Bio::Symbol::SymbolI.3pm

Langue: en

Version: 2008-01-11 (mandriva - 01/05/08)

Section: 3 (Bibliothèques de fonctions)

NAME

Bio::Symbol::SymbolI - Interface for a Symbol

SYNOPSIS

     # get a Bio::Symbol::SymbolI object somehow
 
 
     my ($name,$token) = ($symbol->name, $symbol->token);
     my @symbols       = $symbol->symbols;
     my $matches       = $symbol->matches;
 
 

DESCRIPTION

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.

FEEDBACK


Mailing Lists

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
 
 

Reporting Bugs

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:

   http://bugzilla.open-bio.org/
 
 

AUTHOR - Jason Stajich

Email jason@bioperl.org

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

Bio::Symbol::SymbolI interface methods


name

  Title   : name
  Usage   : my $name = $symbol->name();
  Function: Get/Set Descriptive name for Symbol
  Returns : string
  Args    : (optional) string
 
 

token

  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
 
 

symbols

  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
 
 

matches

  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
 
 

equals

  Title   : equals
  Usage   : if( $symbol->equals($symbol2) ) { }
  Function: Tests if a symbol is equal to another 
  Returns : Boolean
  Args    : Bio::Symbol::SymbolI