Friday, July 9, 2010

The structure of Bio::SimpleAlign

Alignment modifier methods
add_seq
remove_LocatableSeq
remove_Seqs
remove_redundant_Seqs
uniq_seq
remove_columns
sort_alphabetically
sort_by_list
sort_by_pairwise_identity
sort_by_length
sort_by_start
set_new_reference
Alignment selection methods
each_seq
each_alphabetically
each_seq_with_id
get_seq_by_pos
get_seq_by_id
select_Seqs
select_columns
remove_gaps
mask_columns
seq_with_features
Change sequences within the MSA
map_chars
uppercase
lowercase
togglecase
match
unmatch
Consensus sequences
consensus_string
consensus_iupac
consensus_meta
bracket_string
cigar_line
match_line
gap_line
all_gap_line
gap_col_matrix
MSA attributes
id
accession
description
source
missing_char
match_char
gap_char
mask_char
symbol_chars
Alignment descriptors
score
is_flush
length
maxdisplayname_length
max_metaname_length
num_residues
num_sequences
average_percentage_identity
percentage_identity
overall_percentage_identity
pairwise_percentage_identity
column_from_residue_number
Sequence names
displayname
set_displayname_count
set_displayname_flat
set_displayname_normal
set_displayname_safe
restore_displayname
methods implementing Bio::FeatureHolderI
get_SeqFeatures
add_SeqFeature
remove_SeqFeatures
feature_count
get_all_SeqFeatures
methods for Bio::AnnotatableI
annotation

2 comments:

  1. I think we discussed this on the mail list, but it might be worth posting this revised list of methods there in case some have objections. Since this code will go into core after the 1.6 series changes aren't a huge concern, but we want to ensure the bioperl community is comfortable enough with the changes.

    ReplyDelete
  2. Ok, I will post a list of the revised methods, e.g. with an indication of renaming/recoding/debuging events.

    ReplyDelete