allpy: 632a0708ab33 allpy/markups.py

allpy

view allpy/markups.py @ 735:632a0708ab33

blocks3d/www: allow blocks not to be continuous Changes: * javascript * blocks_to_html method of AlignmentMixin * test for blocks viewer (add one non-continuous block) Currently block can have either "start" and "end" or "positions" attribute, but not both. "start" and "end" attributes are not deprecated and can be used if blocks are known to be continuous or while writting blocks javascript by hands. close #71

author	boris <bnagaev@gmail.com>
date	Fri, 08 Jul 2011 20:21:39 +0200
parents	df624c729ab5
children	52ce523138d5

line source

1 import base

3 class IntMarkupMixin(base.Markup):

5 @classmethod

6 def from_record(cls, container, record, name=None):

7 assert record['io-class'] == 'IntMarkup'

8 result = cls(container, name=name)

9 separator = record.get('separator', ',')

10 values = record['markup'].split(separator)

11 assert len(values) == len(result.sorted_keys())

12 for key, value in zip(result.sorted_keys(), values):

13 if value:

14 result[key] = int(value)

15 return result

17 def to_record(self):

18 def fmt(value):

19 if value is None:

20 return ""

21 return str(value)

22 values = [fmt(self.get(key)) for key in self.sorted_keys()]

23 return {'markup': ','.join(values), 'io-class': 'IntMarkup'}

25 class SequenceNumberMarkup(base.SequenceMarkup):

27 name = 'number'

29 def refresh(self):

30 for number, monomer in enumerate(self.sequence, 1):

31 monomer.number = number

33 class SequenceIndexMarkup(base.SequenceMarkup):

35 name = 'index'

37 def refresh(self):

38 for index, monomer in enumerate(self.sequence):

39 monomer.index = index

41 class AlignmentNumberMarkup(base.AlignmentMarkup):

43 name = 'number'

45 def refresh(self):

46 for number, column in enumerate(self.alignment.columns, 1):

47 self[column] = number

49 class AlignmentIndexMarkup(base.AlignmentMarkup):

51 name = 'index'

53 def refresh(self):

54 for index, column in enumerate(self.alignment.columns):

55 self[column] = index

57 class SequenceCaseMarkup(base.SequenceMarkup):

59 name = 'case'

61 def refresh(self):

62 for monomer in self.sequence:

63 if monomer.input_code1.isupper():

64 monomer.case = 'upper'

65 elif monomer.input_code1.islower():

66 monomer.case = 'lower'

68 # vim: set ts=4 sts=4 sw=4 et: