Bio::Map::FPCMarker(3pm)				User Contributed Perl Documentation				  Bio::Map::FPCMarker(3pm)

NAME

       Bio::Map::FPCMarker - An central map object representing a marker

SYNOPSIS

	  # get the marker object of $marker from the Bio::Map::FPCMarker
	  my $markerobj = $physical->get_markerobj($marker);

	  # acquire all the clones that hit this marker
	  foreach my $clone ($markerobj->each_cloneid()) {
	      print "	+++$clone
";
	  }

	  # find the position of this marker in $contig
	  print "Position in contig $contig"," = ",$markerobj->position($contig),
		"
";

	  # find the group of the marker
	  print "Group : ",$markerobj->group();

       See Bio::Map::Position and Bio::Map::PositionI for more information.

DESCRIPTION

       This object handles the notion of a marker.  This object is intended to be used by a map parser like fpc.pm.

FEEDBACK

   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.

	 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. 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.

   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:

	 https://redmine.open-bio.org/projects/bioperl/

AUTHOR - Gaurav Gupta
       Email gaurav@genome.arizona.edu

CONTRIBUTORS

       Sendu Bala  bix@sendu.me.uk

PROJECT LEADERS

       Jamie Hatfield	   jamie@genome.arizona.edu Dr. Cari Soderlund	cari@genome.arizona.edu

PROJECT DESCRIPTION

       The project was done in Arizona Genomics Computational Laboratory (AGCoL) at University of Arizona.

       This work was funded by USDA-IFAFS grant #11180 titled "Web Resources for the Computation and Display of Physical Mapping Data".

       For more information on this project, please refer:
	 http://www.genome.arizona.edu

APPENDIX

       The rest of the documentation details each of the object methods.  Internal methods are usually preceded with a _

   new
	Title	: new
	Usage	: my $clone = Bio::Map::FPCMarker->new
			     (
			      -name    => $marker,
			      -type    => $type,
			      -global  => $global,
			      -frame   => $frame,
			      -group   => $group,
			      -subgroup=> $subgroup,
			      -anchor  => $anchor,
			      -clones  => \%clones,
			      -contigs => \%contigs,
			      -position => \%markerpos,
		      -remark => $remark
			      );

	Function: Initialize a new Bio::Map::FPCMarker object
		  Most people will not use this directly but get Markers
		  through L<Bio::MapIO::fpc>
	Returns : L<Bio::Map::FPCMarker> object
	Args	: -name     => marker name string,
		      -type	=> type string,
		      -global	=> global position for marker,
		      -frame	=> boolean if marker is framework or placement,
		      -group	=> group number for marker,
		      -subgroup => subgroup number of marker,
		      -anchor	=> boolean if marker is anchored,
		      -clones	=> all the clone elements in map (hashref),
		      -contigs	=> all the contig elements (hasref),
		      -position => mapping of marker names to map position (hasref),
		  -remark   => remarks, separated by newlines

Access Methods
       These methods let you get and set the member variables

   name
	Title	: name
	Usage	: my $name = $markerobj->name();
	Function: Get/set the name for this marker
	Returns : scalar representing the current name of this marker
	Args	: none to get, OR string to set

   type
	Title	: type
	Usage	: my $type = $markerobj->type();
	Function: Get/set the type for this marker
	Returns : scalar representing the current type of this marker
	Args	: none to get, OR string to set

   global
	Title	: global
	Usage	: my $type = $markerobj->global();
	Function: Get/set the global position for this marker
	Returns : scalar representing the current global position of this marker
	Args	: none to get, OR string to set

   anchor
	Title	: anchor
	Usage	: my $anchor = $markerobj->anchor();
	Function: indicate if the Marker is anchored or not (True | False)
	Returns : scalar representing the anchor (1 | 0) for this marker
	Args	: none to get, OR 1|0 to set

   framework
	Title	: framework
	Usage	: $frame = $markerobj->framework();
	Function: indicate if the Marker is framework or placement (1 | 0)
	Returns : scalar representing if the marker is framework
		  (1 if framework, 0 if placement)
	Args	: none to get, OR 1|0 to set

   group
	Title	: group
	Usage	: $grpno = $markerobj->group();
	Function: Get/set the group number for this marker. This is a generic term,
		  used for Linkage-Groups as well as for Chromosomes.
	Returns : scalar representing the group number of this marker
	Args	: none to get, OR string to set

   subgroup
	Title	: subgroup
	Usage	: $subgroup = $marker->subgroup();
	Function: Get/set the subgroup for this marker. This is a generic term:
		  subgroup here could represent subgroup of a Chromosome or of a
		  Linkage Group. The user must take care of which subgroup he/she is
		  querying for.
	Returns : scalar representing the subgroup of this marker
	Args	: none to get, OR string to set

   position
	Title	: position
	Usage	: $markerpos = $markerobj->position($ctg);
	Function: get the position of the marker in the contig
	Returns : scalar representing the position of the markernumber of
		  the contig
	Args	: $ctg is necessary to look for the position of the marker
		  in that contig.

	*** This has nothing to do with an actual Bio::Map::PositionI object ***

   remark
	Title	: remark
	Usage	: $markerremark = $markerobj->remark();
	Function: get the remarks for this marker
	Returns : scalar of newline-separated markers
	Args	: none

   each_cloneid
	Title	: each_cloneid
	Usage	: my @clones  = $map->each_cloneid();
	Function: retrieves all the clone ids in a map unordered
	Returns : list of strings (ids)
	Args	: none

	*** This only supplies the ids set with the set_clones method ***
	*** It has nothing to do with actual Bio::Map::MappableI objects ***

   each_contigid
	Title	: each_contigid
	Usage	: my @contigs = $map->each_contigid();
	Function: retrieves all the contig ids in a map unordered
	Returns : list of strings (ids)
	Args	: none

	*** This only supplies the ids set with the set_contigs method ***
	*** It has nothing to do with actual Bio::Map::MapI objects ***

   set_clones
	Title	: set_clones
	Usage	: $marker->set_clones(\%clones)
	Function: Set the clone ids hashref
	Returns : None
	Args	: Hashref of clone ids

	*** This only sets a hash of ids ***
	*** It has nothing to do with actual Bio::Map::MappableI objects ***

   set_contigs
	Title	: set_contigs
	Usage	: $marker->set_contigs(\%contigs)
	Function: Set the contig ids hashref
	Returns : None
	Args	: Hashref of contig ids

	*** This only sets a hash of ids ***
	*** It has nothing to do with actual Bio::Map::MapI objects ***

   set_positions
	Title	: set_positions
	Usage	: $marker->set_positions(\%markerpos)
	Function: Set the positions hashref
	Returns : None
	Args	: Hashref of marker positions

	*** This only sets a hash of numbers ***
	*** It has nothing to do with actual Bio::Map::PositionI objects ***

perl v5.14.2							    2012-03-02						  Bio::Map::FPCMarker(3pm)