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Commit ae21ec7b authored by Simon Potter's avatar Simon Potter
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modules/Bio/EnsEMBL/Mapper/Coordinate.pm
+ 38
− 32
View file @ ae21ec7b
......@@ -2,7 +2,7 @@
#
# Ensembl module for Bio::EnsEMBL::MapperCoordinate
#
# Cared for by Ewan Birney <birney@ebi.ac.uk>
# Written by Ewan Birney <birney@ebi.ac.uk>
#
# Copyright GRL and EBI
#
......@@ -12,23 +12,25 @@
=head1 NAME
Bio::EnsEMBL::Mapper::Coordinate - DESCRIPTION of Object
Bio::EnsEMBL::Mapper::Coordinate
=head1 SYNOPSIS
Give standard usage here
=head1 DESCRIPTION
Describe the object here
Representation of a mapped region in a sequence; returned from
Mapper.pm when the target region maps on to valid sequence.
=head1 CONTACT
Ensembl - ensembl-dev@ebi.ac.uk
This module is part of the Ensembl project http://www.ensembl.org
Post general queries to B<ensembl-dev@ebi.ac.uk>
=head1 APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
......@@ -56,14 +58,15 @@ sub new {
return $self;
}
=head2 start
Title : start
Usage : $obj->start($newval)
Function:
Returns : value of start
Args : newvalue (optional)
=head2 start
Arg 1 int $start
start coordinate of object in mapped region
Function accessor method
Returntype int
Exceptions none
Caller Bio::EnsEMBL::Mapper::Coordinate
=cut
......@@ -77,14 +80,15 @@ sub start{
}
=head2 end
Title : end
Usage : $obj->end($newval)
Function:
Returns : value of end
Args : newvalue (optional)
=head2 end
Arg 1 int $end
end coordinate of object in mapped region
Function accessor method
Returntype int
Exceptions none
Caller Bio::EnsEMBL::Mapper::Coordinate
=cut
......@@ -98,14 +102,15 @@ sub end{
}
=head2 strand
Title : strand
Usage : $obj->strand($newval)
Function:
Returns : value of strand
Args : newvalue (optional)
=head2 strand
Arg 1 int $strand
strand of object in mapped region
Function accessor method
Returntype int
Exceptions none
Caller Bio::EnsEMBL::Mapper::Coordinate
=cut
......@@ -119,15 +124,16 @@ sub strand{
}
=head2 id
Title : id
Usage : $obj->id($newval)
Function:
Example :
Returns : value of id
Args : newvalue (optional)
=head2 id
Arg 1 char|int $id
id of object in mapped region
e.g. RawContig ID/chromosome name
Function accessor method
Returntype char|int
Exceptions none
Caller Bio::EnsEMBL::Mapper::Coordinate
=cut
......
modules/Bio/EnsEMBL/Mapper/Gap.pm
+ 21
− 24
View file @ ae21ec7b
......@@ -3,9 +3,9 @@
#
# Ensembl module for Bio::EnsEMBL::Mapper::Gap
#
# Cared for by Ewan Birney <birney@ebi.ac.uk>
# Written by Ewan Birney <birney@ebi.ac.uk>
#
# Copyright Ewan Birney
# Copyright GRL and EBI
#
# You may distribute this module under the same terms as perl itself
......@@ -13,27 +13,25 @@
=head1 NAME
Bio::EnsEMBL::Mapper::Gap - DESCRIPTION of Object
Bio::EnsEMBL::Mapper::Gap
=head1 SYNOPSIS
Give standard usage here
=head1 DESCRIPTION
Describe the object here
Representation of a gap in a sequence; returned from
Mapper.pm when the target region is in a gap.
=head1 AUTHOR - Ewan Birney
This modules is part of the Ensembl project http://www.ensembl.org
Email birney@ebi.ac.uk
Describe contact details here
Post general queries to B<ensembl-dev@ebi.ac.uk>
=head1 APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
......@@ -65,13 +63,12 @@ sub new {
=head2 start
Title : start
Usage : $obj->start($newval)
Function:
Example :
Returns : value of start
Args : newvalue (optional)
Arg 1 int $start
start coordinate of gap region
Function accessor method
Returntype int
Exceptions none
Caller Bio::EnsEMBL::Mapper::Gap
=cut
......@@ -84,15 +81,15 @@ sub start{
}
=head2 end
Title : end
Usage : $obj->end($newval)
Function:
Example :
Returns : value of end
Args : newvalue (optional)
=head2 end
Arg 1 int $end
end coordinate of gap region
Function accessor method
Returntype int
Exceptions none
Caller Bio::EnsEMBL::Mapper::Gap
=cut
......
modules/Bio/EnsEMBL/Mapper/Pair.pm
+ 29
− 40
View file @ ae21ec7b
......@@ -2,9 +2,9 @@
#
# Ensembl module for Bio::EnsEMBL::Mapper::Pair
#
# Cared for by Ewan Birney <birney@ebi.ac.uk>
# Written by Ewan Birney <birney@ebi.ac.uk>
#
# Copyright Ewan Birney
# Copyright GRL and EBI
#
# You may distribute this module under the same terms as perl itself
......@@ -12,27 +12,26 @@
=head1 NAME
Bio::EnsEMBL::Mapper::Pair - DESCRIPTION of Object
Bio::EnsEMBL::Mapper::Pair
=head1 SYNOPSIS
Give standard usage here
=head1 DESCRIPTION
Describe the object here
Two regions mapped between different coordinate systems are
each represented by a Bio::EnsEMBL::Mapper::Unit and joined
together as a Bio::EnsEMBL::Mapper::Pair.
