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 8b77d3ddbed48dddb5de57dfa44394118c7a1920..99cd68fa7f4b71dfeebffc90ad649a1f01c6564e 100644 (file)
--- a/tree.h
+++ b/tree.h
@@ -10,11 +10,10 @@
  *
  */
 
-using namespace std;
-
 #include "treenode.h"
 #include "globaldata.hpp"
 
+class GlobalData;
 /* This class represents the treefile. */
 
 class Tree {
@@ -22,7 +21,6 @@ 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>);
@@ -36,11 +34,13 @@ public:
        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
-       void assembleTree();            
+       int assembleTree();     
        
        vector<Node> tree;              //the first n nodes are the leaves, where n is the number of sequences.
+               
 private:
        GlobalData* globaldata;
        int numNodes, numLeaves;
@@ -49,14 +49,25 @@ private:
        
        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);
-       int findRoot();  //return index of root node
+       //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