From 2f47cd46c8f2679b3bee1f8b64fbbc6b00860abc Mon Sep 17 00:00:00 2001
From: Graham McVicker <mcvicker@sanger.ac.uk>
Date: Mon, 14 Apr 2003 09:20:24 +0000
Subject: [PATCH] updated POD for display_xref methods, removed species methods
---
modules/Bio/EnsEMBL/Gene.pm | 49 +++++--------------------------
modules/Bio/EnsEMBL/Transcript.pm | 42 +++-----------------------
2 files changed, 11 insertions(+), 80 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Gene.pm b/modules/Bio/EnsEMBL/Gene.pm
index bf62951b08..59cdf64f6a 100755
--- a/modules/Bio/EnsEMBL/Gene.pm
+++ b/modules/Bio/EnsEMBL/Gene.pm
@@ -810,10 +810,10 @@ sub _dump{
=head2 transform
Arg 1 : (optional) Bio::EnsEMBL::Slice $slice
-
Description: when passed a Slice as argument,
it will transform this Gene to the Slice coordinate system.
- Without an argument it transforms the Gene (which should be in a slice) to a RawContig
+ Without an argument it transforms the Gene (which should be
+ in a slice) to a RawContig
coordinate system.
The method changes the Gene in place and returns itself.
Returntype : Bio::EnsEMBL::Gene
@@ -845,7 +845,6 @@ sub transform {
# re-jiggle the exons
$transcript->transform( \%exon_transforms );
-
}
#unset the start, end, and strand - they need to be recalculated
@@ -883,46 +882,12 @@ sub temporary_id {
}
-
-
-=head2 species
-
- Arg [1] : optional Bio::Species $species
- Example : none
- Description: You can set the species for this gene if you want to use species
- specific behaviour. Otherwise species is retrieved from attached
- database.
- Returntype : Bio::Species
- Exceptions : none
- Caller : external_name, external_db, general for setting
-
-=cut
-
-
-sub species {
- my ( $self, $species ) = @_;
-
- if( defined $species ) {
- $self->{species} = $species;
- } else {
- if( ! exists $self->{species} ) {
- if( defined $self->adaptor() ) {
- $self->{species} = $self->adaptor()->db->get_MetaContainer()
- ->get_Species();
- }
- }
- }
-
- return $self->{species};
-}
-
-
=head2 display_xref
- Arg [1] : int $display_xref_id
- Example : $gene->display_xref(42);
- Description: get/set/lazy_loaded display_xref_id for this gene
- Returntype : int
+ Arg [1] : Bio::EnsEMBL::DBEntry $display_xref
+ Example : $gene->display_xref($db_entry);
+ Description: get/set/lazy_loaded display_xref for this gene
+ Returntype : Bio::EnsEMBL::DBEntry
Exceptions : none
Caller : general
@@ -937,7 +902,7 @@ sub display_xref {
return $self->{'display_xref'};
} elsif ( defined $self->adaptor() ) {
$self->{'display_xref'} = $self->adaptor->get_display_xref( $self );
- }
+ }
return $self->{'display_xref'};
}
diff --git a/modules/Bio/EnsEMBL/Transcript.pm b/modules/Bio/EnsEMBL/Transcript.pm
index b6d04396c9..ce566602e5 100755
--- a/modules/Bio/EnsEMBL/Transcript.pm
+++ b/modules/Bio/EnsEMBL/Transcript.pm
@@ -274,10 +274,10 @@ sub adaptor {
=head2 display_xref
- Arg [1] : int $display_xref_id
- Example : $transcript->display_xref(42);
- Description: get/set/lazy_loaded display_xref_id for this transcript
- Returntype : int
+ Arg [1] : Bio::EnsEMBL::DBEntry $display_xref
+ Example : $transcript->display_xref(Bio::EnsEMBL::DBEntry->new(...));
+ Description: get/set/lazy_loaded display_xref for this transcript
+ Returntype : Bio::EnsEMBL::DBEntry
Exceptions : none
Caller : general
@@ -1800,40 +1800,6 @@ sub transform {
}
-
-=head2 species
-
- Arg [1] : optional Bio::Species $species
- Example : none
- Description: You can set the species for this gene if you want to use species
- specific behaviour. Otherwise species is retrieved from attached
- database.
- Returntype : Bio::Species
- Exceptions : none
- Caller : external_name, external_db, general for setting
-
-=cut
-
-
-sub species {
- my ( $self, $species ) = @_;
-
- if( defined $species ) {
- $self->{species} = $species;
- } else {
- if( ! exists $self->{species} ) {
- if( defined $self->adaptor() ) {
- $self->{species} = $self->adaptor()->db->get_MetaContainer()
- ->get_Species();
- }
- }
- }
-
- return $self->{species};
-}
-
-
-
=head2 coding_start
Arg [1] : none
--
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