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#ifndef DOTAXONOMY_H
#define DOTAXONOMY_H
/*
* phylotree.h
*
*
* Created by Pat Schloss on 6/17/09.
* Copyright 2009 Patrick D. Schloss. All rights reserved.
*
*/
#include "mothurout.h"
#include "utils.hpp"
#include "currentfile.h"
/**************************************************************************************************/
struct TaxNode {
vector<string> accessions; //names of seqs in this branch of tree
map<string, int> children; //childs name to index in tree
int parent, childNumber, level;
string name, heirarchyID;
TaxNode(string n) : name(n), level(0), parent(-1) { }
TaxNode(){}
};
/**************************************************************************************************/
class PhyloTree {
#ifdef UNIT_TEST
friend class TestPhyloTree;
#endif
public:
PhyloTree();
PhyloTree(string); //pass it a taxonomy file and it makes the tree
PhyloTree(ifstream&, string); //pass it a taxonomy file and it makes the train.tree
~PhyloTree() = default;;
int addSeqToTree(string, string);
int addSeqToTree(string, vector<Taxon>);
void assignHeirarchyIDs(int);
void printTreeNodes(string); //used by bayesian to save time
vector<int> getGenusNodes();
vector<int> getGenusTotals();
void setUp(string); //used to create file needed for summary file if you use () constructor and add seqs manually instead of passing taxonomyfile
TaxNode get(int i);
TaxNode get(string seqName);
vector<TaxNode> getNodes(int); //returns vector of nodes at given level
string getName(int i);
int getGenusIndex(string seqName);
string getFullTaxonomy(string); //pass a sequence name return taxonomy
vector<string> getSeqs(string); //returns names of sequences in given taxonomy
int getMaxLevel() { return maxLevel; }
int getNumSeqs() { return numSeqs; }
int getNumNodes() { return (int)tree.size(); }
bool ErrorCheck(vector<string>);
private:
void print(ofstream&, vector<TaxNode>&); //used to create static reference taxonomy file
void fillOutTree(int, vector<TaxNode>&); //used to create static reference taxonomy file
void binUnclassified(string);
vector<TaxNode> tree;
vector<int> genusIndex; //holds the indexes in tree where the genus level taxonomies are stored
vector<int> totals; //holds the numSeqs at each genus level taxonomy
map<string, int> name2Taxonomy; //maps name to index in tree
map<string, int> name2GenusNodeIndex;
set<int> uniqueTaxonomies; //map of unique taxonomies
map<int, int> leafNodes; //used to create static reference taxonomy file
//void print(int, ofstream&);
int numNodes;
int numSeqs;
int maxLevel;
bool calcTotals;
MothurOut* m;
CurrentFile* current;
Utils util;
};
/**************************************************************************************************/
#endif
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