*
*/
-using namespace std;
-
-#include <string>
-#include <iostream>
-#include <vector>
-
-struct Node {
- string name;
- string group;
- float branchLength;
- Node* parent;
- Node* lchild;
- Node* rchild;
-};
-
-
+#include "treenode.h"
+#include "counttable.h"
+/* This class represents the treefile. */
class Tree {
- public:
- Tree();
- ~Tree();
-
- Node* getParent(Node);
- Node* getLChild(Node);
- Node* getRChild(Node);
-
- void setParent(Node);
- void setLChild(Node);
- void setRChild(Node);
+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, 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);
+ 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 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();
+
+ 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:
+ 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&, 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;
- Tree generateRandomTree();
-
- vector<Node> leaves; //gives you easy access to the leaves of the tree to generate the parsimony score
-
- private:
};
-
-
-
-#endif
\ No newline at end of file
+#endif
projects / mothur.git / blobdiff