# -*- coding: utf-8 -*-
from ..biotools import find_narrowest_text_wrap

from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
from Bio.SeqFeature import FeatureLocation, SeqFeature

try:
    # Biopython <1.78
    from Bio.Alphabet import DNAAlphabet

    has_dna_alphabet = True
except ImportError:
    # Biopython >=1.78
    has_dna_alphabet = False

from .MatplotlibPlottableMixin import MatplotlibPlottableMixin
from .BokehPlottableMixin import BokehPlottableMixin


class GraphicRecord(MatplotlibPlottableMixin, BokehPlottableMixin):
    """Set of Genetic Features of a same DNA sequence, to be plotted together.

    Parameters
    ----------

    sequence_length
      Length of the DNA sequence, in number of nucleotides.

    features
      list of GraphicalFeature objects.

    feature_level_height
      Width in inches of one "level" for feature arrows.

    annotation_height
      Width in inches of one "level" for feature annotations.

    first_index
      Indicates the first index to plot in case the sequence is actually a
      subsequence of a larger one. For instance, if the Graphic record
      represents the segment (400, 420) of a sequence, we will have
      ``first_index=400`` and ``sequence_length=20``.

    plots_indexing
      Indicates which standard to use to show nucleotide indices in the plots.
      If 'biopython', the standard python indexing is used (starting at 0).
      If 'genbank', the indexing follows the Genbank standard (starting at 1).

    labels_spacing
      Number of pixels that will "pad" every labels to force some horizontal
      space between two labels or between a label and the borders of a feature.

    ticks_resolution
      Leave to "auto" for an auto-selected number of ticks on the ruler, or set
      to e.g. 50 for a tick every 50 nucleotide.

    Attributes
    ----------

      default_font_family
        Default font to use for a feature that doesn't declare a font.

      default_ruler_color
        Default ruler color to use when no color is given at plot() time.

      default_box_color
        Default box color for non-inline annotations. If set to None, no
        boxes will be drawn unless the features declare a box_color.
        If "auto", a color (clearer version of the feature's color) will be
        computed, for all features also declaring their box_color as "auto".

      default_elevate_outline_annotations
        Value to use for elevate_outline_annotations when no specific value is
        given at ``graphic_record.plot(...)`` time. Set to true to have all
        text annotations appears above all features, or false else.
    """

    default_font_family = None
    default_ruler_color = "grey"
    default_box_color = "auto"
    min_y_height_of_text_line = 0.5

    def __init__(
        self,
        sequence_length=None,
        sequence=None,
        features=(),
        feature_level_height=1,
        first_index=0,
        plots_indexing="biopython",
        labels_spacing=8,
        ticks_resolution="auto",
    ):
        if sequence_length is None:
            sequence_length = len(sequence)
        self.features = features
        self.sequence_length = sequence_length
        self.feature_level_height = feature_level_height
        self.sequence = sequence
        self.first_index = first_index
        self.plots_indexing = plots_indexing
        self.labels_spacing = labels_spacing
        self.ticks_resolution = ticks_resolution

    @property
    def last_index(self):
        return self.first_index + self.sequence_length

    @property
    def span(self):
        """Return the display span (start, end) accounting for first_index."""
        return self.first_index, self.last_index

    def to_biopython_record(self, sequence):
        """Export to Biopython record.

        Examples
        --------
        >>> from Bio import SeqIO
        >>> gr_record = GraphicRecord(features=features, sequence_length=len(seq),
        >>>                           sequence=seq)
        >>> bio_record = gr_record.to_biopython_record()
        >>> with open("example.gb", "w+") as f:
        >>>     SeqIO.write(record, f, "genbank")
        """
        features = [
            SeqFeature(
                FeatureLocation(f.start, f.end, f.strand),
                type=f.feature_type,
                qualifiers={"label": f.label},
            )
            for f in self.features
        ]
        if not isinstance(sequence, Seq):
            if has_dna_alphabet:
                sequence = Seq(sequence, alphabet=DNAAlphabet())
            else:
                sequence = Seq(sequence)

        seqrecord = SeqRecord(seq=sequence, features=features)
        seqrecord.annotations["molecule_type"] = "DNA"

        return seqrecord

    def crop(self, window):
        start, end = window
        first_index = self.first_index
        if (start < first_index) or (end > self.last_index):
            raise ValueError("out-of-bound cropping")
        new_features = []
        for f in self.features:
            cropped_feature = f.crop(window)
            if cropped_feature is not None:  # = has ovelap with the window
                new_features.append(cropped_feature)

        return GraphicRecord(
            sequence=(
                self.sequence[start - first_index : end - first_index]
                if self.sequence is not None
                else None
            ),
            sequence_length=end - start,
            features=new_features,
            feature_level_height=self.feature_level_height,
            first_index=start,
            plots_indexing=self.plots_indexing,
            labels_spacing=self.labels_spacing,
            ticks_resolution=self.ticks_resolution,
        )

    def determine_annotation_height(self, levels):
        """By default the ideal annotation level height is the same as the
        feature_level_height."""
        # TODO: Improve me! ideally, annotation width would be linked to the
        # height of one line of text, so dependent on font size and ax
        # height/span.
        return self.feature_level_height

    def coordinates_in_plot(self, x, level):
        """Convert a sequence position and height level into a (x, y) position."""
        return (x, level * self.feature_level_height)

    def split_overflowing_features_circularly(self):
        """Split the features that overflow over the edge for circular
        constructs (inplace)."""
        new_features = []
        for f in self.features:
            if f.start < 0 < f.end:
                f1, f2 = f.split_in_two(-1)
                f1.start, f1.end = (
                    f1.start + self.sequence_length,
                    f1.end + self.sequence_length,
                )
                new_features += [f1, f2]
            elif f.start < self.sequence_length < f.end:
                f1, f2 = f.split_in_two(self.sequence_length - 1)
                f2.start, f2.end = (
                    f2.start - self.sequence_length,
                    f2.end - self.sequence_length,
                )
                new_features += [f1, f2]
            else:
                new_features.append(f)
        self.features = new_features

    def _format_label(self, label, max_label_length=50, max_line_length=40):
        if len(label) > max_label_length:
            label = label[: max_label_length - 1] + "…"
        if len(label) > max_line_length:
            label = find_narrowest_text_wrap(label, max_line_length)
        return label

    def compute_padding(self, ax):
        ax_width = ax.get_window_extent(ax.figure.canvas.get_renderer()).width
        xmin, xmax = ax.get_xlim()
        return self.labels_spacing * (xmax - xmin) / (1.0 * ax_width)
