changes to blastdb to make filenames given to blast unique, changes to split.abund...

[mothur.git] / tree.h

diff --git a/tree.h b/tree.h
index 7157a6f0e43993e8278591d3422caee1eeaa8728..99cd68fa7f4b71dfeebffc90ad649a1f01c6564e 100644 (file)
--- a/tree.h
+++ b/tree.h
@@ -10,48 +10,64 @@
  *
  */
 
-using namespace std;
-
 #include "treenode.h"
 #include "globaldata.hpp"
 
+class GlobalData;
 /* This class represents the treefile. */
 
 class Tree {
-       public: 
-               Tree();         //to generate a tree from a file
-               ~Tree() {};
-               
-               
-               void getCopy(Tree*);  //makes tree a copy of the one passed in.
-               void assembleRandomTree();
-               void assembleRandomUnifracTree();
-               void createNewickFile();
-               int getIndex(string);
-               void setIndex(string, int);
-               int getNumNodes() { return numNodes; }
-               int getNumLeaves(){     return numLeaves; }
-               
-               //this function takes the leaf info and populates the non leaf nodes
-               void assembleTree();            
-               
-               vector<Node> tree;              //the first n nodes are the leaves, where n is the number of sequences.
-               
-       private:
-               GlobalData* globaldata;
-               int numNodes, numLeaves;
-               ofstream out;
-               string filename;
+public: 
+       Tree();         //to generate a tree from a file
+       ~Tree();
+       
+       void getCopy(Tree*);  //makes tree a copy of the one passed in.
+       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 printForBoot(ostream&);
+       int findRoot();  //return index of root node
+       
+       //this function takes the leaf info and populates the non leaf nodes
+       int assembleTree();     
+       
+       vector<Node> tree;              //the first n nodes are the leaves, where n is the number of sequences.
                
-               map<string, int>::iterator it;
-               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> Tree::mergeGcounts(int);
-               void randomTopology();
-               void randomBlengths();
-               void randomLabels();
-               int findRoot();  //return index of root node
-               void printBranch(int);  //recursively print out tree
-               void setGroups();
+private:
+       GlobalData* globaldata;
+       int numNodes, numLeaves;
+       ofstream out;
+       string filename;
+       
+       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();
+       void randomTopology();
+       void randomBlengths();
+       void randomLabels(vector<string>);
+       //void randomLabels(string, string);
+       void printBranch(int, ostream&, string);  //recursively print out tree
+       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&);
+       string readLabel(ifstream&);
+       string readName(ifstream&);
+       string readBranchLength(ifstream&);
+       
+       MothurOut* m;
+       
 };
 
 #endif