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

💖 Bio::Location::Atomic 💖

okay bestie, this is the Bio::Location::Atomic page from the User Contributed Perl Documentation, and it's literally about implementing a Atomic Location on a Sequence. yes it's a real module name, yes the capitalization is like that, we move.

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✨ NAME ✨

Bio::Location::Atomic — the implementation of a Atomic Location on a Sequence. that's it, that's the whole vibe. 💅

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🦋 SYNOPSIS 🦋

so here's how you'd actually use it, bestie:

use Bio::Location::Atomic;

my $location = Bio::Location::Atomic->new(-start => 1, -end => 100,
                                         -strand => 1 );

if( $location->strand == -1 ) {
    printf "complement(%d..%d)\n", $location->start, $location->end;
} else {
    printf "%d..%d\n", $location->start, $location->end;
}

like. look at her. iconic behavior fr fr. 🌸

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🌈 DESCRIPTION 🌈

this is an implementation of Bio::LocationI to manage simple location information on a Sequence. that's the whole point of her existence, no cap. 👑

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🫶 FEEDBACK 🫶

user feedback is an integral part of the evolution of this and other Bioperl modules. so like, send your comments and suggestions preferably to one of the Bioperl mailing lists. your participation is much appreciated. genuinely. we mean it. 🥺

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. because many experienced and reponsive experts will be able look at the problem and quickly address it. (yes, "reponsive" — we are keeping it exactly as written, bestie, that's the original's typo and we respect her. 🙈)

please include a thorough description of the problem with code and data examples if at all possible. the more deets the better, fr.

🐛 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

go off, tell them everything. 💀

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👑 AUTHOR - Jason Stajich 👑

Email jason-at-bioperl-dot-org

(we love a credited author. main character energy. ✨)

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📖 APPENDIX 📖

the rest of the documentation details each of the object methods. internal methods are usually preceded with a _. okay so buckle up, this is the long part, but every single one of these is important so we are NOT skipping. 🎀

🌸 start

Title   : start
Usage   : $start = $loc->start();
Function: get/set the start of this range
Returns : the start of this range
Args    : optionally allows the start to be set
        : using $loc->start($start)

🌸 end

Title   : end
Usage   : $end = $loc->end();
Function: get/set the end of this range
Returns : the end of this range
Args    : optionally allows the end to be set
        : using $loc->end($start)

🌸 strand

Title   : strand
Usage   : $strand = $loc->strand();
Function: get/set the strand of this range
Returns : the strandidness (-1, 0, +1)
Args    : optionally allows the strand to be set
        : using $loc->strand($strand)

"the strandidness" is such a word, and we are keeping it. 💜

🌸 flip_strand

Title   : flip_strand
Usage   : $location->flip_strand();
Function: Flip-flop a strand to the opposite
Returns : None
Args    : None

flip-flop. like a lil acrobat. she returns None and takes None, she's low maintenance. 🦋

🌸 seq_id

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

🌸 length

Title   : length
Usage   : $len = $loc->length();
Function: get the length in the coordinate space this location spans
Example :
Returns : an integer
Args    : none

(yeah the Example : is empty in the original, we're not inventing one, that's a rule. 🙈)

🌸 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 minimum starting point.
Args    : none

🌸 max_start

Title   : max_start
Usage   : my $maxstart = $location->max_start();
Function: Get maximum starting location of feature startpoint.

          In this implementation this is exactly the same as min_start().

Returns : integer or undef if no maximum starting point.
Args    : none

heads up bestie: in this implementation, max_start is exactly the same as min_start(). not a bug, that's just how she is.

🌸 start_pos_type

Title   : start_pos_type
Usage   : my $start_pos_type = $location->start_pos_type();
Function: Get start position type (ie <,>, ^).

          In this implementation this will always be 'EXACT'.

Returns : type of position coded as text
          ('BEFORE', 'AFTER', 'EXACT','WITHIN', 'BETWEEN')
Args    : none

so the position type is like <, >, ^ — and in this implementation it will always be 'EXACT'. periodt. ✨

🌸 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

          In this implementation this is exactly the same as min_end().

Returns : integer or undef if no maximum ending point.
Args    : none

same deal as before: in this implementation, max_end is exactly the same as min_end(). 🫶

🌸 end_pos_type

Title   : end_pos_type
Usage   : my $end_pos_type = $location->end_pos_type();
Function: Get end position type (ie <,>, ^)

          In this implementation this will always be 'EXACT'.

