bio::symbol::alphabet(3pm) [debian man page]
Bio::Symbol::Alphabet(3pm) User Contributed Perl Documentation Bio::Symbol::Alphabet(3pm) NAME
Bio::Symbol::Alphabet - BSANE/BioCORBA compliant symbol list alphabet SYNOPSIS
{ my $alphabet = Bio::Symbols::Alphabet->new(-symbols => [ @s ], -subalphabets => [ @alphas ] ); my @symbols = $alphabet->symbols; my @subalphas = $alphabet->alphabets; if( $alphabet->contains($symbol) ) { # do something } } DESCRIPTION
Alphabet contains set of symbols, which can be concatenated to form symbol lists. Sequence string, for example, is stringified representation of the symbol list (tokens of symbols). 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 Support 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. 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: https://redmine.open-bio.org/projects/bioperl/ 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 _ new Title : new Usage : my $obj = Bio::Symbol::Alphabet->new(); Function: Builds a new Bio::Symbol::Alphabet object Returns : Bio::Symbol::Alphabet Args : -symbols => Array ref of Bio::Symbol::SymbolI objects -subalphas=> Array ref of Bio::Symbol::AlphabetI objects representing sub alphabets AlphabetI Interface methods symbols Title : symbols Usage : my @symbols = $alphabet->symbols(); Function: Get/Set Symbol list for an alphabet List of symbols, which make up this alphabet. Returns : Array of Bio::Symbol::SymbolI objects Args : (optionalalphabets) Array of Bio::Symbol::SymbolI objects alphabets Title : alphabets Usage : my @alphabets = $alphabet->alphabets(); Function: Get/Set Sub Alphabet list for an alphabet Sub-alphabets. E.g. codons made from DNAxDNAxDNA alphabets Returns : Array of Bio::Symbol::AlphabetI objects Args : (optional) Array of Bio::Symbol::AlphabetI objects contains Title : contains Usage : if($alphabet->contains($symbol)) { } Function: Tests of Symbol is contained in this alphabet Returns : Boolean Args : Bio::Symbol::SymbolI perl v5.14.2 2012-03-02 Bio::Symbol::Alphabet(3pm)
Check Out this Related Man Page
Bio::Symbol::Symbol(3pm) User Contributed Perl Documentation Bio::Symbol::Symbol(3pm) NAME
Bio::Symbol::Symbol - A biological symbol SYNOPSIS
use Bio::Symbol::Symbol; my $thymine = Bio::Symbol::Symbol->new(-name => 'Thy', -token=> 'T'); my $a = Bio::Symbol::Symbol->new(-token => 'A' ); my $u = Bio::Symbol::Symbol->new(-token => 'U' ); my $g = Bio::Symbol::Symbol->new(-token => 'G' ); my $M = Bio::Symbol::Symbol->new(-name => 'Met', -token => 'M', -symbols => [ $a, $u, $g ]); my ($name,$token) = ($a->name, $a->token); my @symbols = $a->symbols; my $matches = $a->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 Support 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. 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: https://redmine.open-bio.org/projects/bioperl/ 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 _ new Title : new Usage : my $obj = Bio::Symbol::Symbol->new(); Function: Builds a new Bio::Symbol::Symbol object Returns : Bio::Symbol::Symbol Args : -name => descriptive name (string) [e.g. Met] -token => Shorthand token (string) [e.g. M] -symbols => Symbols that make up this symbol (array) [e.g. AUG] -matches => Alphabet in the event symbol is an ambiguity code. 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 : Ambiguity symbols are made up > 1 base symbol 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 perl v5.14.2 2012-03-02 Bio::Symbol::Symbol(3pm)