNode = tree[currentNode].children[taxon];
-				tree[currentNode].accessions.push_back(seqName);
-				name2Taxonomy[seqName] = currentNode;
-			}
-	
-			if (seqTaxonomy == "") {   uniqueTaxonomies[currentNode] = currentNode;	}
-		}
-		
-		return 0;
-	}
-	catch(exception& e) {
-		m->errorOut(e, "PhyloTree", "addSeqToTree");
-		exit(1);
-	}
-}
-/**************************************************************************************************/
-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);	}
-		
-		return genusIndex;
-	}
-	catch(exception& e) {
-		m->errorOut(e, "PhyloTree", "getGenusNodes");
-		exit(1);
-	}
-}
-/**************************************************************************************************/
-vector<int> PhyloTree::getGenusTotals()	{
-	try {
-	
-		if (calcTotals) {
-			totals.clear();
-			//reset counts because we are on a new word
-			for (int j = 0; j < genusIndex.size(); j++) {
-				totals.push_back(tree[genusIndex[j]].accessions.size());
-			}
-			return totals;
-		}else{
-			return totals;
-		}
-		
-	}
-	catch(exception& e) {
-		m->errorOut(e, "PhyloTree", "getGenusNodes");
-		exit(1);
-	}
-}
-/**************************************************************************************************/
-
-void PhyloTree::assignHeirarchyIDs(int index){
-	try {
-		map<string,int>::iterator it;
-		int counter = 1;
-		
-		for(it=tree[index].children.begin();it!=tree[index].children.end();it++){
-			tree[it->second].heirarchyID = tree[index].heirarchyID + '.' + toString(counter);
-			counter++;
-			tree[it->second].level = tree[index].level + 1;
-						
-			//save maxLevel for binning the unclassified seqs
-			if (tree[it->second].level > maxLevel) { maxLevel = tree[it->second].level; } 
-			
-			assignHeirarchyIDs(it->second);
-		}
-	}
-	catch(exception& e) {
-		m->errorOut(e, "PhyloTree", "assignHeirarchyIDs");
-		exit(1);
-	}
-}
-/**************************************************************************************************/
-void PhyloTree::setUp(string tfile){
-	try{
-		string taxFileNameTest = tfile.substr(0,tfile.find_last_of(".")+1) + "tree.sum";
-		
-		#ifdef USE_MPI
-			int pid;
-			MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
-
-			if (pid == 0) {  binUnclassified(taxFileNameTest);  }
-		
-		#else
-			binUnclassified(taxFileNameTest); 
-		#endif
-	}
-	catch(exception& e) {
-		m->errorOut(e, "PhyloTree", "setUp");
-		exit(1);
-	}
-}
-/**************************************************************************************************/
-void PhyloTree::binUnclassified(string file){
-	try {
-	
-		ofstream 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 extension
-		for (int i = 0; i < copy.size(); i++) {  
-
-			if (copy[i].children.size() == 0) {
-				leafNodes[i] = i;
-			}
-		}
-		
-		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++) {
-			
-			if (m->control_pressed) {  out.close(); break;  }
-			
-			int level = copy[itLeaf->second].level;
-			int currentNode = itLeaf->second;
-			
-			//this sequence is unclassified at some levels
-			while(level < maxLevel){
-		
-				level++;
-			
-				string taxon = "unclassified";	
-				
-				//does the parent have a child names 'unclassified'?
