#!/usr/bin/env python
from tree_likelihood_viz.model import CFNPinv
from tree_likelihood_viz.app_for_model import runApp
from tree_likelihood_viz.simple_tree import TopologyEnum, generate_branch_length_model
import itertools
models = [CFNPinv() for i in TopologyEnum.order]
branches = [generate_branch_length_model(t, m) for m, t in itertools.izip(models, TopologyEnum.order)]
runApp(title='CFN Tree likelihood visualizer',
char_models=models,
branches=branches)
################################################################################
# tree_likelihood_viz is a small package for creating interactive graphical
# depictions of quantities related to the calculation of likelihood on
# phylogenetic trees using a few simple models of character evolution. The
# primary purpose of the package is to assist in teaching.
#
# Copyright (C) 2010 Mark T. Holder [email protected]
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the License, or (at your option) any later version.
#
# This library is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
# Lesser General Public License for more details.
#
fixed_params = []
first_params = []
for branch_set_model in branches:
fpset = []
branch_set = branch_set_model.param_list
first_branch = branch_set[0]
first_params.append(first_branch)
for branch in branch_set[1:]:
first_branch.set_value_listeners.append(branch.set_value)
fpset.append(branch)
fixed_params.append(fpset)
first_branch.value = 0.1
runApp(title='CFN Equal-Branch Length Tree likelihood visualizer',
char_models=models,
branches=branches,
fixed_params=fixed_params,
to_trace=first_params)
################################################################################
# tree_likelihood_viz is a small package for creating interactive graphical
# depictions of quantities related to the calculation of likelihood on
# phylogenetic trees using a few simple models of character evolution. The
# primary purpose of the package is to assist in teaching.
#
# Copyright (C) 2010 Mark T. Holder [email protected]
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the License, or (at your option) any later version.
# the following code makes all of the branches "listen" to value changes to the first for each tree
fixed_params = []
for branch_set_model in branches:
fpset = []
branch_set = branch_set_model.param_list
first_branch = branch_set[0]
for branch in branch_set[1:]:
first_branch.set_value_listeners.append(branch.set_value)
fpset.append(branch)
first_branch.value = 0.2
fpset.append(first_branch)
fixed_params.append(fpset)
runApp(title='CFN Equal-Branch Length Tree likelihood visualizer',
char_models=models,
branches=branches,
fixed_params=fixed_params,
num_possible_patterns=7,
to_trace=epsilon_list)
################################################################################
# tree_likelihood_viz is a small package for creating interactive graphical
# depictions of quantities related to the calculation of likelihood on
# phylogenetic trees using a few simple models of character evolution. The
# primary purpose of the package is to assist in teaching.
#
# Copyright (C) 2010 Mark T. Holder [email protected]
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the License, or (at your option) any later version.