bio::annotatablei(3pm) [debian man page]
Bio::AnnotatableI(3pm) User Contributed Perl Documentation Bio::AnnotatableI(3pm) NAME
Bio::AnnotatableI - the base interface an annotatable object must implement SYNOPSIS
use Bio::SeqIO; # get an annotatable object somehow: for example, Bio::SeqI objects # are annotatable my $seqio = Bio::SeqIO->new(-fh => *STDIN, -format => 'genbank'); while (my $seq = $seqio->next_seq()) { # $seq is-a Bio::AnnotatableI, hence: my $ann_coll = $seq->annotation(); # $ann_coll is-a Bio::AnnotationCollectionI, hence: my @all_anns = $ann_coll->get_Annotations(); # do something with the annotation objects } DESCRIPTION
This is the base interface that all annotatable objects must implement. A good example is Bio::Seq which is an AnnotableI object. 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
Hilmar Lapp E<lt>hlapp@gmx.netE<gt> Allen Day E<lt>allenday@ucla.eduE<gt> APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ annotation Title : annotation Usage : $obj->annotation($newval) Function: Get the annotation collection for this annotatable object. Example : Returns : a Bio::AnnotationCollectionI implementing object, or undef Args : on set, new value (a Bio::AnnotationCollectionI implementing object, optional) (an implementation may not support changing the annotation collection) See Bio::AnnotationCollectionI perl v5.14.2 2012-03-02 Bio::AnnotatableI(3pm)
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Bio::PopGen::GenotypeI(3pm) User Contributed Perl Documentation Bio::PopGen::GenotypeI(3pm) NAME
Bio::PopGen::GenotypeI - A marker and alleles for a specific individual SYNOPSIS
Give standard usage here DESCRIPTION
Describe the interface here 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 email or the web: https://redmine.open-bio.org/projects/bioperl/ AUTHOR - Jason Stajich Email jason-at-bioperl.org APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ marker_name Title : marker_name Usage : my $name = $genotype->marker_name(); Function: Get the marker name for a genotype result Returns : string Args : none individual_id Title : individual_id Usage : my $indid = $genotype->individual_id(); Function: Gets the individual id associated with a genotype This is effectively a back reference since we will typically associate a genotype with an individual with an individual HAS-A genotype relationship. Returns : unique id string for an individual Args : none annotation Title : annotation Usage : my $annotation_collection = $genotype->annotation; Function: Get/set a Bio::AnnotationCollectionI for this genotype Returns : Bio::AnnotationCollectionI object Args : [optional set] Bio::AnnotationCollectionI object get_Alleles Title : get_Alleles Usage : my @alleles = $genotype->get_Alleles(); Function: Get the alleles for a given marker and individual Returns : array of alleles (strings in many implementations) Args : none perl v5.14.2 2012-03-02 Bio::PopGen::GenotypeI(3pm)