Provided by: libbio-perl-perl_1.6.923-1_all 
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\n";
}
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 ***