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

[mothur.git] / tree.h

diff --git a/tree.h b/tree.h
deleted file mode 100644 (file)
index 0660e8a..0000000
--- a/tree.h
+++ /dev/null
@@ -1,82 +0,0 @@
-#ifndef TREE_H
-#define TREE_H
-
-/*
- *  tree.h
- *  Mothur
- *
- *  Created by Sarah Westcott on 1/22/09.
- *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
- *
- */
-
-#include "treenode.h"
-#include "treemap.h"
-/* This class represents the treefile. */
-
-class Tree {
-public: 
-       Tree(string);  //do not use tree generated by this constructor its just to extract the treenames, its a chicken before the egg thing that needs to be revisited.
-       Tree(int, TreeMap*); 
-       Tree(TreeMap*);         //to generate a tree from a file
-    Tree(TreeMap*, vector< vector<double> >&); //create tree from sim matrix
-       ~Tree();
-       
-    TreeMap* getTreeMap() { return tmap; }
-       void getCopy(Tree*);  //makes tree a copy of the one passed in.
-       void getSubTree(Tree*, vector<string>);  //makes tree a that contains only the names passed in.
-    int getSubTree(Tree* originalToCopy, vector<string> seqToInclude, map<string, string> nameMap);  //used with (int, TreeMap) constructor. SeqsToInclude contains subsample wanted - assumes these are unique seqs and size of vector=numLeaves passed into constructor. nameMap is unique -> redundantList can be empty if no namesfile was provided. 
-    
-       void assembleRandomTree();
-       void assembleRandomUnifracTree(vector<string>);
-       void assembleRandomUnifracTree(string, string);
-    
-       void createNewickFile(string);
-       int getIndex(string);
-       void setIndex(string, int);
-       int getNumNodes() { return numNodes; }
-       int getNumLeaves(){     return numLeaves; }
-       map<string, int> mergeUserGroups(int, vector<string>);  //returns a map with a groupname and the number of times that group was seen in the children
-       void printTree();
-       void print(ostream&);
-       void print(ostream&, string);
-    void print(ostream&, map<string, string>);
-       int findRoot();  //return index of root node
-       
-       //this function takes the leaf info and populates the non leaf nodes
-       int assembleTree(map<string, string>);  
-       
-       vector<Node> tree;              //the first n nodes are the leaves, where n is the number of sequences.
-       map< string, vector<int> > groupNodeInfo;       //maps group to indexes of leaf nodes with that group, different groups may contain same node because of names file.
-                       
-private:
-       TreeMap* tmap;
-       int numNodes, numLeaves;
-       ofstream out;
-       string filename;
-       
-    map<string, string> names;
-       map<string, int>::iterator it, it2;
-       map<string, int> mergeGroups(int);  //returns a map with a groupname and the number of times that group was seen in the children
-       map<string,int> mergeGcounts(int);
-       
-       void addNamesToCounts(map<string, string>);
-       void randomTopology();
-       void randomBlengths();
-       void randomLabels(vector<string>);
-       //void randomLabels(string, string);
-       void printBranch(int, ostream&, map<string, string>);  //recursively print out tree
-    void printBranch(int, ostream&, string);
-       void parseTreeFile();   //parses through tree file to find names of nodes and number of them
-                                                       //this is required in case user has sequences in the names file that are
-                                                       //not included in the tree. 
-                                                       //only takes names from the first tree in the tree file and assumes that all trees use the same names.
-       int readTreeString(ifstream&);
-       int populateNewTree(vector<Node>&, int, int&);
-       void printBranch(int, ostream&, string, vector<Node>&);
-               
-       MothurOut* m;
-               
-};
-
-#endif