# geney/tis/ — Translation Initiation Site (TIS) prediction using TITER.
from .model import (
    set_titer_model_dir, get_titer_model_dir, get_codon_score, convert_all_models_to_pytorch,
    set_titer_device, get_titer_device,
)
from .encoding import encode_sequence, encode_sequences
from .prediction import (
    predict_context_score, predict_context_scores_batch,
    predict_tis_score, predict_tis_probability, predict_tis_probabilities_batch,
    extract_tis_context, find_all_atg_positions,
)
from .analysis import TISCandidate, analyze_tis_candidates, predict_alternative_tis
from .metrics import TISShiftResult, compute_tis_shift_metrics, get_tis_summary
from .visualization import plot_tis_comparison, plot_tis_probability_landscape
from .integration import analyze_transcript_tis

__all__ = [
    # Configuration
    "set_titer_model_dir",
    "get_titer_model_dir",
    "set_titer_device",
    "get_titer_device",
    # Codon prior
    "get_codon_score",
    # Encoding
    "encode_sequence",
    "encode_sequences",
    # Prediction
    "predict_context_score",
    "predict_context_scores_batch",
    "predict_tis_score",
    "predict_tis_probability",
    "predict_tis_probabilities_batch",
    "extract_tis_context",
    "find_all_atg_positions",
    # Analysis
    "TISCandidate",
    "analyze_tis_candidates",
    "predict_alternative_tis",
    # Metrics
    "TISShiftResult",
    "compute_tis_shift_metrics",
    "get_tis_summary",
    # Visualization
    "plot_tis_comparison",
    "plot_tis_probability_landscape",
    # Integration
    "analyze_transcript_tis",
    # Model conversion
    "convert_all_models_to_pytorch",
]
