aphylogeo.params

class aphylogeo.params.Params

Bases: object

Class that contains the parameters of the program. Loads the parameters from a yaml file or from a dictionary.

PARAMETER_KEYS = {'alignment_method': '0', 'bootstrap_threshold': 0, 'dist_threshold': 0, 'distance_method': '0', 'file_name': '', 'fit_method': '0', 'makeDebugFiles': False, 'method_similarity': '0', 'preprocessing_climatic': '0', 'preprocessing_genetic': '0', 'preprocessing_threshold_climatic': 0, 'preprocessing_threshold_genetic': 0, 'rate_similarity': 0, 'reference_gene_dir': '', 'reference_gene_file': '', 'specimen': '', 'step_size': 0, 'tree_type': '0', 'window_size': 0}

classmethod load_default_param()

classmethod update_from_dict(params_content)

Method that updates the parameters from a dictionary.

Parameters:

params_content (dict) – the dictionary with the parameters

classmethod validate_and_set_params(params_dict)

Method that validates and sets the parameters.

Parameters:

params_dict (dict) – the dictionary with the parameters