#
# BioPerl module for Bio::Map::clone
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Sendu Bala <bix@sendu.me.uk>
#
# Copyright Gaurav Gupta
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::Map::Clone - An central map object representing a clone
=head1 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 L<Bio::Map::Position> and L<Bio::Map::PositionI> for more information.
=head1 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.
=head1 FEEDBACK
=head2 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
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<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.
=head2 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/
=head1 AUTHOR - Gaurav Gupta
Email gaurav@genome.arizona.edu
=head1 CONTRIBUTORS
Sendu Bala bix@sendu.me.uk
=head1 PROJECT LEADERS
Jamie Hatfield jamie@genome.arizona.edu
Dr. Cari Soderlund cari@genome.arizona.edu
=head1 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
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::Map::Clone;
use strict;
use Bio::Map::Position;
use base qw(Bio::Root::Root Bio::Map::MappableI);
=head2 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 => $endrange)
);
Function: Initialize a new Bio::Map::Clone object
Most people will not use this directly but get Clones
through L<Bio::MapIO::fpc>
Returns : L<Bio::Map::Clone> object
Args : -name => marker name string,
-markers => array ref of markers,
-contig => contig name string,
-type => type string,
-bands => band string,
-gel => gel string,
-group => group name string,
-remark => remark string,
-fpnumber=> FP number string,
-sequencetype => seq type string,
-sequencestatus=> seq status string,
-fpcremark => FPC remark,
-matche => array ref,
-matcha => array ref,
-matchp => array ref,
-range => L<Bio::Range> object,
=cut
sub new {
my ($class,@args) = @_;
my $self= $class->SUPER::new(@args);
my ($name,$markers,$contig,$type,$bands,$gel,$group,
$remark,$fpnumber,$seqtype,$seqstatus,$fpcremark,
$matche,$matcha,$matchp,
$range) = $self->_rearrange([qw(NAME MARKERS CONTIG TYPE
BANDS GEL GROUP REMARK FPNUMBER
SEQUENCETYPE SEQUENCESTATUS
FPCREMARK MATCHE MATCHA MATCHP
RANGE)],@args);
$self->name($name) if defined $name;
$self->markers($markers) if defined $markers;
$self->contigid($contig) if defined $contig;
$self->type($type) if defined $type;
$self->bands($bands) if defined $bands;
$self->gel($gel) if defined $gel;
$self->group($group) if defined $group;
$self->remark($remark) if defined $remark;
$self->fp_number($fpnumber) if defined $fpnumber;
$self->sequence_type($seqtype) if defined $seqtype;
$self->sequence_status($seqstatus) if defined $seqstatus;
$self->fpc_remark($fpcremark) if defined $fpcremark;
$self->range($range) if defined $range;
$self->set_match('approx', $matcha) if defined $matcha;
$self->set_match('pseudo', $matchp) if defined $matchp;
$self->set_match('exact', $matche) if defined $matche;
return $self;
}
=head1 Access Methods
These methods let you get and set the member variables
=head2 name
Title : name
Usage : my $name = $cloneobj->name();
Function: Get/set the name for this Clone
Returns : scalar representing the current name of this clone
Args : none to get, OR string to set
=cut
sub name {
my ($self) = shift;
return $self->{'_name'} = shift if @_;
return $self->{'_name'};
}
=head2 type
Title : type
Usage : my $type = $cloneobj->type();
Function: Get/set the type for this clone
Returns : scalar representing the current type of this clone
Args : none to get, OR string to set
=cut
sub type {
my ($self) = shift;
return $self->{'_type'} = shift if @_;
return $self->{'_type'};
}
=head2 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 = $contigobj->range()->end();
Args : none to get, OR Bio::Range to set
=cut
sub range {
my ($self) = shift;
return $self->{'_range'} = shift if @_;
return $self->{'_range'};
}
=head2 match
Title : match
Usage : @eclone = $cloneobj->match('exact');
@aclone = $cloneobj->match('approximate');
@pclone = $cloneobj->match('pseudo');
Function: get all matching clones
Returns : list
Args : scalar representing the type of clone to be
queried.
=cut
sub match {
my ($self,$type) = @_;
$type = "_match" . lc(substr($type, 0, 1));
return @{$self->{$type} || []};
}
=head2 each_match
Title : each_match
Function: Synonym of the match() method.
