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#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Interface for binary streams of uncompressed mzML.
@author: Sylvain Le Bon
"""
from io import TextIOWrapper
from .. import regex_patterns
from .standardMzml import StandardMzml
class BytesMzml(StandardMzml):
def __init__(self, binary, encoding, build_index_from_scratch=False):
"""
Initalize Wrapper object for standard mzML files.
Arguments:
path (str) : path to the file
encoding (str) : encoding of the file
"""
self.binary = binary
self.file_handler = self.get_file_handler(encoding)
self.offset_dict = dict()
self.spec_open = regex_patterns.SPECTRUM_OPEN_PATTERN
self.spec_close = regex_patterns.SPECTRUM_CLOSE_PATTERN
if build_index_from_scratch is True:
seeker = self.get_binary_file_handler()
self._build_index_from_scratch(seeker)
seeker.close()
def get_binary_file_handler(self):
self.binary.seek(0)
return self.binary
def get_file_handler(self, encoding):
return TextIOWrapper(self.binary, encoding=encoding)
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