Bio::O...Adaptor(3pm)

💖 Bio::O...Adaptor(3pm) — the User Contributed Perl Documentation glow-up 💖

okay bestie, sit down, hydrate, and let me tell you about Bio::Ontology::SimpleGOEngine::GraphAdaptor — yes the name is a whole mouthful, it's giving "my parents picked every syllable" energy, but she's iconic and she WORKS.

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✨ NAME ✨

Bio::Ontology::SimpleGOEngine::GraphAdaptor — a graph adaptor for Bio::Ontology::SimpleGOEngine. that's it, that's the girl 🎀

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🌸 SYNOPSIS 🌸

use Bio::Ontology::SimpleGOEngine::GraphAdaptor;

my $graph = Bio::Ontology::SimpleGOEngine::GraphAdaptor;

look at her. two lines. slay. 💅

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🦋 DESCRIPTION 🦋

so basically 💖 this is an adaptor, right, and her whole job is to make using different versions of the standard CPAN Graph module — old ones being versions 0.2x, new ones being 0.5x and beyond — nice and simple inside Bio::Ontology::SimpleGOEngine.

ngl, previous versions of this module did support Graph versions older than 0.5. but we're removing support for those older versions post BioPerl 1.6.901. so if you absolutely, desperately, cannot live without an old version of Graph? bestie, please just use an older version of BioPerl. no cap. 🙈

also important: this module implements only those Graph methods used by SimpleGOEngine. it is far from a complete compatibility layer, okay?? like, do not come for her expecting a full translator. she also implements workarounds for certain performance problems in the current versions of Graph v0.5x, which is honestly so real of her.

this class provides implementations for the required graph methods using the new version of Graph. in most cases, these are simple pass-throughs. periodt.

the methods implemented here or in the subclasses are listed below. in all cases, we implemented the Graph v0.5x interface. so go consult the Graph v0.5x man page for the deets, iykyk. ✨

add_vertex
has_vertex
add_edge
has_edge
vertices
edges
edges_at
predecessors
successors
set_vertex_attribute
get_vertex_attribute
set_edge_attribute
get_edge_attribute
source_vertices
sink_vertices

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📣 FEEDBACK 📣

💌 Mailing Lists

user feedback is an integral part of the evolution of this and other Bioperl modules — like, the whole glow-up depends on y'all 🫶. send your comments and suggestions preferably to the Bioperl mailing lists. your participation is much appreciated, fr fr.

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. the way that this works is that 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 — the more context, the better the vibes. 💜

🐛 Reporting Bugs

report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. bug reports can be submitted via the web:

https://github.com/bioperl/bioperl-live/issues

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👑 AUTHOR 👑

Nat Goodman

Email: natg at shore.net

Address:

Institute for Systems Biology
1441 N 34th St
Seattle, WA 98103-8904

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🌈 APPENDIX 🌈

the rest of the documentation details each of the object methods. internal methods are usually preceded with a _ — you know, the little secret ones. 🤫

⭐ new

Title   : new
Usage   : $graph = Bio::Ontology::SimpleGOEngine::GraphAdaptor->new()
Function: Creates a new graph
Returns : Bio::Ontology::SimpleGOEngine::GraphAdaptor02 or
          Bio::Ontology::SimpleGOEngine::GraphAdaptor05 object,
          depending on which Graph version is available
Args    : none

she creates a new graph ✨ and the return type depends on which Graph version is available — GraphAdaptor02 or GraphAdaptor05, she's versatile like that.

🎀 _graph

Title   : _graph
Usage   : $self->_graph();
Function: Internal method to access 'real' graph
Returns : Graph::Directed object
Args    : none

internal method to access the 'real' graph. the real one. the main character. 👑

🧚 _vertex_attributes

Title   : _vertex_attributes
Usage   : $self->vertex_attributes();
Function: Internal method to access HASH used to store vertex attributes
Returns : Graph::Directed object
Args    : none

internal method to access the HASH used to store vertex attributes. a whole lil stash of vertex lore. 🍓

🌸 _edge_attributes

Title   : _edge_attributes
Usage   : $self->edge_attributes();
Function: Internal method to access HASH used to store edge attributes
Returns : Graph::Directed object
Args    : none

same energy, but for edges. internal method to access the HASH used to store edge attributes. 💅

💖 _vertex2attributes

Title   : _vertex2attributes
Usage   : $value=$graph->_vertex2attributes($v_->{ATTRIBUTE};
          $graph->_vertex2attributes($v)->{ATTRIBUTE}=$value;
Function: Internal method to access attributes for a specific vertex
Returns : HASH
Args    : none

internal method to access attributes for a specific vertex — one vertex at a time, give her a moment. 🫶

🦋 _edge2attributes

Title   : _edge2attributes
Usage   : $value=$graph->_edge2attributes($u,$v)->{ATTRIBUTE};
          $graph->_edge2attributes($u,$v)->{ATTRIBUTE}=$value;
Function: Internal method to access HASH used to store edge attributes
Returns : HASH
Args    : none

internal method to access the HASH used to store edge attributes. returns a HASH, takes no args, iconic behaviour. ✨

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and that's the whole page, bestie!! 💖 this was perl v5.32.1, dated 2021-08-15, and it lives under the Bio::O...Adaptor(3pm) manual page — go forth and graph responsibly. mwah. 💋👑🌈