University of Connecticut University of UC Title Fallback Connecticut

Test building trees

To test both the buildFromNewick and the makeNewick function, change main.cpp to look like this:

#include <iostream>
#include <string>
#include "node.hpp"
#include "tree.hpp"
#include "tree_manip.hpp"
#include "xstrom.hpp"

using namespace strom;

int main(int argc, const char * argv[])
    {
    std::cout << "Starting..." << std::endl;
    TreeManip tm;
    std::string newick = std::string("(1:0.3,2:0.3,(3:0.2,(4:0.1,5:0.1):0.1):0.1)");
    try
        {
        tm.buildFromNewick(newick, false, false);
        std::cout << tm.makeNewick(3) << std::endl;
        }
    catch (XStrom x)
        {
        std::cout << "Error: " << x.what() << std::endl;
        }
    std::cout << "\nFinished!" << std::endl;

    return 0;
    }

The main function now creates a tree from the newick string

(1:0.3,2:0.3,(3:0.2,(4:0.1,5:0.1):0.1):0.1)

and then uses the makeNewick function to turn the tree in memory into a newick string, which is output. The program is working correctly if the output string represents the same tree as the input string (note that the number of decimal places used to depict edge lengths will differ, but the tree descriptions should depict exactly the same tree topology and edge lengths).

If your program halts at assert(!nd->_left_child);

Assert statements test assumptions that you are making as you write source code. Any time you find yourself thinking "I’m pretty sure that will never happen", then it is probably time to use an assert statement to ensure that if it does happen, you know about it and can find where it happened and under what circumstances it happened. Assert statements disappear in optimized code, so you will only see these trip if you are running the debug (non-optimized) version of your program (usually inside the IDE).

If your program trips the assert(!nd->_left_child); inside the TreeManip::buildFromNewick function, then almost certainly what has happened is that you’ve not removed all traces of Tree::createTestTree(), which you were instructed to do in the very last (Before moving on…) section of the page titled Create the TreeManip class. The problem is that your Tree constructor is building a default tree every time it is called, so you are never starting from a clean slate with respect to the tree that you are building. Thus, you must remove the call to createTestTree() in the Tree::Tree constructor and reinstate the clear() function there.

Handling exceptions

If you would like to test the exception mechanism, try introducing an error in the newick tree description. For example, changing taxon "3" to "Z" because only newick descriptions with taxon names that can be converted to positive integers are allowed:

std::string newick = std::string("(1:0.3,2:0.3,(Z:0.2,(4:0.1,5:0.1):0.1):0.1)");

Running the program now should produce the following error message:

Error: node name (Z) not interpretable as a positive integer

(Be sure to change the "Z" back to a "3" before continuing.)