allpy
view allpy/markup.py @ 704:80043822a41e
Added fileio.File.read_alignment and fileio.File.write_alignment [closes #57]
This is now the recommended interface.
In the following commits this interface will be used to write markup together
with alignment.
Previously, fileio received the alignment torn-apart into sequence
representations as strings with gaps, sequence names and descriptions.
Now, fileio tears the alignment apart by itself.
author | Daniil Alexeyevsky <dendik@kodomo.fbb.msu.ru> |
---|---|
date | Thu, 07 Jul 2011 19:21:12 +0400 |
parents | 3566d253c994 |
children |
line source
4 """ object for use as key for default value """
7 """ Markup for Sequence or Alignment
9 container is iterable collection of items.
10 item is object getting markup data (new attribute).
12 container: Alignment, item: Column
13 container: Sequence, item: Monomer
15 Markup stored in attributes of item is internal value.
16 When export or import, it is mapped to or from external value.
17 Internal value could be of any type.
18 External value should be single character.
20 Data:
21 * name -- name (str) of attribute of object
22 * container
23 * map_out -- dict, mapping internal values to external
24 * map_in -- dict, mapping external values to internal
26 map_in and map_out can have key markup.default, which used when
27 input key is not in map. To drop this defaults, drop this key
28 from map_out and map_in dicts. In this case to_string() and
29 from_string() methods can raise KeyError
30 """
33 """ Note: add convenient defaults to maps """
55 """ return internal value for given item
57 markup[monomer] <==> monomer.name, where name is markup.name
58 """
62 """ set attribute of item to value """
66 """ return item has attribute
68 usage: if item in markup
69 """
73 """ delete all attributes from items """
78 """ return string representing markup """
87 @classmethod
89 """ return new markup
91 add (or replaces) attributes to items
92 """
104 """ return list of tuples (item, self[item]) for items with attribute """
110 """ return list of items for with attribute is determined """