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.\"
.IX Title "Bio::Map::OrderedPositionWithDistance 3pm"
.TH Bio::Map::OrderedPositionWithDistance 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::OrderedPositionWithDistance \- 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::OrderedPositionWithDistance;
\&        # the first marker in the sequence
\&    my $position = Bio::Map::OrderedPositionWithDistance\->new(\-positions => 1,
\&                        \-distance => 22.3 );
\&        # the second marker in the sequence, 15.6 units from the fist one
\&    my $position2 = Bio::Map::OrderedPositionWithDistance\->new(\-positions => 2,
\&                        \-distance => 15.6 );
\&        # the third marker in the sequence, coincidental with the second
\&        # marker
\&    my $position3 = Bio::Map::OrderedPositionWithDistance\->new(\-positions => 3,
\&                        \-distance => 0 );
.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.
OrderedPositionWithDistance 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
.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 8
\& Title   : new
\& Usage   : my $obj = Bio::Map::OrderedPositionWithDistance\->new();
\& Function: Builds a new Bio::Map::OrderedPositionWithDistance object 
\& Returns : Bio::Map::OrderedPositionWithDistance
\& Args    : \-positions  \- Should be a single value representing the order
\&        of this marker within the list of markers
\&        \-distance \- The distance this marker is from the marker before it.
\&                0 reflects coincidentality.
.Ve
.SS "distance($new_distance)"
.IX Subsection "distance($new_distance)"
.Vb 7
\& Title   : distance($new_distance)
\& Usage   : $position\->distance(new_distance) _or_
\&        $position\->distance()
\& Function: get/set the distance of this position from the previous marker
\& Returns : A scalar representing the current distance for this position.
\& Args    : If $new_distance is provided the distance of this Position will
\&        be set to $new_distance
.Ve