# Copyright 2026 AlQuraishi Laboratory
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
#      http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.

import argparse
import concurrent
import os
import pickle
import tempfile
from concurrent.futures import ProcessPoolExecutor

from openfold3.core.data.legacy import parsers


def parse_stockholm_file(alignment_dir: str, stockholm_file: str):
    path = os.path.join(alignment_dir, stockholm_file)
    file_name, _ = os.path.splitext(stockholm_file)
    with open(path) as infile:
        msa = parsers.parse_stockholm(infile.read())
        infile.close()
    return {file_name: msa}


def parse_a3m_file(alignment_dir: str, a3m_file: str):
    path = os.path.join(alignment_dir, a3m_file)
    file_name, _ = os.path.splitext(a3m_file)
    with open(path) as infile:
        msa = parsers.parse_a3m(infile.read())
        infile.close()
    return {file_name: msa}


def run_parse_all_msa_files_multiprocessing(
    stockholm_files: list, a3m_files: list, alignment_dir: str
):
    # Number of workers based on the tasks
    msa_results = {}
    a3m_tasks = [(alignment_dir, f) for f in a3m_files]
    sto_tasks = [(alignment_dir, f) for f in stockholm_files]
    with ProcessPoolExecutor(max_workers=len(a3m_tasks) + len(sto_tasks)) as executor:
        a3m_futures = {
            executor.submit(parse_a3m_file, *task): task for task in a3m_tasks
        }
        sto_futures = {
            executor.submit(parse_stockholm_file, *task): task for task in sto_tasks
        }

        for future in concurrent.futures.as_completed(a3m_futures | sto_futures):
            try:
                result = future.result()
                msa_results.update(result)
            except Exception as exc:
                print(f"Task generated an exception: {exc}")
        return msa_results


def main():
    parser = argparse.ArgumentParser(description="Process msa files in parallel")
    parser.add_argument("--alignment_dir", type=str, help="path to alignment dir")
    args = parser.parse_args()
    alignment_dir = args.alignment_dir
    stockholm_files = [
        i
        for i in os.listdir(alignment_dir)
        if all([i.endswith(".sto"), "hmm_output" not in i, "uniprot_hits" not in i])
    ]
    a3m_files = [i for i in os.listdir(alignment_dir) if i.endswith(".a3m")]
    msa_data = run_parse_all_msa_files_multiprocessing(
        stockholm_files, a3m_files, alignment_dir
    )
    with tempfile.NamedTemporaryFile("wb", suffix=".pkl", delete=False) as outfile:
        pickle.dump(msa_data, outfile)
        print(outfile.name)


if __name__ == "__main__":
    main()