Returns : type of position coded as text
          ('BEFORE', 'AFTER', 'EXACT','WITHIN', 'BETWEEN')
Args    : none

again: always 'EXACT' in this implementation. no surprises, we love consistency. 💅

🌸 location_type

Title   : location_type
Usage   : my $location_type = $location->location_type();
Function: Get location type encoded as text
Returns : string ('EXACT', 'WITHIN', 'IN-BETWEEN')
Args    : none

🌸 is_remote

Title   : is_remote
Usage   : $is_remote_loc = $loc->is_remote()
Function: Whether or not a location is a remote location.

          A location is said to be remote if it is on a different
          'object' than the object which 'has' this
          location. Typically, features on a sequence will sometimes
          have a remote location, which means that the location of
          the feature is on a different sequence than the one that is
          attached to the feature. In such a case, $loc->seq_id will
          be different from $feat->seq_id (usually they will be the
          same).

          While this may sound weird, it reflects the location of the
          kind of AL445212.9:83662..166657 which can be found in GenBank/EMBL
          feature tables.

Example :
Returns : TRUE if the location is a remote location, and FALSE otherwise
Args    : Value to set to

okay so like, a location is remote when it's chillin' on a different 'object' than the object that 'has' this location. so $loc->seq_id will be different from $feat->seq_id — although usually they will be the same. and yeah, it "may sound weird", but it's literally how the AL445212.9:83662..166657 kind of location works in GenBank/EMBL feature tables. iykyk. 🧚

🌸 each_Location

Title   : each_Location
Usage   : @locations = $locObject->each_Location($order);
Function: Conserved function call across Location:: modules - will
          return an array containing the component Location(s) in
          that object, regardless if the calling object is itself a
          single location or one containing sublocations.
Returns : an array of Bio::LocationI implementing objects - for
          Simple locations, the return value is just itself.
Args    :

the vibe: it returns an array of Bio::LocationI implementing objects — and for Simple locations, the return value is just itself. she's self-sufficient, we stan. 👑

🌸 to_FTstring

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

🌸 valid_Location

Title   : valid_Location
Usage   : if ($location->valid_location) {...};
Function: boolean method to determine whether location is considered valid
          (has minimum requirements for Simple implementation)
Returns : Boolean value: true if location is valid, false otherwise
Args    : none

yes, the Title says valid_Location but the Usage calls valid_location. we are reporting this faithfully because we do not change the facts, bestie. 🙈

🌸 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 L<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
          L<Bio::Location::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 L<Bio::Location::CoordinatePolicyI> implementing object.
Args    : On set, a L<Bio::Location::CoordinatePolicyI> implementing object.

okay this one's meaty so let's break it down:

• it's the coordinate computing policy</c>)> this object is using.
• 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. however, the implementation provided here does allow one to do so. slay.
• implementors of this interface are expected to initialize every new instance with a Bio::Location::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. but note: in this case only subsequently created Location objects will be affected. so like, no take-backsies on the ones already out there. 💀

see Bio::Location::CoordinatePolicyI for more information.

🌸 trunc

Title   : trunc
      Usage   : $trunc_location = $location->trunc($start, $end, $relative_ori);
      Function: To truncate a location and keep annotations and features
                within the truncated segment intact.

                                              This might do things differently where the truncation
                                              splits the location in half.
      CAVEAT  : As yet, this is an untested and unannounced method. Use
                with caution!
      Returns : A L<Bio::Location::Atomic> object.
      Args    : The start and end position for the trunction, and the relative
                orientation.

⚠️ CAVEAT, READ THIS BESTIE ⚠️ — as yet, this is an untested and unannounced method. use with caution! she might do things differently where the truncation splits the location in half. we are telling you exactly what the original says, no more, no less. 🚨

also yes, "trunction" is in the original. we love her, we keep her, typos are heritage. 💖

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okay that's the whole page!! 🎀 this documentation came from perl v5.32.1, dated 2021-08-15, and it's the Bio::Location::Atomic(3pm) page, lovingly delivered to you by the User Contributed Perl Documentation. go forth and locate things atomically, bestie. 🦋💜✨