From cb07a1144007815716defa3ee60f43f075e90967 Mon Sep 17 00:00:00 2001
From: Ian Longden <ianl@sanger.ac.uk>
Date: Mon, 15 Aug 2005 10:35:08 +0000
Subject: [PATCH] Mapper methods basically all set to be stable.
---
modules/Bio/EnsEMBL/Mapper/Coordinate.pm | 49 +++++++++++++++++++--
modules/Bio/EnsEMBL/Mapper/Gap.pm | 4 ++
modules/Bio/EnsEMBL/Mapper/Pair.pm | 2 +
modules/Bio/EnsEMBL/Mapper/RangeRegistry.pm | 3 ++
modules/Bio/EnsEMBL/Mapper/Unit.pm | 3 ++
5 files changed, 57 insertions(+), 4 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Mapper/Coordinate.pm b/modules/Bio/EnsEMBL/Mapper/Coordinate.pm
index b059963605..ee61da4977 100644
--- a/modules/Bio/EnsEMBL/Mapper/Coordinate.pm
+++ b/modules/Bio/EnsEMBL/Mapper/Coordinate.pm
@@ -35,6 +35,22 @@ package Bio::EnsEMBL::Mapper::Coordinate;
use vars qw(@ISA);
use strict;
+=head2 new
+
+ Arg [1] char|int id of object in mapped region
+ Arg [2] int start of region
+ Arg [3] int end of region
+ Arg [4] int strand if region
+ Arg [5] Bio::EnsEMBL::CoordSystem coordsytem of the region
+ Function creates a new Coordinate object
+ Returntype Bio::EnsEMBL::Mapper::Coordinate
+ Exceptions none
+ Status Stable
+
+=cut
+
+
+
sub new {
my($class, $id, $start, $end, $strand, $coord_system) = @_;
@@ -50,10 +66,11 @@ sub new {
Arg 1 int $start
start coordinate of object in mapped region
- Function accessor method
+ Function getter/setter method
Returntype int
Exceptions none
Caller Bio::EnsEMBL::Mapper::Coordinate
+ Status Stable
=cut
@@ -68,10 +85,11 @@ sub start{
Arg 1 int $end
end coordinate of object in mapped region
- Function accessor method
+ Function getter/setter method
Returntype int
Exceptions none
Caller Bio::EnsEMBL::Mapper::Coordinate
+ Status Stable
=cut
@@ -86,10 +104,11 @@ sub end{
Arg 1 int $strand
strand of object in mapped region
- Function accessor method
+ Function getter/setter method
Returntype int
Exceptions none
Caller Bio::EnsEMBL::Mapper::Coordinate
+ Status Stable
=cut
@@ -105,10 +124,11 @@ sub strand{
Arg 1 char|int $id
id of object in mapped region
e.g. seq_region_id / seq_region_name
- Function accessor method
+ Function getter/setter method
Returntype char|int
Exceptions none
Caller Bio::EnsEMBL::Mapper::Coordinate
+ Status Stable
=cut
@@ -119,12 +139,33 @@ sub id{
}
+=head2 coord_system
+
+ Arg 1 Bio::EnsEMBL::CoordSystem
+ Function getter/setter method
+ Returntype Bio::EnsEMBL::CoordSystem
+ Exceptions none
+ Caller Bio::EnsEMBL::Mapper::Coordinate
+ Status Stable
+
+=cut
+
sub coord_system {
my $self = shift;
$self->{'coord_system'} = shift if(@_);
return $self->{'coord_system'};
}
+=head2 length
+
+ Function getter method
+ Returntype int
+ Exceptions none
+ Caller ?
+ Status Stable
+
+=cut
+
sub length {
my $self = shift;
return $self->{'end'} - $self->{'start'} + 1;
diff --git a/modules/Bio/EnsEMBL/Mapper/Gap.pm b/modules/Bio/EnsEMBL/Mapper/Gap.pm
index b22cc7899a..eb1e388433 100644
--- a/modules/Bio/EnsEMBL/Mapper/Gap.pm
+++ b/modules/Bio/EnsEMBL/Mapper/Gap.pm
@@ -45,6 +45,7 @@ use strict;
Returntype : Bio::EnsEMBL::Mapper::Gap
Exceptions : none
Caller : Bio::EnsEMBL::Mapper
+ Status : Stable
=cut
@@ -66,6 +67,7 @@ sub new {
Returntype : int
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -88,6 +90,7 @@ sub start{
Returntype : string
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -108,6 +111,7 @@ sub end{
Returntype : int
Exceptions : none
Caller : general
+ Status : Stable
=cut
diff --git a/modules/Bio/EnsEMBL/Mapper/Pair.pm b/modules/Bio/EnsEMBL/Mapper/Pair.pm
index 40015a1e55..14c9a04af5 100644
--- a/modules/Bio/EnsEMBL/Mapper/Pair.pm
+++ b/modules/Bio/EnsEMBL/Mapper/Pair.pm
@@ -52,6 +52,7 @@ sub new {
Returntype Bio::EnsEMBL::Mapper::Unit
Exceptions none
Caller Bio::EnsEMBL::Mapper::Pair
+ Status : Stable
=cut
@@ -83,6 +84,7 @@ sub from {
Returntype Bio::EnsEMBL::Mapper::Unit
Exceptions none
Caller Bio::EnsEMBL::Mapper::Pair
+ Status : Stable
=cut
diff --git a/modules/Bio/EnsEMBL/Mapper/RangeRegistry.pm b/modules/Bio/EnsEMBL/Mapper/RangeRegistry.pm
index 205743b215..966a0ea9a1 100644
--- a/modules/Bio/EnsEMBL/Mapper/RangeRegistry.pm
+++ b/modules/Bio/EnsEMBL/Mapper/RangeRegistry.pm
@@ -73,6 +73,7 @@ use integer;
Returntype : Bio::EnsEMBL::Mapper::RangeRegistry
Exceptions : none
Caller : AssemblyMapperAdaptor
+ Status : Stable
=cut
@@ -124,6 +125,7 @@ sub flush {
throw if end is less than start
throw if id, start, or end are not defined
Caller : AssemblyMapperAdaptor
+ Status : Stable
=cut
@@ -274,6 +276,7 @@ sub check_and_register {
Returntype : int
Exceptions : none
Caller : general
+ Status : Stable
=cut
diff --git a/modules/Bio/EnsEMBL/Mapper/Unit.pm b/modules/Bio/EnsEMBL/Mapper/Unit.pm
index 13ff5b6c3e..7e36eb119d 100644
--- a/modules/Bio/EnsEMBL/Mapper/Unit.pm
+++ b/modules/Bio/EnsEMBL/Mapper/Unit.pm
@@ -52,6 +52,7 @@ sub new {
Returntype int|char
Exceptions none
Caller Bio::EnsEMBL::Mapper::Unit
+ Status Stable
=cut
@@ -74,6 +75,7 @@ sub id{
Returntype int
Exceptions none
Caller Bio::EnsEMBL::Mapper::Unit
+ Status Stable
=cut
@@ -96,6 +98,7 @@ sub start{
Returntype int
Exceptions none
Caller Bio::EnsEMBL::Mapper::Unit
+ Status Stable
=cut
--
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