Unimplemented methods in BioPerl
From BioPerl
These are a collection of modules which contain unimplemented methods. These do not include interface classes (as described in Advanced BioPerl), but are modules which haven't implemented methods described in an interface.
Bio::Assembly::Contig
Total unimplemented methods: 25
- average_percentage_identity
- column_from_residue_number
- consensus_iupac
- consensus_string
- each_alphabetically
- each_seq_with_id
- gap_char
- is_flush
- length
- map_chars
- match
- match_char
- match_line
- maxname_length
- missing_char
- overall_percentage_identity
- purge
- select
- select_noncont
- set_displayname_count
- slice
- sort_alphabetically
- symbol_chars
- unmatch
- uppercase
Bio::Restriction::IO
- Modules haven't implemented all write() methods. Bio::Restriction::IO::base
write()is only partially implemented (i.e. doesn't recognize multisite/multicut enzymes). - Bio::Restriction::IO::bairoch format works somewhat, but does not work for multisite/multicut enzymes.
- Bio::Restriction::IO inherits from Bio::SeqIO for some unknown reason at the moment (maybe as a quick way to access methods).
Bio::AlignIO
The following modules currently do not have write_aln() methods implemented. Note also that a few of these also do not completely parse data in the file, such as meta data. A notable exception is Stockholm multiple alignment format, which now has implemented a write_aln() method and parses annotation and meta data.
