from phylogenie.draw import Coloring, draw_tree
from phylogenie.generators import (
    AliSimDatasetGenerator,
    BDEITreeDatasetGenerator,
    BDSSTreeDatasetGenerator,
    BDTreeDatasetGenerator,
    CanonicalTreeDatasetGenerator,
    DatasetGenerator,
    DatasetGeneratorConfig,
    EpidemiologicalTreeDatasetGenerator,
    FBDTreeDatasetGenerator,
    TreeDatasetGeneratorConfig,
)
from phylogenie.io import load_fasta
from phylogenie.msa import MSA
from phylogenie.skyline import (
    SkylineMatrix,
    SkylineMatrixCoercible,
    SkylineParameter,
    SkylineParameterLike,
    SkylineVector,
    SkylineVectorCoercible,
    SkylineVectorLike,
    skyline_matrix,
    skyline_parameter,
    skyline_vector,
)
from phylogenie.treesimulator import (
    Birth,
    BirthWithContactTracing,
    Death,
    Event,
    EventType,
    Feature,
    Migration,
    Mutation,
    Sampling,
    SamplingWithContactTracing,
    Tree,
    compute_mean_leaf_pairwise_distance,
    compute_sackin_index,
    dump_newick,
    generate_trees,
    get_BD_events,
    get_BDEI_events,
    get_BDSS_events,
    get_canonical_events,
    get_contact_tracing_events,
    get_distance,
    get_epidemiological_events,
    get_FBD_events,
    get_mrca,
    get_mutation_id,
    get_node_depth_levels,
    get_node_depths,
    get_node_height_levels,
    get_node_heights,
    get_node_leaf_counts,
    get_node_state,
    load_newick,
    load_nexus,
    set_features,
    simulate_tree,
)

__all__ = [
    "Coloring",
    "draw_tree",
    "AliSimDatasetGenerator",
    "BDEITreeDatasetGenerator",
    "BDSSTreeDatasetGenerator",
    "BDTreeDatasetGenerator",
    "CanonicalTreeDatasetGenerator",
    "DatasetGenerator",
    "DatasetGeneratorConfig",
    "EpidemiologicalTreeDatasetGenerator",
    "FBDTreeDatasetGenerator",
    "TreeDatasetGeneratorConfig",
    "load_fasta",
    "MSA",
    "SkylineMatrix",
    "SkylineMatrixCoercible",
    "SkylineParameter",
    "SkylineParameterLike",
    "SkylineVector",
    "SkylineVectorCoercible",
    "SkylineVectorLike",
    "skyline_matrix",
    "skyline_parameter",
    "skyline_vector",
    "Birth",
    "BirthWithContactTracing",
    "Death",
    "Event",
    "EventType",
    "Feature",
    "Migration",
    "Mutation",
    "Sampling",
    "SamplingWithContactTracing",
    "Tree",
    "compute_mean_leaf_pairwise_distance",
    "compute_sackin_index",
    "dump_newick",
    "generate_trees",
    "get_BD_events",
    "get_BDEI_events",
    "get_BDSS_events",
    "get_canonical_events",
    "get_contact_tracing_events",
    "get_distance",
    "get_epidemiological_events",
    "get_FBD_events",
    "get_mrca",
    "get_mutation_id",
    "get_node_depth_levels",
    "get_node_depths",
    "get_node_height_levels",
    "get_node_heights",
    "get_node_leaf_counts",
    "get_node_state",
    "load_newick",
    "load_nexus",
    "set_features",
    "simulate_tree",
]
