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[mothur.git] / phylotree.h

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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 "mothur.h"
+#include "mothurout.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 {
+
+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() {};
+       int addSeqToTree(string, string);
+       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);
+       string getName(int i);                  
+       int getIndex(string seqName);   
+       string getFullTaxonomy(string);  //pass a sequence name return taxonomy
+       
+       int getMaxLevel()               {       return maxLevel;        }
+       int getNumSeqs()                {       return numSeqs;         }
+       int getNumNodes()               {       return tree.size();     }
+       
+       bool ErrorCheck(vector<string>);
+       
+private:
+       string getNextTaxon(string&, string);
+       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<int, 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;
+};
+
+/**************************************************************************************************/
+
+#endif
+
+