printBranch(tree[node].getRChild());
out << ")";
}else { //you are a leaf
- tree[node].printNode(out); //prints out name and branch length
+ tree[node].printNode(); //prints out name and branch length
}
}
}
/*****************************************************************/
+
void Tree::setGroups() {
try {
//if the user has not entered specific groups to analyze then do them all
}
+/*****************************************************************/
+
+void Tree::printTree() {
+
+ for(int i=0;i<numNodes;i++){
+ cout << i << '\t';
+ tree[i].printNode();
+ }
+
+}
+
+/*****************************************************************/
+
+
/* 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
-
- 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();
+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
+ void printTree();
+
+ //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
+
+ 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();
};
#endif
int Node::getIndex() { return vectorIndex; }
/****************************************************************/
//to be used by printTree in the Tree class to print the leaf info
-void Node::printNode(ostream& out) {
+void Node::printNode() {
try{
- out << name;
-
+ cout << parent << ' ' << lchild << ' ' << rchild << ' ' << group;
//there is a branch length
if (branchLength != -1) {
- out << ":" << setprecision(4) << branchLength;
+ cout << ' ' << setprecision(4) << branchLength;
+ }
+ cout << " |";
+ map<string, int>::iterator it;
+ for(it=pGroups.begin();it!=pGroups.end();it++){
+ cout << ' ' << it->first << ':' << it->second;
+ }
+ cout << " |";
+ for(it=pcount.begin();it!=pcount.end();it++){
+ cout << ' ' << it->first << ':' << it->second;
}
+ cout << endl;
}
catch(exception& e) {