# Copyright 2026 AlQuraishi Laboratory
# Copyright 2021 DeepMind Technologies Limited
#
# 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.

"""A Python wrapper for hmmsearch - search profile against a sequence db."""

import os
import subprocess
from collections.abc import Sequence

from absl import logging

from openfold3.core.data.legacy import parsers
from openfold3.core.data.tools import hmmbuild, utils


class Hmmsearch:
    """Python wrapper of the hmmsearch binary."""

    def __init__(
        self,
        *,
        binary_path: str,
        hmmbuild_binary_path: str,
        database_path: str,
        flags: Sequence[str] | None = None,
    ):
        """Initializes the Python hmmsearch wrapper.

        Args:
            binary_path: The path to the hmmsearch executable.
            hmmbuild_binary_path: The path to the hmmbuild executable. Used to build
                an hmm from an input a3m.
            database_path: The path to the hmmsearch database (FASTA format).
            flags: List of flags to be used by hmmsearch.

        Raises:
            RuntimeError: If hmmsearch binary not found within the path.
        """
        self.binary_path = binary_path
        self.hmmbuild_runner = hmmbuild.Hmmbuild(binary_path=hmmbuild_binary_path)
        self.database_path = database_path
        if flags is None:
            # Default hmmsearch run settings.
            flags = [
                "--F1",
                "0.1",
                "--F2",
                "0.1",
                "--F3",
                "0.1",
                "--incE",
                "100",
                "-E",
                "100",
                "--domE",
                "100",
                "--incdomE",
                "100",
            ]
        self.flags = flags

        if not os.path.exists(self.database_path):
            logging.error("Could not find hmmsearch database %s", database_path)
            raise ValueError(f"Could not find hmmsearch database {database_path}")

    @property
    def output_format(self) -> str:
        return "sto"

    @property
    def input_format(self) -> str:
        return "sto"

    def query(self, msa_sto: str, output_dir: str | None = None) -> str:
        """Queries the database using hmmsearch using a given stockholm msa."""
        hmm = self.hmmbuild_runner.build_profile_from_sto(
            msa_sto, model_construction="hand"
        )
        return self.query_with_hmm(hmm, output_dir)

    def query_with_hmm(self, hmm: str, output_dir: str | None = None) -> str:
        """Queries the database using hmmsearch using a given hmm."""
        with utils.tmpdir_manager() as query_tmp_dir:
            hmm_input_path = os.path.join(query_tmp_dir, "query.hmm")
            output_dir = query_tmp_dir if output_dir is None else output_dir
            out_path = os.path.join(output_dir, "hmm_output.sto")
            with open(hmm_input_path, "w") as f:
                f.write(hmm)

            cmd = [
                self.binary_path,
                "--noali",  # Don't include the alignment in stdout.
                "--cpu",
                "8",
            ]
            # If adding flags, we have to do so before the output and input:
            if self.flags:
                cmd.extend(self.flags)
            cmd.extend(
                [
                    "-A",
                    out_path,
                    hmm_input_path,
                    self.database_path,
                ]
            )

            logging.info("Launching sub-process %s", cmd)
            process = subprocess.Popen(
                cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE
            )
            with utils.timing(
                f"hmmsearch ({os.path.basename(self.database_path)}) query"
            ):
                stdout, stderr = process.communicate()
                retcode = process.wait()

            if retcode:
                raise RuntimeError(
                    f"hmmsearch failed:\nstdout:\n{stdout.decode('utf-8')}\n\n"
                    f"stderr:\n{stderr.decode('utf-8')}\n"
                )

            with open(out_path) as f:
                out_msa = f.read()

        return out_msa

    @staticmethod
    def get_template_hits(
        output_string: str, input_sequence: str
    ) -> Sequence[parsers.TemplateHit]:
        """Gets parsed template hits from the raw string output by the tool."""
        template_hits = parsers.parse_hmmsearch_sto(
            output_string,
            input_sequence,
        )
        return template_hits