=cut
*each_match = \&match;
=head2 set_match
Title : set_match
Usage : $clone->set_match($type,$values);
Function: Set the Matches per type
Returns : None
Args : type (one of 'exact' 'approx' 'pseudo')
array ref of match values
=cut
sub set_match{
my ($self,$type,$val) = @_;
$type = "_match" . lc(substr($type, 0, 1));
$self->{$type} = $val;
}
=head2 gel
Title : gel
Usage : $clonegel = $cloneobj->gel();
Function: Get/set the gel number for this clone
Returns : scalar representing the gel number of this clone
Args : none to get, OR string to set
=cut
sub gel {
my ($self) = shift;
return $self->{'_gel'} = shift if @_;
return $self->{'_gel'};
}
=head2 remark
Title : remark
Usage : $cloneremark = $cloneobj->remark();
Function: Get/set the remark for this clone
Returns : scalar representing the current remark of this clone
Args : none to get, OR string to set
=cut
sub remark {
my ($self) = shift;
return $self->{'_remark'} = shift if @_;
return $self->{'_remark'};
}
=head2 fp_number
Title : fp_number
Usage : $clonefpnumber = $cloneobj->fp_number();
Function: Get/set the fp number for this clone
Returns : scalar representing the fp number of this clone
Args : none to get, OR string to set
=cut
sub fp_number {
my ($self) = shift;
return $self->{'_fpnumber'} = shift if @_;
return $self->{'_fpnumber'};
}
=head2 sequence_type
Title : sequence_type
Usage : $cloneseqtype = $cloneobj->sequence_type();
Function: Get/set the sequence type for this clone
Returns : scalar representing the sequence type of this clone
Args : none to get, OR string to set
=cut
sub sequence_type {
my ($self) = shift;
return $self->{'_sequencetype'} = shift if @_;
return $self->{'_sequencetype'};
}
=head2 sequence_status
Title : sequence_status
Usage : $cloneseqstatus = $cloneobj->sequence_status();
Function: Get/set the sequence status for this clone
Returns : scalar representing the sequence status of this clone
Args : none to get, OR string to set
=cut
sub sequence_status {
my ($self) = shift;
return $self->{'_sequencestatus'} = shift if @_;
return $self->{'_sequencestatus'};
}
=head2 fpc_remark
Title : fpc_remark
Usage : $clonefpcremark = $cloneobj->fpc_remark();
Function: Get/set the fpc remark for this clone
Returns : scalar representing the fpc remark of this clone
Args : none to get, OR string to set
=cut
sub fpc_remark {
my ($self) = shift;
return $self->{'_fpcremark'} = shift if @_;
return $self->{'_fpcremark'};
}
=head2 bands
Title : bands
Usage : @clonebands = $cloneobj->bands();
Function: Get/set the bands for this clone
Returns : liat representing the band of this clone, if
readcor = 1 while creating the MapIO object and the
.cor exists
Args : none to get, OR string to set
=cut
sub bands {
my ($self) = shift;
return $self->{'_bands'} = shift if @_;
return $self->{'_bands'};
}
=head2 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
=cut
sub group {
my ($self) = shift;
return $self->{'_group'} = shift if @_;
return $self->{'_group'};
}
=head2 contigid
Title : contigid
Usage : my $ctg = $cloneobj->contigid();
Function: Get/set the contig this clone belongs to
Returns : scalar representing the contig
Args : none to get, OR string to set
=cut
sub contigid {
my ($self) = shift;
$self->{'_contig'} = shift if @_;
return $self->{'_contig'} || 0;
}
=head2 each_markerid
Title : each_markerid
Usage : @markers = $cloneobj->each_markerid();
Function: retrieves all the elements in a map unordered
Returns : list of strings (ids)
Args : none
*** This only supplies the ids set with the set_markers method ***
*** It has nothing to do with actual Bio::Map::MarkerI objects ***
=cut
sub each_markerid {
my ($self,$value) = @_;
return @{$self->{"_markers"}};
}
=head2 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 ***
=cut
sub set_markers {
my ($self,$markers) = @_;
if( defined $markers && ref($markers) =~ /ARRAY/ ) {
$self->{'_markers'} = $markers;
}
}
1;