# Copyright 2001 by Katharine Lindner.  All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license.  Please see the LICENSE file that should have been included
# as part of this package.

__all__ = [
    'Record',
    'kabat_format'
    ]

# standard library
import string
import array
import os
import re
import sgmllib
import urlparse

# XML from python 2.0
from xml.sax import handler

# Martel
import Martel
from Martel import RecordReader

from Bio.ParserSupport import EventGenerator
from Bio.ParserSupport import AbstractConsumer
from Bio.SeqFeature import Reference
from Bio import File
import kabat_format
import Record
class Iterator:
    """Iterator interface to move over a file of Kabat entries one at a time.
    """
    def __init__(self, handle, parser = None):
        """Initialize the iterator.

        Arguments:
        o handle - A handle with Kabat entries to iterate through.
        o parser - An optional parser to pass the entries through before
        returning them. If None, then the raw entry will be returned.
        """
        self._reader = RecordReader.StartsWith(handle, "KADBID")
#        self._reader = RecordReader.EndsWith(handle, "RECEND|\n")
        self._parser = parser

    def next(self):
        """Return the next Kabat record from the handle.

        Will return None if we ran out of records.
        """
        data = self._reader.next()

        if self._parser is not None:
            if data:
                dumpfile = open( 'dump', 'w' )
                dumpfile.write( data )
                dumpfile.close()
                return self._parser.parse(File.StringHandle(data))

        return data

class _Scanner:
    """Start up Martel to do the scanning of the file.

    This initialzes the Martel based parser and connects it to a handler
    that will generate events for a Feature Consumer.
    """
    def __init__(self, debug = 0):
        """Initialize the scanner by setting up our caches.

        Creating the parser takes a long time, so we want to cache it
        to reduce parsing time.

        Arguments:
        o debug - The level of debugging that the parser should
        display. Level 0 is no debugging, Level 2 displays the most
        debugging info (but is much slower). See Martel documentation
        for more info on this.
        """
        # a listing of all tags we are interested in scanning for
        # in the MartelParser
        self.interest_tags = ["kabatid", "creation_date", "last_mod_date",
                              "definition", "species", "nucleotide_sequence_name",
                              "amino_acid_sequence_name", "nucleotide_ref_author",
                              "nucleotide_ref_pubmed", "nucleotide_ref_journal",
                              "amino_acid_ref_author", "amino_acid_ref_pubmed",
                              "amino_acid_ref_journal", "annotation_key",
                              "annotation_val", "codon",
                               "amino_1_letter_code" ]

        # make a parser that returns only the tags we are interested in
        expression = Martel.select_names(kabat_format.kabat_record, self.interest_tags)
        self._parser = expression.make_parser(debug_level = debug)

    def feed(self, handle, consumer):
        """Feeed a set of data into the scanner.

        Arguments:
        o handle - A handle with the information to parse.
        o consumer - The consumer that should be informed of events.
        """
        self._parser.setContentHandler( EventGenerator(consumer,
                                                       self.interest_tags))
#        self._parser.setErrorHandler(handle.ErrorHandler())

        self._parser.parseFile(handle)

class _RecordConsumer:
    """Create a Kabat Record object from scanner generated information.
    """
    def __init__(self):
        self.data = Record.Record()

        self._cur_nucleotide_ref = None
        self._cur_amino_acid_ref = None

    def kabatid(self, content):
        next_line = content[ 0 ]
        self.data.kabatid = next_line

    def creation_date(self, content):
        next_line = content[ 0 ]
        self.data.creation_date = next_line

    def last_mod_date(self, content):
        next_line = content[ 0 ]
        self.data.date_last_mod = next_line

    def definition(self, content):
        next_line = content[ 0 ]
        self.data.definition = next_line

    def species(self, content):
        next_line = content[ 0 ]
        self.data.species = next_line

    def nucleotide_sequence_name(self, content):
        self.data.nucleotide_sequence_name = content[ 0 ]

    def amino_acid_sequence_name(self, content):
        self.data.nucleotide_sequence_name = content[ 0 ]

