allpy
annotate allpy/rna.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 | df571a5233fb |
| children | 4a9b4503a027 |
| rev | line source |
|---|---|
| bnagaev@240 | 1 import base |
| me@353 | 2 import data.codes |
| me@281 | 3 |
| dendik@382 | 4 import rna |
| dendik@382 | 5 |
| me@328 | 6 class Monomer(base.Monomer): |
| me@328 | 7 """RNA monomers: nucleotides.""" |
| me@328 | 8 type = 'rna' |
| dendik@382 | 9 types = rna |
| me@281 | 10 by_code1 = {} |
| me@281 | 11 by_code3 = {} |
| me@281 | 12 by_name = {} |
| me@353 | 13 Monomer._initialize(data.codes.rna) |
| bnagaev@240 | 14 |
| bnagaev@240 | 15 class Sequence(base.Sequence): |
| dendik@382 | 16 types = rna |
| bnagaev@240 | 17 |
| dendik@623 | 18 class Alignment(base.Alignment): |
| dendik@623 | 19 types = rna |
| dendik@623 | 20 |
| me@341 | 21 class Block(Alignment, base.Block): |
| me@341 | 22 pass |
| me@341 | 23 |
| me@281 | 24 # vim: set ts=4 sts=4 sw=4 et: |