fixed summary.shared bug and set jumble default to 1.

[mothur.git] / tree.cpp

diff --git a/tree.cpp b/tree.cpp
index 1aba4ede5e3d810d603d4f21a869b90fa26f76fc..03eb17127d5ebc174c8c3018452eb36290fb9346 100644 (file)
--- a/tree.cpp
+++ b/tree.cpp
@@ -9,3 +9,155 @@
 
 #include "tree.h"
 
+
+/*****************************************************************/
+Tree::Tree() {
+       try {
+               globaldata = GlobalData::getInstance();
+
+               numLeaves = globaldata->gTreemap->getNumSeqs();
+               numNodes = 2*numLeaves - 1;
+               
+               tree.resize(numNodes);
+
+               //initialize tree with correct number of nodes, name and group info.
+               for (int i = 0; i < numNodes; i++) {
+
+                       //initialize leaf nodes
+                       if (i <= (numLeaves-1)) {
+                               tree[i].setName(globaldata->gTreemap->namesOfSeqs[i]);
+                               tree[i].setGroup(globaldata->gTreemap->getGroup(globaldata->gTreemap->namesOfSeqs[i]));
+                               //the node knows its index
+                               tree[i].setIndex(i);
+                               //Treemap knows name, group and index to speed up search
+                               globaldata->gTreemap->setIndex(globaldata->gTreemap->namesOfSeqs[i], i);
+                       //intialize non leaf nodes
+                       }else if (i > (numLeaves-1)) {
+                               tree[i].setName("");
+                               tree[i].setGroup("");
+                               //the node knows its index
+                               tree[i].setIndex(i);
+                       }
+               }
+       }
+       catch(exception& e) {
+               cout << "Standard Error: " << e.what() << " has occurred in the Tree class Function Tree. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
+       catch(...) {
+               cout << "An unknown error has occurred in the Tree class function Tree. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }               
+}
+
+/*****************************************************************/
+
+int Tree::getIndex(string searchName) {
+       try {
+               //Treemap knows name, group and index to speed up search
+               // getIndex function will return the vector index or -1 if seq is not found.
+               int index = globaldata->gTreemap->getIndex(searchName);
+               return index;
+               
+       }
+       catch(exception& e) {
+               cout << "Standard Error: " << e.what() << " has occurred in the Tree class Function getIndex. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
+       catch(...) {
+               cout << "An unknown error has occurred in the Tree class function getIndex. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }               
+}
+/*****************************************************************/
+
+void Tree::setIndex(string searchName, int index) {
+       try {
+               //set index in treemap
+               globaldata->gTreemap->setIndex(searchName, index);
+       }
+       catch(exception& e) {
+               cout << "Standard Error: " << e.what() << " has occurred in the Tree class Function setIndex. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
+       catch(...) {
+               cout << "An unknown error has occurred in the Tree class function setIndex. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }               
+}
+
+
+/*****************************************************************/
+// This prints out the tree in Newick form.
+void Tree::createNewickFile() {
+       try {
+               int root = findRoot();
+               filename = getRootName(globaldata->getTreeFile()) + "newick";
+               openOutputFile(filename, out);
+               
+               printBranch(root);
+               
+               // you are at the end of the tree
+               out << ";" << endl;
+       }
+       catch(exception& e) {
+               cout << "Standard Error: " << e.what() << " has occurred in the Tree class Function createNewickFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
+       catch(...) {
+               cout << "An unknown error has occurred in the Tree class function createNewickFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }               
+}
+
+/*****************************************************************/
+//This function finds the index of the root node.
+
+int Tree::findRoot() {
+       try {
+               for (int i = 0; i < numNodes; i++) {
+                       //you found the root
+                       if (tree[i].getParent() == -1) { return i; }
+               }
+               return -1;
+       }
+       catch(exception& e) {
+               cout << "Standard Error: " << e.what() << " has occurred in the Tree class Function findRoot. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
+       catch(...) {
+               cout << "An unknown error has occurred in the Tree class function findRoot. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }               
+}
+
+/*****************************************************************/
+void Tree::printBranch(int node) {
+       try {
+               
+               // you are not a leaf
+               if (tree[node].getLChild() != -1) {
+                       out << "(";
+                       printBranch(tree[node].getLChild());
+                       out << ",";
+                       printBranch(tree[node].getRChild());
+                       out << ")";
+               }else { //you are a leaf
+                       tree[node].printNode(out);  //prints out name and branch length
+               }
+               
+       }
+       catch(exception& e) {
+               cout << "Standard Error: " << e.what() << " has occurred in the Tree class Function printBranch. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
+       catch(...) {
+               cout << "An unknown error has occurred in the Tree class function printBranch. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }               
+}
+
+/*****************************************************************/
+
+
+