| Bio::Symbol::SymbolI(3pm) | User Contributed Perl Documentation | Bio::Symbol::SymbolI(3pm) |
Bio::Symbol::SymbolI - Interface for a Symbol
# get a Bio::Symbol::SymbolI object somehow
my ($name,$token) = ($symbol->name, $symbol->token);
my @symbols = $symbol->symbols;
my $matches = $symbol->matches;
Symbol represents a single token in the sequence. Symbol can have multiple synonyms or matches within the same Alphabet, which makes possible to represent ambiguity codes and gaps.
Symbols can be also composed from ordered list other symbols. For example, codons can be represented by single Symbol using a compound Alphabet made from three DNA Alphabets.
This module was implemented for the purposes of meeting the BSANE/BioCORBA spec 0.3 only.
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.
Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web:
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Email jason@bioperl.org
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : name Usage : my $name = $symbol->name(); Function: Get/Set Descriptive name for Symbol Returns : string Args : (optional) string
Title : token Usage : my $token = $self->token(); Function: Get/Set token for this symbol Example : Letter A,C,G,or T for a DNA alphabet Symbol Returns : string Args : (optional) string
Title : symbols Usage : my @symbols = $self->symbols(); Function: Get/Set Symbols this Symbol is composed from Example : A codon is composed of 3 DNA symbols Returns : Array of Bio::Symbol::SymbolI objects Args : (optional) Array of Bio::Symbol::SymbolI objects
Title : matches
Usage : my $matchalphabet = $symbol->matches();
Function: Get/Set (Sub) alphabet of symbols matched by this symbol
including the symbol itself (i.e. if symbol is DNA
ambiguity code W then the matches contains symbols for W
and T)
Returns : Bio::Symbol::AlphabetI
Args : (optional) Bio::Symbol::AlphabetI
Title : equals
Usage : if( $symbol->equals($symbol2) ) { }
Function: Tests if a symbol is equal to another
Returns : Boolean
Args : Bio::Symbol::SymbolI
| 2018-10-27 | perl v5.26.2 |