#
# BioPerl module for Bio::Map::fpcmarker
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Gaurav Gupta <gaurav@genome.arizona.edu>
#
# 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::FPCMarker - An central map object representing a marker
=head1 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\n";
}
# find the position of this marker in $contig
print "Position in contig $contig"," = ",$markerobj->position($contig),
"\n";
# find the group of the marker
print "Group : ",$markerobj->group();
See L<Bio::Map::Position> and L<Bio::Map::PositionI> for more information.
=head1 DESCRIPTION
This object handles the notion of a marker.
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://github.com/bioperl/bioperl-live/issues
=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::FPCMarker;
use strict;
use Bio::Map::Position;
use Time::Local;
use base qw(Bio::Root::Root Bio::Map::MappableI);
=head2 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 => $remark
);
Function: Initialize a new Bio::Map::FPCMarker object
Most people will not use this directly but get Markers
through L<Bio::MapIO::fpc>
Returns : L<Bio::Map::FPCMarker> object
Args : -name => marker name string,
-type => type string,
-global => global position for marker,
-frame => boolean if marker is framework or placement,
-group => group number for marker,
-subgroup => subgroup number of marker,
-anchor => boolean if marker is anchored,
-clones => all the clone elements in map (hashref),
-contigs => all the contig elements (hasref),
-position => mapping of marker names to map position (hasref),
-remark => remarks, separated by newlines
=cut
sub new {
my ($class,@args) = @_;
my $self= $class->SUPER::new(@args);
my ($name,$type,$global,$frame,$group,
$subgroup, $anchor, $clones,$contigs,
$positions, $remark) = $self->_rearrange([qw(NAME TYPE GLOBAL FRAME
GROUP SUBGROUP ANCHOR
CLONES CONTIGS POSITIONS REMARK)],@args);
$self->name($name) if defined $name;
$self->type($type) if defined $type;
$self->global($global) if defined $global;
$self->group($group) if defined $group;
$self->subgroup($group) if defined $subgroup;
$self->anchor($anchor) if defined $anchor;
$self->remark($remark) if defined $remark;
$self->set_clones($clones) if defined $clones;
$self->set_contigs($contigs) if defined $contigs;
$self->set_positions($positions) if defined $positions;
return $self;
}
=head1 Access Methods
These methods let you get and set the member variables
=head2 name
Title : name
Usage : my $name = $markerobj->name();
Function: Get/set the name for this marker
Returns : scalar representing the current name of this marker
Args : none to get, OR string to set
=cut
sub name {
my ($self) = shift;
return $self->{'_name'} = shift if @_;
return $self->{'_name'};
}
=head2 type
Title : type
Usage : my $type = $markerobj->type();
Function: Get/set the type for this marker
Returns : scalar representing the current type of this marker
Args : none to get, OR string to set
=cut
sub type {
my ($self) = shift;
return $self->{'_type'} = shift if @_;
return $self->{'_type'};
}
=head2 global
Title : global
Usage : my $type = $markerobj->global();
Function: Get/set the global position for this marker
Returns : scalar representing the current global position of this marker
Args : none to get, OR string to set
=cut
sub global {
my ($self) = shift;
return $self->{'_global'} = shift if @_;
return $self->{'_global'};
}
=head2 anchor
Title : anchor
Usage : my $anchor = $markerobj->anchor();
Function: indicate if the Marker is anchored or not (True | False)
Returns : scalar representing the anchor (1 | 0) for this marker
Args : none to get, OR 1|0 to set
=cut
sub anchor {
my ($self) = shift;
return $self->{'_anchor'} = shift if @_;
return $self->{'_anchor'};
}
=head2 framework
Title : framework
Usage : $frame = $markerobj->framework();
Function: indicate if the Marker is framework or placement (1 | 0)
Returns : scalar representing if the marker is framework
(1 if framework, 0 if placement)
Args : none to get, OR 1|0 to set
=cut
sub framework {
my ($self) = shift;
return $self->{'_frame'} = shift if @_;
return $self->{'_frame'};
}
=head2 group
Title : group
Usage : $grpno = $markerobj->group();
Function: Get/set the group number for this marker. This is a generic term,
used for Linkage-Groups as well as for Chromosomes.
