Class List

Here are the classes, structs, unions and interfaces with brief descriptions:

[detail level 123]

combination_utils	Contains functions that generate different kinds of combinations from an iterable
computation	Contains just the ptreegen::computation::Computation class
distance_functions	Contains implementations of possible distance measures
distance_matrix	Constains just the ptreegen::distance_matrix::DistanceMatrix class
enums	Contains all enums used in the project
main	The main module with the main method
neighbor_joining	Contains just the ptreegen::neighbor_joining::NeighborJoining class
parsimony	Contains two classes (ptreegen::parsimony::SmallParsimony and ptreegen::parsimony::LargeParsimony) that implement the basic steps of the parsimony approach to tree building
ptreegen	This package contains all that is needed by the main module to do its thing :)
computation
Computation	Parses user specified options and delegetes appropriate actions to other modules
distance_functions
distance_matrix
DistanceMatrix	Basically a wrapper around a numpy array obejct representing the alignment distance matrix
enums
neighbor_joining
NeighborJoining	Contains an implementation of the Neighbor-Joining algorithm
parsimony
SmallParsimony	Represents a solution to the small parsimony problem (tree is known and we are intersted in the parsimony score of the tree)
LargeParsimony	Represents a solution to the large parsimony problem (the tree toplogy is unknown as oposed to the small parsimony problem)
utilities
visualization
Visualization	Similar to the ptreegen::computation::Computation class
tree_utils	Defines a number of functions that can be used to manipulate a tree
utilities	Contains some universally usefull stuff
visualization	Contains just the ptreegen::visualization::Visualization class