allpy
annotate allpy/dna.py @ 666:d9a3e99ae19b
blocks3d/www: mark conservative columns inside blocks
Previously letters were marked if column is conservative over all
sequences of alignment. Currently it was changed to conservatism
over block including this letter.
Additional attribute storing conservatism of columns inside block
was added to block. This caused all colors of blocks to be changed.
| author | boris <bnagaev@gmail.com> |
|---|---|
| date | Fri, 01 Jul 2011 03:21:08 +0400 |
| parents | 5639138f619a |
| children | 5f9e9c4e9ed6 e461a5529338 |
| rev | line source |
|---|---|
| bnagaev@240 | 1 import base |
| me@353 | 2 import data.codes |
| me@280 | 3 |
| dendik@382 | 4 import dna |
| dendik@382 | 5 |
| me@328 | 6 class Monomer(base.Monomer): |
| me@328 | 7 """DNA monomers: nucleotides.""" |
| me@328 | 8 type = 'dna' |
| dendik@382 | 9 types = dna |
| me@280 | 10 by_code1 = {} |
| me@280 | 11 by_code3 = {} |
| me@280 | 12 by_name = {} |
| me@353 | 13 Monomer._initialize(data.codes.dna) |
| bnagaev@240 | 14 |
| bnagaev@240 | 15 class Sequence(base.Sequence): |
| dendik@382 | 16 types = dna |
| dendik@382 | 17 |
| dendik@382 | 18 class Alignment(base.Alignment): |
| dendik@382 | 19 types = dna |
| bnagaev@240 | 20 |
| me@341 | 21 class Block(Alignment, base.Block): |
| me@341 | 22 pass |
| me@341 | 23 |
| me@280 | 24 # vim: set ts=4 sts=4 sw=4 et: |