#! /usr/bin/env python
# -*- coding: utf-8 -*-

##############################################################################
##  DendroPy Phylogenetic Computing Library.
##
##  Copyright 2010-2015 Jeet Sukumaran and Mark T. Holder.
##  All rights reserved.
##
##  See "LICENSE.rst" for terms and conditions of usage.
##
##  If you use this work or any portion thereof in published work,
##  please cite it as:
##
##     Sukumaran, J. and M. T. Holder. 2010. DendroPy: a Python library
##     for phylogenetic computing. Bioinformatics 26: 1569-1571.
##
##############################################################################

"""
Implementation of multiple-alignment PHYLIP-format data reader.
"""

import re
from dendropy.dataio import ioservice
from dendropy.dataio import phylipreader
from dendropy.utility import filesys
from dendropy.utility import error
from dendropy.utility.textprocessing import StringIO

class MultiPhylipReader(ioservice.DataReader):

    data_block_start_pattern = re.compile(r'^\s*(\d+\s+\d+)\s*\n', re.MULTILINE)

    def __init__(self, **kwargs):
        """
        See ``dendropy.dataio.phylipreader.PhylipReader`` for keyword arguments.
        """
        self._phylip_reader = phylipreader.PhylipReader(**kwargs)

    def _read(self,
            stream,
            taxon_namespace_factory=None,
            tree_list_factory=None,
            char_matrix_factory=None,
            state_alphabet_factory=None,
            global_annotations_target=None):
        data = stream.read()
        start_positions = []
        for match in MultiPhylipReader.data_block_start_pattern.finditer(data):
            start_positions.append(match.start(1))
        if not start_positions:
            raise error.DataParseError("No PHYLIP data blocks found in source", stream=stream)
        char_matrices = []
        for idx, start_pos in enumerate(start_positions):
            if idx == len(start_positions) - 1:
                end_pos = len(data)
            else:
                end_pos = start_positions[idx+1]
            block = data[start_pos:end_pos]
            src = StringIO(block)
            subproduct = self._phylip_reader._read(
                    stream=src,
                    taxon_namespace_factory=taxon_namespace_factory,
                    tree_list_factory=tree_list_factory,
                    char_matrix_factory=char_matrix_factory,
                    state_alphabet_factory=state_alphabet_factory,
                    global_annotations_target=global_annotations_target,
                    )
            char_matrices.extend(subproduct.char_matrices)
        product = self.Product(
                taxon_namespaces=None,
                tree_lists=None,
                char_matrices=char_matrices)
        return product