Raw content of Bio::EnsEMBL::Analysis::Tools::Pmatch::CoordPair
<![CDATA[# holds a Coordinate Pair; name of the protein and contig that are hit (as a cross check) and
# the start and end positions of the
package Bio::EnsEMBL::Analysis::Tools::Pmatch::CoordPair;
use Bio::EnsEMBL::Utils::Exception qw(throw warning);
use Bio::EnsEMBL::Utils::Argument qw( rearrange );
@ISA = qw();
=head2 new
Title : new
Usage :
Function: constructor
Example :
Returns :
Args :
=cut
sub new {
my ($class, @args) = @_;
my $self = bless {}, $class;
my ($query, $target, $qstart, $qend, $tstart, $tend, $percent, $strand) =
rearrange(['QUERY',
'TARGET',
'QSTART',
'QEND',
'TSTART',
'TEND',
'PERCENT',
'STRAND'],@args);
throw("No query") unless defined $query;
$self->query($query);
throw("No target") unless defined $target;
$self->target($target);
throw("No query start") unless defined $qstart;
$self->qstart($qstart);
throw("No query end") unless defined $qend;
$self->qend($qend);
throw("No target start") unless defined $tstart;
$self->tstart($tstart);
throw("No target end") unless defined $tend;
$self->tend($tend);
throw("No percent") unless defined $percent;
$self->percent($percent);
throw("No strand") unless defined $strand;
$self->strand($strand);
return $self;
}
=head2 query
Title : query
Usage :
Function: get/set for query (contig name)
Example :
Returns :
Args :
=cut
sub query {
my ($self,$arg) = @_;
if ($arg) {
$self->{'query'} = $arg;
}
return $self->{'query'};
}
=head2 target
Title : target
Usage :
Function: get/set for target (protein name)
Example :
Returns :
Args :
=cut
sub target {
my ($self,$arg) = @_;
if ($arg) {
$self->{'target'} = $arg;
}
return $self->{'target'};
}
sub qstart {
my ($self,$arg) = @_;
if ($arg) {
$self->{'qstart'} = $arg;
}
return $self->{'qstart'};
}
sub qend {
my ($self,$arg) = @_;
if ($arg) {
$self->{'qend'} = $arg;
}
return $self->{'qend'};
}
sub tstart {
my ($self,$arg) = @_;
if ($arg) {
$self->{'tstart'} = $arg;
}
return $self->{'tstart'};
}
sub tend {
my ($self,$arg) = @_;
if ($arg) {
$self->{'tend'} = $arg;
}
return $self->{'tend'};
}
sub percent {
my ($self,$arg) = @_;
if ($arg) {
$self->{'percent'} = $arg;
}
return $self->{'percent'};
}
sub strand {
my ($self,$arg) = @_;
if ($arg) {
$self->{'strand'} = $arg;
}
return $self->{'strand'};
}
1;
]]>