Returns : scalar representing the group number of this marker
Args : none to get, OR string to set
=cut
sub group {
my ($self) = shift;
$self->{'_group'} = shift if @_;
return $self->{'_group'} || 0;
}
=head2 subgroup
Title : subgroup
Usage : $subgroup = $marker->subgroup();
Function: Get/set the subgroup for this marker. This is a generic term:
subgroup here could represent subgroup of a Chromosome or of a
Linkage Group. The user must take care of which subgroup he/she is
querying for.
Returns : scalar representing the subgroup of this marker
Args : none to get, OR string to set
=cut
sub subgroup {
my ($self) = shift;
$self->{'_subgroup'} = shift if @_;
return $self->{'_subgroup'} || 0;
}
=head2 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 : $ctg is necessary to look for the position of the marker
in that contig.
*** This has nothing to do with an actual Bio::Map::PositionI object ***
=cut
sub position {
my ($self,$ctg) = @_;
return 0 unless defined $ctg;
return 0 unless( defined $self->{'_position'} &&
defined $self->{'_position'}{$ctg});
return $self->{'_position'}{$ctg};
}
=head2 remark
Title : remark
Usage : $markerremark = $markerobj->remark();
Function: get the remarks for this marker
Returns : scalar of newline-separated markers
Args : none
=cut
sub remark {
my ($self) = shift;
return $self->{'_remark'} = shift if @_;
return $self->{'_remark'};
}
=head2 each_cloneid
Title : each_cloneid
Usage : my @clones = $map->each_cloneid();
Function: retrieves all the clone ids in a map unordered
Returns : list of strings (ids)
Args : none
*** This only supplies the ids set with the set_clones method ***
*** It has nothing to do with actual Bio::Map::MappableI objects ***
=cut
sub each_cloneid {
my ($self) = @_;
return $self->_each_element('clones');
}
=head2 each_contigid
Title : each_contigid
Usage : my @contigs = $map->each_contigid();
Function: retrieves all the contig ids in a map unordered
Returns : list of strings (ids)
Args : none
*** This only supplies the ids set with the set_contigs method ***
*** It has nothing to do with actual Bio::Map::MapI objects ***
=cut
sub each_contigid {
my ($self) = @_;
return $self->_each_element('contigs');
}
sub _each_element{
my ($self, $type) = @_;
$type = 'clones' unless defined $type;
$type = lc("_$type");
return keys %{$self->{$type} || {}};
}
=head2 set_clones
Title : set_clones
Usage : $marker->set_clones(\%clones)
Function: Set the clone ids hashref
Returns : None
Args : Hashref of clone ids
*** This only sets a hash of ids ***
*** It has nothing to do with actual Bio::Map::MappableI objects ***
=cut
sub set_clones{
my ($self,$clones) = @_;
if( defined $clones && ref($clones) =~ /HASH/ ) {
$self->{'_clones'} = $clones;
}
}
=head2 set_contigs
Title : set_contigs
Usage : $marker->set_contigs(\%contigs)
Function: Set the contig ids hashref
Returns : None
Args : Hashref of contig ids
*** This only sets a hash of ids ***
*** It has nothing to do with actual Bio::Map::MapI objects ***
=cut
sub set_contigs{
my ($self,$contigs) = @_;
if( defined $contigs && ref($contigs) =~ /HASH/ ) {
$self->{'_contigs'} = $contigs;
}
}
=head2 set_positions
Title : set_positions
Usage : $marker->set_positions(\%markerpos)
Function: Set the positions hashref
Returns : None
Args : Hashref of marker positions
*** This only sets a hash of numbers ***
*** It has nothing to do with actual Bio::Map::PositionI objects ***
=cut
sub set_positions{
my ($self,$pos) = @_;
if( defined $pos && ref($pos) =~ /HASH/ ) {
$self->{'_positions'} = $pos;
}
}
1;