Bio::Graphics::FeatureBase - Base class for Bio::Graphics::Feature
See Bio::Graphics::Feature for full synopsis.
This is the base class for Bio::Graphics::Feature. It has all the methods of Bio::Graphics::Feature except for those that are required to interface with Bio::Graphics::FeatureFile, namely factory(), configurator(), url(), and make_link(). Please see Bio::Graphics::Feature for full documentation.
Title : display_name Usage : $id = $obj->display_name or $obj->display_name($newid); Function: Gets or sets the display id, also known as the common name of the Seq object. The semantics of this is that it is the most likely string to be used as an identifier of the sequence, and likely to have "human" readability. The id is equivalent to the LOCUS field of the GenBank/EMBL databanks and the ID field of the Swissprot/sptrembl database. In fasta format, the >(\S+) is presumed to be the id, though some people overload the id to embed other information. Bioperl does not use any embedded information in the ID field, and people are encouraged to use other mechanisms (accession field for example, or extending the sequence object) to solve this. Notice that $seq->id() maps to this function, mainly for legacy/convenience issues. Returns : A string Args : None or a new id
Title : accession_number Usage : $unique_biological_key = $obj->accession_number; Function: Returns the unique biological id for a sequence, commonly called the accession_number. For sequences from established databases, the implementors should try to use the correct accession number. Notice that primary_id() provides the unique id for the implemetation, allowing multiple objects to have the same accession number in a particular implementation. For sequences with no accession number, this method should return "unknown". Returns : A string Args : None
Title : alphabet Usage : if( $obj->alphabet eq 'dna' ) { /Do Something/ } Function: Returns the type of sequence being one of 'dna', 'rna' or 'protein'. This is case sensitive. This is not called <type> because this would cause upgrade problems from the 0.5 and earlier Seq objects. Returns : a string either 'dna','rna','protein'. NB - the object must make a call of the type - if there is no type specified it has to guess. Args : none Status : Virtual
Title : desc Usage : $seqobj->desc($string) or $seqobj->desc() Function: Sets or gets the description of the sequence Example : Returns : The description Args : The description or none
Title : location Usage : my $location = $seqfeature->location() Function: returns a location object suitable for identifying location of feature on sequence or parent feature Returns : Bio::LocationI object Args : none
Title : location_string Usage : my $string = $seqfeature->location_string() Function: Returns a location string in a format recognized by gbrowse Returns : a string Args : none
This is a convenience function used by the generic genome browser. It returns the location of the feature and its subfeatures in the compact form "start1..end1,start2..end2,...". Use $seqfeature->location()->toFTString() to obtain a standard GenBank/EMBL location representation.
Title : clone Usage : my $feature = $seqfeature->clone Function: Create a deep copy of the feature Returns : A copy of the feature Args : none
Bio::Graphics::Feature, Bio::Graphics::FeatureFile, Bio::Graphics::Panel,Bio::Graphics::Glyph, GD
Lincoln Stein <lstein@cshl.org>.
Copyright (c) 2006 Cold Spring Harbor Laboratory
This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. See DISCLAIMER.txt for disclaimers of warranty.
To install Bio::Seq, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Seq
CPAN shell
perl -MCPAN -e shell install Bio::Seq
For more information on module installation, please visit the detailed CPAN module installation guide.