From ae21ec7b3c6766d8641813c4bbbe3ecbd6fafd86 Mon Sep 17 00:00:00 2001
From: Simon Potter <scp@sanger.ac.uk>
Date: Fri, 1 Mar 2002 16:52:49 +0000
Subject: [PATCH] pod changes
---
modules/Bio/EnsEMBL/Mapper/Coordinate.pm | 70 +++++++++++++-----------
modules/Bio/EnsEMBL/Mapper/Gap.pm | 45 +++++++--------
modules/Bio/EnsEMBL/Mapper/Pair.pm | 69 ++++++++++-------------
modules/Bio/EnsEMBL/Mapper/Unit.pm | 66 +++++++++++-----------
4 files changed, 122 insertions(+), 128 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Mapper/Coordinate.pm b/modules/Bio/EnsEMBL/Mapper/Coordinate.pm
index b2c17900b3..65b2a781b2 100644
--- a/modules/Bio/EnsEMBL/Mapper/Coordinate.pm
+++ b/modules/Bio/EnsEMBL/Mapper/Coordinate.pm
@@ -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
diff --git a/modules/Bio/EnsEMBL/Mapper/Gap.pm b/modules/Bio/EnsEMBL/Mapper/Gap.pm
index 9ee3615e37..b234adbaa3 100644
--- a/modules/Bio/EnsEMBL/Mapper/Gap.pm
+++ b/modules/Bio/EnsEMBL/Mapper/Gap.pm
@@ -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
diff --git a/modules/Bio/EnsEMBL/Mapper/Pair.pm b/modules/Bio/EnsEMBL/Mapper/Pair.pm
index 10e6da10a2..f3b4be7576 100644
--- a/modules/Bio/EnsEMBL/Mapper/Pair.pm
+++ b/modules/Bio/EnsEMBL/Mapper/Pair.pm
@@ -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;
diff --git a/modules/Bio/EnsEMBL/Mapper/Unit.pm b/modules/Bio/EnsEMBL/Mapper/Unit.pm
index 754d0f1137..eae6fff107 100644
--- a/modules/Bio/EnsEMBL/Mapper/Unit.pm
+++ b/modules/Bio/EnsEMBL/Mapper/Unit.pm
@@ -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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