from rnavigate.data.data import Sequence, Data, normalize_sequence
from rnavigate.data.secondary_structure import (
    SecondaryStructure,
    SequenceCircle,
    StructureCoordinates,
)
from rnavigate.data.alignments import (
    AlignmentChain,
    lookup_alignment,
    set_alignment,
    set_multiple_sequence_alignment,
    SequenceAlignment,
    StructureAlignment,
)
from rnavigate.data.colors import ScalarMappable
from rnavigate.data.interactions import (
    Interactions,
    SHAPEJuMP,
    RINGMaP,
    PAIRMaP,
    PairingProbability,
    AllPossible,
    StructureAsInteractions,
    StructureCompareMany,
    StructureCompareTwo,
)
from rnavigate.data.pdb import PDB
from rnavigate.data.profile import (
    DanceMaP,
    DeltaProfile,
    Profile,
    RNPMaP,
    SHAPEMaP,
)
from rnavigate.data.annotation import Annotation, Motif, ORFs, domains

__all__ = [
    # from data
    "Sequence",
    "Data",
    # from secondary_structure
    "SecondaryStructure",
    "StructureCoordinates",
    "SequenceCircle",
    # from alignment
    "set_alignment",
    "set_multiple_sequence_alignment",
    "lookup_alignment",
    "SequenceAlignment",
    "AlignmentChain",
    "StructureAlignment",
    # from colors
    "ScalarMappable",
    # from interactions
    "Interactions",
    "SHAPEJuMP",
    "RINGMaP",
    "PAIRMaP",
    "PairingProbability",
    "AllPossible",
    "StructureAsInteractions",
    "StructureCompareMany",
    "StructureCompareTwo",
    # from PDB
    "PDB",
    # from profile
    "Profile",
    "SHAPEMaP",
    "DanceMaP",
    "RNPMaP",
    "DeltaProfile",
    # from annotations
    "Annotation",
    "Motif",
    "ORFs",
    "domains",
]
