*/
#include "treenode.h"
-#include "treemap.h"
+#include "counttable.h"
/* This class represents the treefile. */
class Tree {
public:
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, TreeMap*);
- Tree(TreeMap*); //to generate a tree from a file
- Tree(TreeMap*, vector< vector<double> >&); //create tree from sim matrix
+ Tree(int, CountTable*);
+ Tree(CountTable*); //to generate a tree from a file
+ Tree(CountTable*, vector< vector<double> >&); //create tree from sim matrix
~Tree();
- TreeMap* getTreeMap() { return tmap; }
+ CountTable* getCountTable() { return ct; }
void getCopy(Tree*); //makes tree a copy of the one passed in.
- void getCopy(Tree* copy, map<string, string>); //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 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.
+ //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>);
int findRoot(); //return index of root node
//this function takes the leaf info and populates the non leaf nodes
- int assembleTree(map<string, string>);
+ 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:
- TreeMap* tmap;
+ CountTable* ct;
int numNodes, numLeaves;
ofstream out;
string filename;
- map<string, string> names;
+ //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 randomLabels(string, string);
void printBranch(int, ostream&, map<string, string>); //recursively print out tree
void printBranch(int, ostream&, string);
- void parseTreeFile(); //parses through tree file to find names of nodes and number of them
+ 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.