added phylotype command which reads a taxonomy file and creates a .list, .rabund...

[mothur.git] / doTaxonomy.h

diff --git a/doTaxonomy.h b/doTaxonomy.h
deleted file mode 100644 (file)
index 6f83f19..0000000
--- a/doTaxonomy.h
+++ /dev/null
@@ -1,57 +0,0 @@
-#ifndef DOTAXONOMY_H
-#define DOTAXONOMY_H
-
-/*
- *  doTaxonomy.h
- *  
- *
- *  Created by Pat Schloss on 6/17/09.
- *  Copyright 2009 Patrick D. Schloss. All rights reserved.
- *
- */
-
-#include "mothur.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() {};
-       void addSeqToTree(string, string);
-       void assignHeirarchyIDs(int);
-       void print(ofstream&);
-       vector<int> getGenusNodes();    
-       TaxNode get(int i)                              {       return tree[i]; }
-       TaxNode get(string seqName)             {       return tree[name2Taxonomy[seqName]];    }
-       int getIndex(string seqName)    {       return name2Taxonomy[seqName];  }
-       string getName(int i)                   {       return tree[i].name;    }
-private:
-       string getNextTaxon(string&);
-       vector<TaxNode> tree;
-       vector<int> genusIndex; //holds the indexes in tree where the genus level taxonomies are stored
-       map<string, int> name2Taxonomy;  //maps name to index in tree
-       map<int, int> uniqueTaxonomies;  //map of unique taxonomies
-       void print(int, ofstream&);
-       int numNodes;
-       int numSeqs;
-};
-
-/**************************************************************************************************/
-
-#endif
-
-