moved mothur's source into a folder to make grabbing just the source easier on github

[mothur.git] / phylotree.h

diff --git a/phylotree.h b/phylotree.h
deleted file mode 100644 (file)
index 7aae8f1..0000000
--- a/phylotree.h
+++ /dev/null
@@ -1,80 +0,0 @@
-#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
-
-