broke up globaldata and moved error checking and help into commands

[mothur.git] / tree.h

diff --git a/tree.h b/tree.h
index 6404db784eec791783e609dfc8ff8d8a971c61aa..b6d5ea807a38801a872daf96b23557d53a241f4e 100644 (file)
--- a/tree.h
+++ b/tree.h
@@ -10,8 +10,6 @@
  *
  */
 
-using namespace std;
-
 #include "treenode.h"
 #include "globaldata.hpp"
 
@@ -20,19 +18,22 @@ using namespace std;
 class Tree {
 public: 
        Tree();         //to generate a tree from a file
-       ~Tree() {};
-       
+       ~Tree();
        
        void getCopy(Tree*);  //makes tree a copy of the one passed in.
        void assembleRandomTree();
-       void assembleRandomUnifracTree();
-       void createNewickFile();
+       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);  //returns a map with a groupname and the number of times that group was seen in the children
+       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
        void assembleTree();            
@@ -47,13 +48,17 @@ 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> Tree::mergeGcounts(int);
+       map<string,int> mergeGcounts(int);
        void randomTopology();
        void randomBlengths();
-       void randomLabels();
-       int findRoot();  //return index of root node
-       void printBranch(int);  //recursively print out tree
-       void setGroups();
+       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.
+       void readTreeString(ifstream&);
 };
 
 #endif