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

NAME

       Bio::Map::Clone - An central map object representing a clone

SYNOPSIS

	  # get the clone object of $clone from the Bio::Map::Clone
	  my $cloneobj = $physical->get_cloneobj($clone);

	  # acquire all the markers that hit this clone
	  foreach my $marker ($cloneobj->each_markerid()) {
	      print "	+++$marker
";
	  }

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

DESCRIPTION

       This object handles the notion of a clone. This clone will have a name and a position in a map.

       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::Clone->new
			     (
			      -name    => $clone,
			      -markers => @markers,
			      -contig  => $contig,
			      -type    => $type,
			      -bands   => $bands,
			      -gel     => $gel,
			      -group   => $group,
			      -remark  => $remark,
			      -fpnumber=> $fp_number,
			      -sequencetype  => $seq_type,
			      -sequencestatus=> $seq_status,
			      -fpcremark => $fpc_remark,
			      -matche	 => @ematch,
			      -matcha	 => @amatch,
			      -matchp	 => @pmatch,
			      -range	 => Bio::Range->new(-start => $startrange,
							    -end   => $endrange)
			      );
	Function: Initialize a new Bio::Map::Clone object
		  Most people will not use this directly but get Clones
		  through L<Bio::MapIO::fpc>
	Returns : L<Bio::Map::Clone> object
	Args	:   -name => marker name string,
		    -markers => array ref of markers,
		    -contig  => contig name string,
		    -type    => type string,
		    -bands   => band string,
		    -gel     => gel string,
		    -group   => group name string,
		    -remark  => remark string,
		    -fpnumber=> FP number string,
		    -sequencetype  => seq type string,
		    -sequencestatus=> seq status string,
		    -fpcremark => FPC remark,
		    -matche    => array ref,
		    -matcha    => array ref,
		    -matchp    => array ref,
		    -range     => L<Bio::Range> object,

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

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

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

   range
	Title	: range
	Usage	: my $range = $cloneobj->range();
	Function: Get/set the range of the contig that this clone covers
	Returns : Bio::Range representing the current range of this contig,
		  start and end of the contig can be thus found using:
		  my $start = $contigobj->range()->start();
		  my $end   = $contigobj->range()->end();
	Args	: none to get, OR Bio::Range to set

   match
	Title	: match
	Usage	: @eclone = $cloneobj->match('exact');
		  @aclone = $cloneobj->match('approximate');
		  @pclone = $cloneobj->match('pseudo');
	Function: get all matching clones
	Returns : list
	Args	: scalar representing the type of clone to be
		  queried.

   each_match
	Title	: each_match
	Function: Synonym of the match() method.

   set_match
	Title	: set_match
	Usage	: $clone->set_match($type,$values);
	Function: Set the Matches per type
	Returns : None
	Args	: type (one of 'exact' 'approx' 'pseudo')
		  array ref of match values

   gel
	Title	: gel
	Usage	: $clonegel = $cloneobj->gel();
	Function: Get/set the gel number for this clone
	Returns : scalar representing the gel number of this clone
	Args	: none to get, OR string to set

   remark
	Title	: remark
	Usage	: $cloneremark = $cloneobj->remark();
	Function: Get/set the remark for this clone
	Returns : scalar representing the current remark of this clone
	Args	: none to get, OR string to set

   fp_number
	Title	: fp_number
	Usage	: $clonefpnumber = $cloneobj->fp_number();
	Function: Get/set the fp number for this clone
	Returns : scalar representing the fp number of this clone
	Args	: none to get, OR string to set

   sequence_type
	Title	: sequence_type
	Usage	: $cloneseqtype = $cloneobj->sequence_type();
	Function: Get/set the sequence type for this clone
	Returns : scalar representing the sequence type of this clone
	Args	: none to get, OR string to set

   sequence_status
	Title	: sequence_status
	Usage	: $cloneseqstatus = $cloneobj->sequence_status();
	Function: Get/set the sequence status for this clone
	Returns : scalar representing the sequence status of this clone
	Args	: none to get, OR string to set

   fpc_remark
	Title	: fpc_remark
	Usage	: $clonefpcremark = $cloneobj->fpc_remark();
	Function: Get/set the fpc remark for this clone
	Returns : scalar representing the fpc remark of this clone
	Args	: none to get, OR string to set

   bands
	Title	: bands
	Usage	: @clonebands = $cloneobj->bands();
	Function: Get/set the bands for this clone
	Returns : liat representing the band of this clone, if
		  readcor = 1 while creating the MapIO object and the
		  .cor exists
	Args	: none to get, OR string to set

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

   contigid
	Title	: contigid
	Usage	: my $ctg = $cloneobj->contigid();
	Function: Get/set the contig this clone belongs to
	Returns : scalar representing the contig
	Args	: none to get, OR string to set

   each_markerid
	Title	: each_markerid
	Usage	: @markers = $cloneobj->each_markerid();
	Function: retrieves all the elements in a map unordered
	Returns : list of strings (ids)
	Args	: none

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

   set_markers
	Title	: markers
	Usage	: $obj->set_markers($newval)
	Function: Set list of Marker ids (arrayref)
	Returns : None
	Args	: arrayref of strings (ids)

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

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