Bio::L...cationI(3pm)

💖 Bio::L...cationI(3pm) 💖

okay bestie, welcome to Bio::L...cationI(3pm) — it's the User Contributed Perl Documentation for the BioPerl gang, and I'm literally so hype to walk you through it. this one's a whole interface, not a real class, so no cap, you don't instantiate it directly — you just vibe with its methods. 🦋

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✨ NAME ✨

Bio::Location::SplitLocationI — the abstract interface of a Location on a Sequence which has multiple locations (start/end points). it's giving "one feature, many address labels." 💅

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🌸 SYNOPSIS 🌸

# get a SplitLocationI somehow
  print $splitlocation->start, "..", $splitlocation->end, "\n";
  my @sublocs = $splitlocation->sub_Location();

  my $count = 1;
  # print the start/end points of the sub locations
  foreach my $location ( sort { $a->start <=> $b->start }  @sublocs ) {
              printf "sub feature %d [%d..%d]\n", $location->start,$location->end;
      $count++;
  }

look at that sort block sorting by start like the little icon it is 🎀

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🧚 DESCRIPTION 🧚

so this interface wraps up every method you need to represent the location of a sequence feature that has more than just one single start/end pair. the classics are the annotated exons in a gene, or the annotated CDS in a sequence file. multiple spots, one feature, main character energy. 👑

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🫶 FEEDBACK 🫶

user feedback is, like, integral to the evolution of this and every other Bioperl module. send your comments and suggestions to one of the Bioperl mailing lists, preferably — 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. lots of experienced and responsive experts will be able to look at the problem and address it quickly. and if you can, include a thorough description of the problem with code and data examples. the more deets the better, bestie. 🙈

🐛 Reporting Bugs

report bugs to the Bioperl bug tracking system so we can keep track of the bugs and their resolutions. bug reports can be submitted via the web:

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

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⭐ AUTHOR - Jason Stajich ⭐

Email jason-at-bioperl-dot-org

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👑 APPENDIX 👑

the rest of the documentation details each of the object methods. internal methods are usually preceded with a _. iykyk. 🔥

🌈 sub_Location

• Title: sub_Location
• Usage: @locations = $feat->sub_Location();
• Function: Returns an array of LocationI objects
• Returns: An array
• Args: none

🌈 splittype

• Title: splittype
• Usage: $splittype = $fuzzy->splittype();
• Function: get/set the split splittype
• Returns: the splittype of split feature (join, order)
• Args: splittype to set

🌈 is_single_sequence

• Title: is_single_sequence
• Usage:

if($splitloc->is_single_sequence()) {
    print "Location object $splitloc is split ".
          "but only across a single sequence\n";
}

• Function: Determine whether this location is split across a single or multiple sequences.
• Returns: TRUE if all sublocations lie on the same sequence as the root location (feature), and FALSE otherwise.
• Args: none

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💜 Bio::LocationI methods 💜

Bio::LocationI inherited methods follow, periodt.

🌟 min_start

• Title: min_start
• Usage: my $minstart = $location->min_start();
• Function: Get minimum starting location of feature startpoint
• Returns: integer or undef if no maximum starting point.
• Args: none

🌟 max_start

• Title: max_start
• Usage: my $maxstart = $location->max_start();
• Function: Get maximum starting location of feature startpoint
• Returns: integer or undef if no maximum starting point.
• Args: none

🌟 start_pos_type

• Title: start_pos_type
• Usage: my $start_pos_type = $location->start_pos_type();
• Function: Get start position type (ie <, >, ^)
• Returns: type of position coded as text ('BEFORE', 'AFTER', 'EXACT', 'WITHIN', 'BETWEEN')
• Args: none

🌟 min_end

• Title: min_end
• Usage: my $minend = $location->min_end();
• Function: Get minimum ending location of feature endpoint
• Returns: integer or undef if no minimum ending point.
• Args: none

🌟 max_end

• Title: max_end
• Usage: my $maxend = $location->max_end();
• Function: Get maximum ending location of feature endpoint
• Returns: integer or undef if no maximum ending point.
• Args: none

🌟 end_pos_type

• Title: end_pos_type
• Usage: my $end_pos_type = $location->end_pos_type();
• Function: Get end position type (ie <, >, ^)
• Returns: type of position coded as text ('BEFORE', 'AFTER', 'EXACT', 'WITHIN', 'BETWEEN')
• Args: none

🌟 seq_id

• Title: seq_id
• Usage: my $seqid = $location->seq_id();
• Function: Get/Set seq_id that location refers to
• Returns: seq_id
• Args: [optional] seq_id value to set

🌟 coordinate_policy

• Title: coordinate_policy
• Usage:

$policy = $location->coordinate_policy();
$location->coordinate_policy($mypolicy); # set may not be possible

• Function: Get the coordinate computing policy employed by this object.

See Bio::Location::CoordinatePolicyI for documentation about the policy object and its use.

The interface does not require implementing classes to accept setting of a different policy. The implementation provided here does, however, allow one to do so.

Implementors of this interface are expected to initialize every new instance with a CoordinatePolicyI object. The implementation provided here will return a default policy object if none has been set yet. To change this default policy object call this method as a class method with an appropriate argument. Note that in this case only subsequently created Location objects will be affected.

• Returns: A Bio::Location::CoordinatePolicyI implementing object.
• Args: On set, a Bio::Location::CoordinatePolicyI implementing object.

🌟 to_FTstring

• Title: to_FTstring
• Usage: my $locstr = $location->to_FTstring()
• Function: returns the FeatureTable string of this location
• Returns: string
• Args: none

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💀 heads up: coordinate_policy says the set might not be possible, and the interface doesn't require implementers to accept a new policy — so don't just assume your setter slayed. and changing the default as a class method only affects Locations created after that. no retroactive glow-ups. ✨

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and that's the whole page, bestie 🎀 this one shipped as perl v5.32.1, dated 2021-08-15, and it's all filed under Bio::L...cationI(3pm). go forth and split those locations. 💖🦋🌸