from phylogenie.draw import (
    draw_colored_dated_tree_categorical,
    draw_colored_dated_tree_continuous,
    draw_colored_tree_categorical,
    draw_colored_tree_continuous,
    draw_dated_tree,
    draw_tree,
)
from phylogenie.generators import (
    AliSimDatasetGenerator,
    BDEITreeDatasetGenerator,
    BDSSTreeDatasetGenerator,
    BDTreeDatasetGenerator,
    CanonicalTreeDatasetGenerator,
    DatasetGenerator,
    DatasetGeneratorConfig,
    EpidemiologicalTreeDatasetGenerator,
    FBDTreeDatasetGenerator,
    TreeDatasetGeneratorConfig,
)
from phylogenie.io import dump_fasta, dump_newick, load_fasta, load_newick, load_nexus
from phylogenie.main import run
from phylogenie.msa import MSA, Sequence
from phylogenie.skyline import (
    SkylineMatrix,
    SkylineMatrixCoercible,
    SkylineParameter,
    SkylineParameterLike,
    SkylineVector,
    SkylineVectorCoercible,
    SkylineVectorLike,
    skyline_matrix,
    skyline_parameter,
    skyline_vector,
)
from phylogenie.tree_node import TreeNode
from phylogenie.treesimulator import (
    EXPOSED_STATE,
    INFECTIOUS_STATE,
    SUPERSPREADER_STATE,
    Model,
    UnboundedPopulationModel,
    generate_trees,
    get_BD_model,
    get_BDEI_model,
    get_BDSS_model,
    get_canonical_model,
    get_epidemiological_model,
    get_FBD_model,
    simulate_tree,
)

__all__ = [
    "draw_colored_dated_tree_categorical",
    "draw_colored_dated_tree_continuous",
    "draw_colored_tree_categorical",
    "draw_colored_tree_continuous",
    "draw_dated_tree",
    "draw_tree",
    "AliSimDatasetGenerator",
    "BDEITreeDatasetGenerator",
    "BDSSTreeDatasetGenerator",
    "BDTreeDatasetGenerator",
    "CanonicalTreeDatasetGenerator",
    "DatasetGenerator",
    "DatasetGeneratorConfig",
    "EpidemiologicalTreeDatasetGenerator",
    "FBDTreeDatasetGenerator",
    "TreeDatasetGeneratorConfig",
    "dump_fasta",
    "dump_newick",
    "load_fasta",
    "load_newick",
    "load_nexus",
    "run",
    "MSA",
    "Sequence",
    "SkylineMatrix",
    "SkylineMatrixCoercible",
    "SkylineParameter",
    "SkylineParameterLike",
    "SkylineVector",
    "SkylineVectorCoercible",
    "SkylineVectorLike",
    "skyline_matrix",
    "skyline_parameter",
    "skyline_vector",
    "TreeNode",
    "EXPOSED_STATE",
    "INFECTIOUS_STATE",
    "SUPERSPREADER_STATE",
    "Model",
    "UnboundedPopulationModel",
    "generate_trees",
    "get_BD_model",
    "get_BDEI_model",
    "get_BDSS_model",
    "get_canonical_model",
    "get_epidemiological_model",
    "get_FBD_model",
    "simulate_tree",
]
