*
*/
-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; }
- map<string, int> mergeUserGroups(int); //returns a map with a groupname and the number of times that group was seen in the children
-
- //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;
-
- 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
+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> 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