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.\" ========================================================================
.\"
.IX Title "Bio::Map::MarkerI 3pm"
.TH Bio::Map::MarkerI 3pm "2018-10-27" "perl v5.26.2" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.SH "NAME"
Bio::Map::MarkerI \- Interface for basic marker functionality
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 3
\&    # do not use this module directly
\&    # See Bio::Map::Marker for an example of
\&    # implementation.
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
A Marker is a Bio::Map::Mappable with some properties particular to markers.
It also offers a number of convienience methods to make dealing with map
elements easier.
.SH "FEEDBACK"
.IX Header "FEEDBACK"
.SS "Mailing Lists"
.IX Subsection "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.
.PP
.Vb 2
\&  bioperl\-l@bioperl.org                  \- General discussion
\&  http://bioperl.org/wiki/Mailing_lists  \- About the mailing lists
.Ve
.SS "Support"
.IX Subsection "Support"
Please direct usage questions or support issues to the mailing list:
.PP
\&\fIbioperl\-l@bioperl.org\fR
.PP
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.
.SS "Reporting Bugs"
.IX Subsection "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:
.PP
.Vb 1
\&  https://github.com/bioperl/bioperl\-live/issues
.Ve
.SH "AUTHOR \- Jason Stajich"
.IX Header "AUTHOR - Jason Stajich"
Email jason@bioperl.org
.SH "CONTRIBUTORS"
.IX Header "CONTRIBUTORS"
Heikki Lehvaslaiho heikki-at-bioperl-dot-org
Lincoln Stein      lstein@cshl.org
Jason Stajich      jason@bioperl.org
Chad Matsalla      bioinformatics1@dieselwurks.com
Sendu Bala         bix@sendu.me.uk
.SH "APPENDIX"
.IX Header "APPENDIX"
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
.SS "get_position_object"
.IX Subsection "get_position_object"
.Vb 10
\& Title   : get_position_class
\& Usage   : my $position = $marker\->get_position_object();
\& Function: To get an object of the default Position class
\&           for this Marker. Subclasses should redefine this method.
\&           The Position returned needs to be a L<Bio::Map::PositionI> with
\&                   \-element set to self.
\& Returns : L<Bio::Map::PositionI>
\& Args    : none for an \*(Aqempty\*(Aq PositionI object, optionally
\&           Bio::Map::MapI and value string to set the Position\*(Aqs \-map and \-value
\&           attributes.
.Ve
.SS "position"
.IX Subsection "position"
.Vb 12
\& Title   : position
\& Usage   : my $position = $mappable\->position();
\&                   $mappable\->position($position);
\& Function: Get/Set the Position of this Marker (where it is on which map),
\&           purging all other positions before setting.
\& Returns : L<Bio::Map::PositionI>
\& Args    : Bio::Map::PositionI
\&            OR
\&           Bio::Map::MapI AND
\&           scalar
\&            OR
\&           scalar, but only if the marker has a default map
.Ve
.SS "positions"
.IX Subsection "positions"
.Vb 5
\& Title   : positions
\& Usage   : $marker\->positions([$pos1, $pos2, $pos3]);
\& Function: Add multiple Bio::Map::PositionI to this marker
\& Returns : n/a
\& Args    : array ref of $map/value tuples or array ref of Bio::Map::PositionI
.Ve
.SS "default_map"
.IX Subsection "default_map"
.Vb 5
\& Title   : default_map
\& Usage   : my $map = $marker\->default_map();
\& Function: Get/Set the default map for the marker.
\& Returns : L<Bio::Map::MapI>
\& Args    : [optional] new L<Bio::Map::MapI>
.Ve
.SS "in_map"
.IX Subsection "in_map"
.Vb 5
\& Title   : in_map
\& Usage   : if ( $marker\->in_map($map) ) {}
\& Function: Tests if this marker is found on a specific map
\& Returns : boolean
\& Args    : a map unique id OR Bio::Map::MapI
.Ve