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.\" ========================================================================
.\"
.IX Title "Bio::Map::CytoMarker 3pm"
.TH Bio::Map::CytoMarker 3pm "2014-07-13" "perl v5.18.2" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.SH "NAME"
Bio::Map::CytoMarker \- An object representing a marker.
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 2
\&  $o_usat = Bio::Map::CytoMarker\->new(\-name=>\*(AqChad Super Marker 2\*(Aq,
\&                                 \-position => $pos);
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
This object handles markers with a positon in a cytogenetic map known.
This marker will have a name and a position.
.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 \- Heikki Lehvaslaiho"
.IX Header "AUTHOR - Heikki Lehvaslaiho"
Email heikki-at-bioperl-dot-org
.SH "CONTRIBUTORS"
.IX Header "CONTRIBUTORS"
Chad Matsalla      bioinformatics1@dieselwurks.com
Lincoln Stein      lstein@cshl.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 "Bio::Map::MarkerI methods"
.IX Subsection "Bio::Map::MarkerI methods"
.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 "Comparison methods"
.IX Subsection "Comparison methods"
The numeric values for cutogeneic loctions go from the p tip of
chromosome 1, down to the q tip and similarly throgh consecutive
chromosomes, through X and end the the q tip of X. See
Bio::Map::CytoPosition::cytorange for more details.
.SS "New methods"
.IX Subsection "New methods"
.SS "get_chr"
.IX Subsection "get_chr"
.Vb 6
\& Title   : get_chr
\& Usage   : my $mychr = $marker\->get_chr();
\& Function: Read only method for the  chromosome string of the location.
\&           A shortcut to $marker\->position\->chr().
\& Returns : chromosome value
\& Args    : [optional] new chromosome value
.Ve