=head1 AUTHOR - Ewan Birney
This modules is part of the Ensembl project http://www.ensembl.org
Email birney@ebi.ac.uk
This module is part of the Ensembl project http://www.ensembl.org
Describe contact details here
Post general queries to B<ensembl-dev@ebi.ac.uk>
=head1 APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
......@@ -62,19 +61,20 @@ sub new {
return $self;
}
=head2 to
Title : to
Usage : $obj->to($newval)
Function:
Example :
Returns : value of to
Args : newvalue (optional)
=head2 from, to
Arg 1 Bio::EnsEMBL::Mapper::Unit $seqobj
from and to represent the two regions
which are mapped to each other
Function accessor method
Returntype Bio::EnsEMBL::Mapper::Unit
Exceptions none
Caller Bio::EnsEMBL::Mapper::Pair
=cut
sub to{
sub to {
my ($self,$value) = @_;
if( defined $value) {
$self->{'to'} = $value;
......@@ -83,19 +83,7 @@ sub to{
}
=head2 from
Title : from
Usage : $obj->from($newval)
Function:
Example :
Returns : value of from
Args : newvalue (optional)
=cut
sub from{
sub from {
my ($self,$value) = @_;
if( defined $value) {
$self->{'from'} = $value;
......@@ -104,19 +92,20 @@ sub from{
}
=head2 ori
Title : ori
Usage : $obj->ori($newval)
Function:
Example :
Returns : value of ori
Args : newvalue (optional)
=head2 ori
Arg 1 Bio::EnsEMBL::Mapper::Unit $ori
Function accessor method
relative orientation of the the
two mapped regions
Returntype Bio::EnsEMBL::Mapper::Unit
Exceptions none
Caller Bio::EnsEMBL::Mapper::Pair
=cut
sub ori{
sub ori {
my ($self,$value) = @_;
if( defined $value) {
$self->{'ori'} = $value;
......
modules/Bio/EnsEMBL/Mapper/Unit.pm
+ 34
− 32
View file @ ae21ec7b
......@@ -2,9 +2,9 @@
#
# Ensembl module for Bio::EnsEMBL::Mapper::Unit
#
# Cared for by Ewan Birney <birney@ebi.ac.uk>
# Written by Ewan Birney <birney@ebi.ac.uk>
#
# Copyright Ewan Birney
# Copyright GRL and EBI
#
# You may distribute this module under the same terms as perl itself
......@@ -16,23 +16,22 @@ Bio::EnsEMBL::Mapper::Unit - One side of a map pair
=head1 SYNOPSIS
Give standard usage here
=head1 DESCRIPTION
Describe the object here
Two regions mapped between different coordinate systems are
each represented by a Bio::EnsEMBL::Mapper::Unit and joined
together as a Bio::EnsEMBL::Mapper::Pair.
=head1 AUTHOR - Ewan Birney
This modules is part of the Ensembl project http://www.ensembl.org
Email birney@ebi.ac.uk
This module is part of the Ensembl project http://www.ensembl.org
Describe contact details here
Post general queries to B<ensembl-dev@ebi.ac.uk>
=head1 APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
......@@ -62,15 +61,16 @@ sub new {
return $self;
}
=head2 id
Title : id
Usage : $obj->id($newval)
Function:
Example :
Returns : value of id
Args : newvalue (optional)
=head2 id
Arg 1 int|char $id
the id of the object (e.g. chromosome
or RawContig) which is mapped
Function accessor method
Returntype int|char
Exceptions none
Caller Bio::EnsEMBL::Mapper::Unit
=cut
......@@ -83,15 +83,16 @@ sub id{
}
=head2 start
Title : start
Usage : $obj->start($newval)
Function:
Example :
Returns : value of start
Args : newvalue (optional)
=head2 start
Arg 1 int $start
the start coordinate of the mapped
region which this object represents
Function accessor method
Returntype int
Exceptions none
Caller Bio::EnsEMBL::Mapper::Unit
=cut
......@@ -104,15 +105,16 @@ sub start{
}
=head2 end
Title : end
Usage : $obj->end($newval)
Function:
Example :
Returns : value of end
Args : newvalue (optional)
=head2 end
Arg 1 int $end
the end coordinate of the mapped
region which this object represents
Function accessor method
Returntype int
Exceptions none
Caller Bio::EnsEMBL::Mapper::Unit
=cut
......
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