    def nucleotide_ref_author(self, content):
        next_line = content[ 0 ]
        author_info = next_line[ 6: ]
        self._cur_nucleotide_ref = Record.KabatReference()
        self._cur_nucleotide_ref.authors = author_info
        continuation = next_line[ :6 ]
        continuation = continuation.strip()
        if( continuation != '1' ):
            self.data.nucleotide_refs.append( self._cur_nucleotide_ref )
            self._cur_nucleotide_ref = None

    def nucleotide_ref_journal(self, content):
        next_line = content[ 0 ]
        journal_info = next_line[ 6: ]
        self._cur_nucleotide_ref.journal = journal_info
        continuation = next_line[ :6 ]
        continuation = continuation.strip()
        if( continuation != '1' ):
            self.data.nucleotide_refs.append( self._cur_nucleotide_ref )
            self._cur_nucleotide_ref = None


    def nucleotide_ref_pubmed(self, content):
        next_line = content[ 0 ]
        pubmed_info = next_line[ 6: ]
        self._cur_nucleotide_ref.pubmed_id = pubmed_info.strip()
        continuation = next_line[ :6 ]
        continuation = continuation.strip()
        if( continuation != '1' ):
            self.data.nucleotide_refs.append( self._cur_nucleotide_ref )
            self._cur_nucleotide_ref = None

    def amino_acid_ref_author(self, content):
        next_line = content[ 0 ]
        author_info = next_line[ 6: ]
        self._cur_amino_acid_ref = Record.KabatReference()
        self._cur_amino_acid_ref.authors = author_info
        continuation = next_line[ :6 ]
        try:
            continuation = continuation.strip()
        except:
            print 'continuation is %s' % continuation
        if( continuation != '1' ):
            self.data.amino_acid_refs.append( self._cur_amino_acid_ref )
            self._cur_amino_acid_ref = None

    def amino_acid_ref_journal(self, content):
        next_line = content[ 0 ]
        journal_info = next_line[ 6: ]
        self._cur_amino_acid_ref.journal = journal_info
        continuation = next_line[ :6 ]
        continuation = continuation.strip()
        if( continuation != '1' ):
            self.data.amino_acid_refs.append( self._cur_amino_acid_ref )
            self._cur_amino_acid_ref = None

    def amino_acid_ref_pubmed(self, content):
        next_line = content[ 0 ]
        pubmed_info = next_line[ 6: ]
        self._cur_amino_acid_ref.pubmed_id = pubmed_info.strip()
        continuation = next_line[ :6 ]
        continuation = continuation.strip()
        if( continuation != '1' ):
            self.data.amino_acid_refs.append( self._cur_amino_acid_ref )
            self._cur_amino_acid_ref = None


    def codon(self, content):
        for item in array.array( 'c', content[ 0 ] ):
            self.data.nucleotide_sequence.append( item )

    def amino_1_letter_code(self, content):
        for item in array.array( 'c', content[ 0 ] ):
            self.data.amino_acid_sequence.append( item )


    def annotation_key( self, content ):
        text = content[ 0 ]
        self.pending_key = text

    def annotation_val( self, content ):
        val = content[ 0 ]
        val = val.strip()

        if( self.pending_key != None ):
            key = self.pending_key
            if( self.data.annotation.has_key( key ) ):
                val = self.data.annotation[ key ] + val
            self.data.annotation[ key ] = val
            self.pending_key = None


class RecordParser:
    """Parse Kabat files into Record objects
    """
    def __init__(self, debug_level = 0):
        """Initialize the parser.

        Arguments:
        o debug_level - An optional argument that species the amount of
        debugging information Martel should spit out. By default we have
        no debugging info (the fastest way to do things), but if you want
        you can set this as high as two and see exactly where a parse fails.
        """
        self._scanner = _Scanner(debug_level)

    def parse(self, handle):
        """Parse the specified handle into a GenBank record.
        """
        self._consumer = _RecordConsumer()
        self._scanner.feed(handle, self._consumer)
        return self._consumer.data

