Package Bio :: Module Decode
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Module Decode

source code

Decode elements from a Std/Martel parsed XML stream (OBSOLETE).

Andrew Dalke is no longer maintaining Martel or Bio.Mindy, and these modules (and therefore Bio.Decode) have been deprecated. They are no longer used in any of the current Biopython parsers, and are likely to be removed in a future release.

Classes [hide private]
  Token
  ValueToken
  Integer
  Float
  String
  FunctionName
  DecodeScanner
  Function
  DecodeParser
  FunctionCall
  FunctionCallChain
Functions [hide private]
 
unescape_C(s) source code
 
join_english(fields) source code
 
chomp(s, c) source code
 
lchomp(s, c) source code
 
chompchomp(s, c) source code
 
fixspaces(s) source code
 
join_fixspaces(lines) source code
 
tr(s, frm, to) source code
 
safe_int(s)
converts to int if the number is small, long if it's large
source code
 
_fixup_defs() source code
 
scan(input) source code
 
parse(tokens) source code
 
make_decoder(s) source code
 
_verify_subtypes(subset, total, old_name, new_name) source code
 
make_typechecked_decoder(s, input_types=None, output_types=None) source code
 
test() source code
Variables [hide private]
  decode_functions = {'add': (<function <lambda> at 0x8ce317c>, ...
  _decoder_cache = {}
  _typechecked_decoder_cache = {}
  __package__ = 'Bio'
  __warningregistry__ = {('Martel and those parts of Biopython d...
Variables Details [hide private]

decode_functions

Value:
{'add': (<function <lambda> at 0x8ce317c>,
         (<type 'int'>),
         (<type 'int'>)),
 'chomp': (<function chomp at 0x8cdecdc>,
           (<type 'str'>),
           (<type 'str'>)),
 'chompchomp': (<function chompchomp at 0x8cded4c>,
                (<type 'str'>),
...

__warningregistry__

Value:
{('Martel and those parts of Biopython depending on it directly (such \
as Bio.Mindy and Bio.Decode) are now deprecated, and will be removed i\
n a future release of Biopython.  If you want to continue to use this \
code, please get in contact with the Biopython developers via the mail\
ing lists to avoid its permanent removal from Biopython.',
  <type 'exceptions.DeprecationWarning'>,
  21): True}