allpy: 4d1f5ece3f0a allpy/markups.py

allpy

Added module markups with sample *Index and *Number markups

author	Daniil Alexeyevsky <dendik@kodomo.fbb.msu.ru>
date	Fri, 01 Jul 2011 15:46:32 +0400
parents
children	df624c729ab5

line source

1 import base

3 class SequenceNumberMarkup(base.SequenceMarkup):

5 name = 'number'

7 def refresh(self):

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

9 monomer.number = number

11 class SequenceIndexMarkup(base.SequenceMarkup):

13 name = 'index'

15 def refresh(self):

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

17 monomer.index = index

19 class AlignmentNumberMarkup(base.AlignmentMarkup):

21 name = 'number'

23 def refresh(self):

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

25 self[column] = number

27 class AlignmentIndexMarkup(base.AlignmentMarkup):

29 name = 'index'

31 def refresh(self):

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

33 self[column] = index

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