changing command name classify.shared to classifyrf.shared

[mothur.git] / tree.h

diff --git a/tree.h b/tree.h
index 1c44d8c919805c24072e0f6ab314789393ed63ce..c8e8478edb8f313ab16d4dbeebf0a3d60a0a2698 100644 (file)
--- a/tree.h
+++ b/tree.h
@@ -11,21 +11,27 @@
  */
 
 #include "treenode.h"
-#include "globaldata.hpp"
-
-class GlobalData;
+#include "counttable.h"
 /* This class represents the treefile. */
 
 class Tree {
 public: 
-       Tree(string); 
-       Tree();         //to generate a tree from a file
+       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, CountTable*); 
+       Tree(CountTable*);              //to generate a tree from a file
+    Tree(CountTable*, vector< vector<double> >&); //create tree from sim matrix
        ~Tree();
        
+    CountTable* getCountTable() { return ct; }
        void getCopy(Tree*);  //makes tree a copy of the one passed in.
+    void getCopy(Tree* copy, bool); //makes a copy of the tree structure passed in, (just parents, children and br). Used with the Tree(TreeMap*) constructor. Assumes the tmap already has set seqs groups you want.  Used by subsample to reassign seqs you don't want included to group "doNotIncludeMe".
+       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);
@@ -34,37 +40,42 @@ public:
        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&);
+       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();     
-       int assembleTree(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:
-       GlobalData* globaldata;
+       CountTable* ct;
        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);
+    map<string, int> indexes; //maps seqName -> index in tree vector
        
-       void addNamesToCounts();
+       void addNamesToCounts(map<string, string>);
        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
+       void printBranch(int, ostream&, map<string, string>);  //recursively print out tree
+    void printBranch(int, ostream&, string);
+       int 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;