-				childPointer = copy[currentNode].children.find(taxon);
-				
-				if(childPointer != copy[currentNode].children.end()){	//if the node already exists, move on
-					currentNode = childPointer->second; //currentNode becomes 'unclassified'
-				}
-				else{											//otherwise, create it
-					copy.push_back(TaxNode(taxon));
-					copyNodes++;
-					copy[currentNode].children[taxon] = copyNodes-1;
-					copy[copyNodes-1].parent = currentNode;
-					copy[copyNodes-1].level = copy[currentNode].level + 1;
-									
-					currentNode = copy[currentNode].children[taxon];
-				}
-			}
-		}
-		
-		if (!m->control_pressed) {
-			//print copy tree
-			print(out, copy);
-		}
-				
-	}
-	catch(exception& e) {
-		m->errorOut(e, "PhyloTree", "binUnclassified");
-		exit(1);
-	}
-}
-/**************************************************************************************************/
-void PhyloTree::fillOutTree(int index, vector<TaxNode>& copy) {
-	try {
-	
-		map<string,int>::iterator it;
-		
-		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;
-		}
-		
-		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");
-		exit(1);
-	}
-}
-/**************************************************************************************************/
-string PhyloTree::getFullTaxonomy(string seqName) {
-	try {
-		string tax = "";
-		
-		int currentNode = name2Taxonomy[seqName];
-		
-		while (tree[currentNode].parent != -1) {
-			tax = tree[currentNode].name + ";" + tax;
-			currentNode = tree[currentNode].parent;
-		}
-		
-		return tax;
-	}
-	catch(exception& e) {
-		m->errorOut(e, "PhyloTree", "getFullTaxonomy");
-		exit(1);
-	}
-}
-/**************************************************************************************************/
-
-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;
-			for(it=copy[i].children.begin();it!=copy[i].children.end();it++){
-				out << it->first << '\t' << it->second << '\t';
-			}
-			out << endl;
-		}
-		
-		out.close();
-	}
-	catch(exception& e) {
-		m->errorOut(e, "PhyloTree", "print");
-		exit(1);
-	}
-}
-/**************************************************************************************************/
-void PhyloTree::printTreeNodes(string treefilename) {
-	try {
-	
-		#ifdef USE_MPI
-			int pid;
-			MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
-
-			if (pid == 0) {  
-		
-		#endif
-
-			ofstream outTree;
-			m->openOutputFile(treefilename, outTree);
-			
-			//output mothur version
-			outTree << "#" << m->getVersion() << endl;
-			
-			//print treenodes
-			outTree << tree.size() << endl;
-			for (int i = 0; i < tree.size(); i++) {
-				outTree << tree[i].name << '\t' << tree[i].level << '\t' << tree[i].parent << endl;
-			}
-			
-			//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;	}
-			outTree << endl;
-			
-			outTree.close();
-		
-		#ifdef USE_MPI
-			}
-		#endif
-
-		
-	}
-	catch(exception& e) {
-		m->errorOut(e, "PhyloTree", "printTreeNodes");
-		exit(1);
-	}
-}
-/**************************************************************************************************/
-TaxNode PhyloTree::get(int i ){
-	try {
-		if (i < tree.size()) {  return tree[i];	 }
-		else {  cout << i << '\t' << tree.size() << endl ; m->mothurOut("Mismatch with taxonomy and template files. Cannot continue."); m->mothurOutEndLine(); exit(1); }
-	}
-	catch(exception& e) {
-		m->errorOut(e, "PhyloTree", "get");
-		exit(1);
-	}
-}
-/**************************************************************************************************/
-TaxNode PhyloTree::get(string seqName){
-	try {
-		map<string, int>::iterator itFind = name2Taxonomy.find(seqName);
-	
-		if (itFind != name2Taxonomy.end()) {  return tree[name2Taxonomy[seqName]];  }
-		else { m->mothurOut("Cannot find " + seqName + ". Mismatch with taxonomy and template files. Cannot continue."); m->mothurOutEndLine(); exit(1);}
-	}
-	catch(exception& e) {
-		m->errorOut(e, "PhyloTree", "get");
-		exit(1);
-	}
-}
-/**************************************************************************************************/
-string PhyloTree::getName(int i ){
-	try {
-		if (i < tree.size()) {  return tree[i].name;	 }
-		else { m->mothurOut("Mismatch with taxonomy and template files. Cannot continue."); m->mothurOutEndLine(); exit(1); }
-	}
-	catch(exception& e) {
-		m->errorOut(e, "PhyloTree", "get");
-		exit(1);
-	}
-}
-/**************************************************************************************************/
-int PhyloTree::getIndex(string seqName){
-	try {
-		map<string, int>::iterator itFind = name2Taxonomy.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);}
-	}
-	catch(exception& e) {
-		m->errorOut(e, "PhyloTree", "get");
-		exit(1);
-	}
-}
-/**************************************************************************************************/
-bool PhyloTree::ErrorCheck(vector<string> templateFileNames){
-	try {
-	
-		bool okay = true;
-		templateFileNames.push_back("unknown");
-		
-		map<string, int>::iterator itFind;
-		map<string, int> taxonomyFileNames = name2Taxonomy;
-		
-		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();
-				okay = false;
-			}
-			
-			//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;
-			
-			for (itFind = taxonomyFileNames.begin(); itFind != taxonomyFileNames.end(); itFind++) {
-				m->mothurOut(itFind->first + " is in your taxonomy file and is not in your template file. Please correct."); m->mothurOutEndLine();
-			}
-		}
-		
-		return okay;
-	}
-	catch(exception& e) {
-		m->errorOut(e, "PhyloTree", "ErrorCheck");
-		exit(1);
-	}
-}
-/**************************************************************************************************/
-	
-
-
-