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Дата изменения: Unknown
Дата индексирования: Mon Feb 4 03:44:01 2013
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allpy: 88c246f20918 allpy/markup.py

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Fixed monomer pickling to avoid name clashes. This breaks pickle backwards-compatiblity! [see #35] Previosly all monomer classes were stored a single namespace, allpy.data.monomers. This caused a few name clashes, which were mostly resolved, and one name clash, that was not. (This caused one class to be named differently depending on the order in which modules were loaded). Now, instead of one allpy.data.monomers module we have allpy.data.monomers package with modules dna, rna, protein. This ensures that all name clashes are resolved uniformly upon any sequence of modules loading. This may also help in future to keep backward-compatibility longer in case we replace dynaminc monomer class creation with storing the classes in the module - if we want to retain independent loading of dna/rna/protein parts.
author Daniil Alexeyevsky <dendik@kodomo.fbb.msu.ru>
date Wed, 08 Jun 2011 21:31:02 +0400
parents 3566d253c994
children
line source
1 import base
2
3 default = object()
4 """ object for use as key for default value """
5
6 class Markup(object):
7 """ Markup for Sequence or Alignment
8
9 container is iterable collection of items.
10 item is object getting markup data (new attribute).
11
12 container: Alignment, item: Column
13 container: Sequence, item: Monomer
14
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.
19
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
25
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 """
31
32 def __init__(self, name, container, map_out={}):
33 """ Note: add convenient defaults to maps """
34 self.name = name
35 self.container = container
36 self.set_map_out(map_out)
37 self.set_internal_default()
38 self.set_external_default()
39
40 def set_map_out(self, map_out):
41 self.map_out = map_out
42 self.map_in = dict([(v, k) for (k, v) in self.map_out.items()])
43
44 def set_map_in(self, map_in):
45 self.map_in = map_in
46 self.map_out = dict([(v, k) for (k, v) in self.map_in.items()])
47
48 def set_internal_default(self, default_value=None):
49 self.map_in[default] = default_value
50
51 def set_external_default(self, default_value='-'):
52 self.map_out[default] = default_value
53
54 def __getitem__(self, item):
55 """ return internal value for given item
56
57 markup[monomer] <==> monomer.name, where name is markup.name
58 """
59 return getattr(item, self.name)
60
61 def __setitem__(self, item, value):
62 """ set attribute of item to value """
63 setattr(item, self.name, value)
64
65 def __contains__(self, item):
66 """ return item has attribute
67
68 usage: if item in markup
69 """
70 return hasattr(item, self.name)
71
72 def clear(self):
73 """ delete all attributes from items """
74 for item in self.keys():
75 delattr(item, self.name)
76
77 def to_string(self):
78 """ return string representing markup """
79 internal_values = []
80 for item in self.container:
81 if item in self and self[item] in self.map_out:
82 internal_values.append(self[item])
83 else:
84 internal_values.append(default)
85 return ''.join(self.map_out[i] for i in internal_values)
86
87 @classmethod
88 def from_string(cls, string, name, container, map_out={}):
89 """ return new markup
90
91 add (or replaces) attributes to items
92 """
93 assert len(string) == len(container)
94 self = cls(name, container, map_out)
95 for char, item in zip(list(string), self.container):
96 if char in self.map_in:
97 internal = self.map_in[char]
98 else:
99 internal = self.map_in[default]
100 setattr(item, self.name, internal)
101 return self
102
103 def items(self):
104 """ return list of tuples (item, self[item]) for items with attribute """
105 for item in self.container:
106 if item in self:
107 yield (item, self[item])
108
109 def keys(self):
110 """ return list of items for with attribute is determined """
111 for item in self.container:
112 if item in self:
113 yield item
114