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.\" ========================================================================
.\"
.IX Title "Bio::Map::OrderedPosition 3pm"
.TH Bio::Map::OrderedPosition 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::OrderedPosition \- Abstracts the notion of a member
	of an ordered list of markers. Each marker is a certain distance
	from the one in the ordered list before it.
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 11
\&    use Bio::Map::OrderedPosition;
\&        # the first marker in the sequence
\&    my $position = Bio::Map::OrderedPosition\->new(\-order => 1,
\&                        \-positions => [ [ $map, 22.3] ] );
\&        # the second marker in the sequence, 15.6 units from the fist one
\&    my $position2 = Bio::Map::OrderedPosition\->new(\-order => 2,
\&                        \-positions => [ [ $map, 37.9] ] );
\&        # the third marker in the sequence, coincidental with the second
\&        # marker
\&    my $position3 = Bio::Map::OrderedPosition\->new(\-order => 3,
\&                        \-posititions => [ [ $map, 37.9]] );
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
This object is an implementation of the PositionI interface and the
Position object handles the specific values of a position.
OrderedPosition is intended to be slightly more specific then Position
but only specific enough for a parser from the MarkerIO subsystem to
create and then pass to a client application to bless into the proper
type. For an example of how this is intended to work, see the
Mapmaker.pm.
.PP
No units are assumed here \- units are handled by context of which Map
a position is placed in.
.PP
Se Bio::Map::Position for additional information.
.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 \- Chad Matsalla"
.IX Header "AUTHOR - Chad Matsalla"
Email bioinformatics1@dieselwurks.com
.SH "CONTRIBUTORS"
.IX Header "CONTRIBUTORS"
Lincoln Stein, lstein@cshl.org
Heikki Lehvaslaiho, heikki-at-bioperl-dot-org
Jason Stajich, jason@bioperl.org
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 "new"
.IX Subsection "new"
.Vb 5
\& Title   : new
\& Usage   : my $obj = Bio::Map::OrderedPosition\->new();
\& Function: Builds a new Bio::Map::OrderedPosition object 
\& Returns : Bio::Map::OrderedPosition
\& Args    : \-order : The order of this position
.Ve
.SS "order"
.IX Subsection "order"
.Vb 6
\& Title   : order
\& Usage   : $o_position\->order($new_order);
\&           my $order = $o_position\->order();
\& Function: Get/set the order position of this position in a map.
\& Returns : int, the order of this position
\& Args    : none to get, OR int to set
.Ve
.SS "sortable"
.IX Subsection "sortable"
.Vb 8
\& Title   : sortable
\& Usage   : my $num = $position\->sortable();
\& Function: Read\-only method that is guaranteed to return a value suitable
\&           for correctly sorting this kind of position amongst other positions
\&           of the same kind on the same map. Note that sorting different kinds
\&           of position together is unlikely to give sane results.
\& Returns : numeric
\& Args    : none
.Ve
.SS "equals"
.IX Subsection "equals"
.Vb 5
\& Title   : equals
\& Usage   : if ($mappable\->equals($mapable2)) {...}
\& Function: Test if a position is equal to another position.
\& Returns : boolean
\& Args    : Bio::Map::PositionI
.Ve
.SS "less_than"
.IX Subsection "less_than"
.Vb 6
\& Title   : less_than
\& Usage   : if ($mappable\->less_than($m2)) {...}
\& Function: Tests if a position is less than another position
\&           It is assumed that 2 positions are in the same map.
\& Returns : boolean
\& Args    : Bio::Map::PositionI
.Ve
.SS "greater_than"
.IX Subsection "greater_than"
.Vb 6
\& Title   : greater_than
\& Usage   : if ($mappable\->greater_than($m2)) {...}
\& Function: Tests if position is greater than another position.
\&           It is assumed that 2 positions are in the same map.
\& Returns : boolean
\& Args    : Bio::Map::PositionI
.Ve