#!/usr/bin/env python
"""Parser for NCBI Sequence Set XML format.
DOCTYPE Bioseq-set PUBLIC "-//NCBI//NCBI Seqset/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_Seqset.dtd"
"""
import io
import xml.dom.minidom

from cogent3.core import annotation, moltype


__author__ = "Matthew Wakefield"
__copyright__ = "Copyright 2007-2022, The Cogent Project"
__credits__ = ["Matthew Wakefield", "Peter Maxwell", "Gavin Huttley", "Rob Knight"]
__license__ = "BSD-3"
__version__ = "2022.8.24a1"
__maintainer__ = "Matthew Wakefield"
__email__ = "wakefield@wehi.edu.au"
__status__ = "Production"

"""
CAUTION:
This XML PARSER uses minidom. This means a bad performance for
big files (>5MB), and huge XML files will for sure crash the program!
"""


def GbSeqXmlParser(doc):
    """Parser for NCBI Sequence Set XML format.
    DOCTYPE Bioseq-set PUBLIC "-//NCBI//NCBI Seqset/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_Seqset.dtd"

    Parameters
    ----------
    doc
        An xml.dom.minidom.Document, file object of string

    Returns
    -------
    name, cogent sequence

    CAUTION:
    This XML PARSER uses minidom. This means a bad performance for
    big files (>5MB), and huge XML files will for sure crash the program!
    """
    if isinstance(doc, xml.dom.minidom.Document):
        dom_obj = doc
    elif isinstance(doc, io.IOBase):
        dom_obj = xml.dom.minidom.parse(doc)
    elif isinstance(doc, str):
        dom_obj = xml.dom.minidom.parseString(doc)
    else:
        raise TypeError
    for record in dom_obj.getElementsByTagName("GBSeq"):
        raw_seq = (
            record.getElementsByTagName("GBSeq_sequence")[0].childNodes[0].nodeValue
        )
        name = (
            record.getElementsByTagName("GBSeq_accession-version")[0]
            .childNodes[0]
            .nodeValue
        )

        # cast as string to de-unicode
        raw_string = str(raw_seq).upper()
        name = str(name)

        if (
            record.getElementsByTagName("GBSeq_moltype")[0].childNodes[0].nodeValue
            == "9"
        ):
            alphabet = moltype.PROTEIN
        else:
            alphabet = moltype.DNA

        seq = alphabet.make_seq(raw_string, name=name)

        all = annotation.Map([(0, len(seq))], parent_length=len(seq))
        seq.add_annotation(annotation.Source, all, name, all)

        organism = str(
            record.getElementsByTagName("GBSeq_organism")[0].childNodes[0].nodeValue
        )

        seq.add_annotation(annotation.Feature, "organism", organism, [(0, len(seq))])

        features = record.getElementsByTagName("GBFeature")
        for feature in features:
            key = str(
                feature.getElementsByTagName("GBFeature_key")[0].childNodes[0].nodeValue
            )

            if key == "source":
                continue

            spans = []
            feature_name = ""

            for interval in feature.getElementsByTagName("GBInterval"):
                try:
                    start = int(
                        interval.getElementsByTagName("GBInterval_from")[0]
                        .childNodes[0]
                        .nodeValue
                    )
                    end = int(
                        interval.getElementsByTagName("GBInterval_to")[0]
                        .childNodes[0]
                        .nodeValue
                    )
                    spans.append((start - 1, end))
                except IndexError:
                    point = int(
                        interval.getElementsByTagName("GBInterval_point")[0]
                        .childNodes[0]
                        .nodeValue
                    )
                    spans.append((point - 1, point))
            if spans == []:
                spans = [(0, len(seq))]
            for qualifier in feature.getElementsByTagName("GBQualifier"):
                qname = (
                    qualifier.getElementsByTagName("GBQualifier_name")[0]
                    .childNodes[0]
                    .nodeValue
                )
                if qname == "gene":
                    feature_name = (
                        qualifier.getElementsByTagName("GBQualifier_value")[0]
                        .childNodes[0]
                        .nodeValue
                    )
            seq.add_annotation(annotation.Feature, key, feature_name, spans)
        yield (name, seq)


def parse(*args):
    return GbSeqXmlParser(*args).next()[1]
