NAMESPACE

# CellProgramMapper Package Namespace
# Generated and maintained manually for precise control

# =============================================================================
# Exports - User-facing functions
# =============================================================================

# Main function
export(CellProgramMapper)

# Reference management
export(available_references)
export(load_reference)
export(download_reference)

# Consensus reference building
export(BuildConsensusReference)

# Scoring
export(compute_scores)
export(create_score_definition)
export(create_score_data)

# Built-in models
export(list_builtin_models)
export(get_lineage_probabilities)

# Data I/O
export(load_counts)
export(save_results)
export(read_npz)
export(read_df_from_npz)

# Result accessors
export(get_usage)
export(get_scores)

# Seurat integration
export(add_results_to_seurat)

# S3 methods
S3method(print, CellProgramMapperResult)
S3method(summary, CellProgramMapperResult)

# =============================================================================
# Imports - Package dependencies
# =============================================================================

import(Matrix)
import(methods)

importFrom(Rcpp, sourceCpp)
importFrom(stats, cor, sd, setNames, predict)
importFrom(utils, read.table, write.table, download.file, packageVersion, untar)
importFrom(tools, file_path_sans_ext, file_ext)
importFrom(data.table, fread, fwrite)
importFrom(curl, curl_download, new_handle)
importFrom(yaml, read_yaml)
importFrom(future, plan, multisession)
importFrom(future.apply, future_lapply)
importFrom(rappdirs, user_cache_dir)
importFrom(jsonlite, fromJSON)

# =============================================================================
# C++ Registration
# =============================================================================

useDynLib(CellProgramMapper, .registration = TRUE)