*/
#include "treenode.h"
-#include "globaldata.hpp"
-
+#include "counttable.h"
/* This class represents the treefile. */
class Tree {
public:
- 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);
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
- void assembleTree();
+ int assembleTree();
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(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 randomLabels(string, string);
+ 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.
- void readTreeString(ifstream&);
+ int readTreeString(ifstream&);
+ int populateNewTree(vector<Node>&, int, int&);
+ void printBranch(int, ostream&, string, vector<Node>&);
+
+ MothurOut* m;
+
};
#endif