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

NAME

       Bio::Map::Physical - A class for handling a Physical Map (such as FPC)

SYNOPSIS

	   use Bio::MapIO;

	   # accquire a Bio::Map::Physical using Bio::MapIO::fpc
	   my $mapio = Bio::MapIO->new(-format => "fpc",-file => "rice.fpc",
				      -readcor => 0);

	   my $physical = $mapio->next_map();

	   # get all the markers ids
	   foreach my $marker ( $physical->each_markerid() ) {
	     print "Marker $marker
";

	     # acquire the marker object using Bio::Map::FPCMarker
	     my $markerobj = $physical->get_markerobj($marker);

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

DESCRIPTION

       This class is basically a continer class for a collection of Contig maps and other physical map information.

       Bio::Map::Physical has been tailored to work for FPC physical maps, but could probably be used for others as well (with the appropriate
       MapIO module).

       This class also has some methods with specific functionalities:

	 print_gffstyle()     : Generates GFF; either Contigwise[Default] or
				Groupwise

	 print_contiglist()   : Prints the list of Contigs, markers that hit the
				contig, the global position and whether the marker
				is a placement (<P>) or a Framework (<F>) marker.

	 print_markerlist()   : Prints the markers list; contig and corresponding
				number of clones.

	 matching_bands()     : Given two clones [and tolerence], this method
				calculates how many matching bands do they have.

	 coincidence_score()  : Given two clones [,tolerence and gellen], this
				method calculates the Sulston Coincidence score.

       For faster access and better optimization, the data is stored internally in hashes. The corresponding objects are created on request.

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 _

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

   version
	Title	: version
	Usage	: my $version = $map->version();
	Function: Get/set the version of the program used to
		  generate this map
	Returns : scalar representing the version
	Args	: none to get, OR string to set

   modification_user
	Title	: modification_user
	Usage	: my $modification_user = $map->modification_user();
	Function: Get/set the name of the user who last modified this map
	Returns : scalar representing the username
	Args	: none to get, OR string to set

   group_type
	Title	: group_type
	Usage	: $map->group_type($grptype);
		      my $grptype = $map->group_type();
	Function: Get/set the group type of this map
	Returns : scalar representing the group type
	Args	: none to get, OR string to set

   group_abbr
	Title	: group_abbr
	Usage	: $map->group_abbr($grpabbr);
		      my $grpabbr = $map->group_abbr();
	Function: get/set the group abbrev of this map
	Returns : string representing the group abbrev
	Args	: none to get, OR string to set

   core_exists
	Title	: core_exists
	Usage	: my $core_exists = $map->core_exists();
	Function: Get/set if the FPC file is accompanied by COR file
	Returns : boolean
	Args	: none to get, OR 1|0 to set

   each_cloneid
	Title	: each_cloneid
	Usage	: my @clones = $map->each_cloneid();
	Function: returns an array of clone names
	Returns : list of clone names
	Args	: none

   get_cloneobj
	Title	: get_cloneobj
	Usage	: my $cloneobj = $map->get_cloneobj('CLONEA');
	Function: returns an object of the clone given in the argument
	Returns : object of the clone
	Args	: scalar representing the clone name

   each_markerid
	Title	: each_markerid
	Usage	: my @markers = $map->each_markerid();
	Function: returns list of marker names
	Returns : list of marker names
	Args	: none

   get_markerobj
	Title	: get_markerobj
	Usage	: my $markerobj = $map->get_markerobj('MARKERA');
	Function: returns an object of the marker given in the argument
	Returns : object of the marker
	Args	: scalar representing the marker name

   each_contigid
	Title	: each_contigid
	Usage	: my @contigs = $map->each_contigid();
	Function: returns a list of contigs (numbers)
	Returns : list of contigs
	Args	: none

   get_contigobj
	Title	: get_contigobj
	Usage	: my $contigobj = $map->get_contigobj('CONTIG1');
	Function: returns an object of the contig given in the argument
	Returns : object of the contig
	Args	: scalar representing the contig number

   matching_bands
	Title	: matching_bands
	Usage	: $self->matching_bands('cloneA','cloneB',[$tol]);
	Function: given two clones [and tolerence], this method calculates how many
		  matching bands do they have.
		  (this method is ported directly from FPC)
	Returns : scalar representing the number of matching bands
	Args	: names of the clones ('cloneA', 'cloneB') [Default tolerence=7]

   coincidence_score
	Title	: coincidence_score
	Usage	: $self->coincidence_score('cloneA','cloneB'[,$tol,$gellen]);
	Function: given two clones [,tolerence and gellen], this method calculates
		  the Sulston Coincidence score.
		  (this method is ported directly from FPC)
	Returns : scalar representing the Sulston coincidence score.
	Args	: names of the clones ('cloneA', 'cloneB')
		  [Default tol=7 gellen=3300.0]

   print_contiglist
	Title	: print_contiglist
	Usage	: $map->print_contiglist([showall]); #[Default 0]
	Function: prints the list of contigs, markers that hit the contig, the
		  global position and whether the marker is a placement (P) or
		  a Framework (F) marker.
	Returns : none
	Args	: [showall] [Default 0], 1 includes all the discrepant markers

   print_markerlist
	Title	 : print_markerlist
	Usage	 : $map->print_markerlist();
	Function : prints the marker list; contig and corresponding number of
		   clones for each marker.
	Returns  : none
	Args	 : none

   print_gffstyle
	Title	 : print_gffstyle
	Usage	 : $map->print_gffstyle([style]);
	Function : prints GFF; either Contigwise (default) or Groupwise
	Returns  : none
	Args	 : [style] default = 0 contigwise, else
				     1 groupwise (chromosome-wise).

   _calc_markerposition
	Title	: _calc_markerposition
	Usage	: $map->_calc_markerposition();
	Function: Calculates the position of the marker in the contig
	Returns : none
	Args	: none

   _calc_contigposition
	Title	: _calc_contigposition
	Usage	: $map->_calc_contigposition();
	Function: calculates the position of the contig in the group
	Returns : none
	Args	: none

   _calc_contiggroup
	Title	: _calc_contiggroup
	Usage	: $map->_calc_contiggroup();
	Function: calculates the group of the contig
	Returns : none
	Args	: none

   _set<Type>Ref
	Title	: _set<Type>Ref
	Usage	: These are used for initializing the reference of the hash in
		  Bio::MapIO (fpc.pm) to the corresponding hash in Bio::Map
		  (physical.pm). Should be used only from Bio::MapIO System.
		      $map->setCloneRef(\%_clones);
		      $map->setMarkerRef(\%_markers);
		      $map->setContigRef(\%_contigs);
	Function: sets the hash references to the corresponding hashes
	Returns : none
	Args	: reference of the hash.

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