From 813f08cb0bee09f2c2934cc40387c0732a76dea0 Mon Sep 17 00:00:00 2001
From: Patrick Meidl <pm2@sanger.ac.uk>
Date: Wed, 30 May 2007 08:51:51 +0000
Subject: [PATCH] - added new methods: - current_version(): retrieves current
version of stable ID from db - is_current(): test if this is the current
version - get_latest_incarnation(): get latest incarnation of stable ID
from db - is_latest(): test if this is the latest version
- version() no longer lazy-loaded (now always set by adaptor)
- removed deprecated methods
---
modules/Bio/EnsEMBL/ArchiveStableId.pm | 175 +++++++++++++++++++------
1 file changed, 134 insertions(+), 41 deletions(-)
diff --git a/modules/Bio/EnsEMBL/ArchiveStableId.pm b/modules/Bio/EnsEMBL/ArchiveStableId.pm
index 4fcc6790df..855d550eff 100644
--- a/modules/Bio/EnsEMBL/ArchiveStableId.pm
+++ b/modules/Bio/EnsEMBL/ArchiveStableId.pm
@@ -83,6 +83,7 @@ use Bio::EnsEMBL::Utils::Exception qw(deprecate);
Arg [STABLE_ID] : String $stable_id
Arg [VERSION] : Int $version
+ Arg [CURRENT_VERSION] : Int $current_version
Arg [DB_NAME] : String $db_name
Arg [RELEASE] : String $release
Arg [ASSEMBLY_NAME] : String $assembly
@@ -105,12 +106,13 @@ sub new {
my $self = bless {}, $class;
- my ($stable_id, $version, $db_name, $release, $assembly, $type, $adaptor) =
- rearrange([qw( STABLE_ID VERSION DB_NAME RELEASE ASSEMBLY TYPE ADAPTOR)],
- @_ );
+ my ($stable_id, $version, $current_version, $db_name, $release, $assembly,
+ $type, $adaptor) = rearrange([qw( STABLE_ID VERSION CURRENT_VERSION DB_NAME
+ RELEASE ASSEMBLY TYPE ADAPTOR)], @_ );
$self->{'stable_id'} = $stable_id;
$self->{'version'} = $version;
+ $self->{'current_version'} = $current_version;
$self->{'db_name'} = $db_name;
$self->{'release'} = $release;
$self->{'assembly'} = $assembly;
@@ -130,6 +132,7 @@ sub new {
Arg [5] : String $assembly
Arg [6] : String $type - "Gene", "Transcript", "Translation", "Exon"
Arg [7] : Bio::EnsEMBL::DBSQL::ArchiveStableIdAdaptor $adaptor
+ Arg [8] : Int $current_version
Example : none
Description : faster version of above constructor
Returntype : Bio::EnsEMBL::ArchiveStableId
@@ -153,6 +156,7 @@ sub new_fast {
'assembly' => $_[4],
'type' => $_[5],
'adaptor' => $_[6],
+ 'current_version' => $_[7],
}, $class;
return $self;
@@ -178,8 +182,13 @@ sub new_fast {
sub get_history_tree {
my ($self, $num_high_scorers, $max_rows) = @_;
- return $self->adaptor->fetch_history_tree_by_stable_id(
- $self->stable_id, $num_high_scorers, $max_rows);
+
+ unless ($self->{'history'}) {
+ $self->{'history'} = $self->adaptor->fetch_history_tree_by_stable_id(
+ $self->stable_id, $num_high_scorers, $max_rows);
+ }
+
+ return $self->{'history'};
}
@@ -334,7 +343,114 @@ sub get_all_translation_archive_ids {
}
+=head2 current_version
+
+ Example : if (my $v = $arch_id->current_version) {
+ print "Current version of this stable ID: ", $v, "\n";
+ } else {
+ print "This stable ID is not in the current db.\n";
+ }
+ Description : Lazy-loads the current version of stable ID
+ Return type : Boolean (TRUE is current version found, else FALSE)
+ Exceptions : none
+ Caller : general
+ Status : At Risk
+ : under development
+
+=cut
+
+sub current_version {
+ my $self = shift;
+
+ if (@_) {
+ $self->{'current_version'} = shift;
+ } elsif (! defined $self->{'current_version'}) {
+ if (defined $self->{'adaptor'}) {
+ # lazy load
+ $self->{'adaptor'}->lookup_current($self);
+ }
+ }
+
+ return $self->{'current_version'};
+}
+
+
+=head2 is_current
+
+ Example : if ($arch_id->is_current) {
+ print $arch_id->version, " is the current version of this
+ stable ID.\n";
+ }
+ Description : Determines if the version of this object is the current version
+ of this stable ID.
+ Return type : Boolean (TRUE if it is current, else FALSE)
+ Exceptions : none
+ Caller : general
+ Status : At Risk
+ : under development
+
+=cut
+
+sub is_current {
+ my $self = shift;
+ return ($self->{'version'} == $self->{'current_version'});
+}
+
+
+=head2 get_latest_incarnation
+
+ Example : my $latest = $arch_id->get_latest_incarnation;
+ print "Latest version of ".$arch_id->stable_id." is ".
+ $latest->version."\n";
+ Description : Returns the ArchiveStableId representing the latest version
+ of this stable ID. Returns itself if this already is the latest
+ version, otherwise fetches it from the db.
+ Return type : Bio::EnsEMBL::ArchiveStableId
+ Exceptions : none
+ Caller : general
+ Status : At Risk
+ : under development
+
+=cut
+
+sub get_latest_incarnation {
+ my $self = shift;
+
+ return $self if ($self->is_latest);
+
+ my $latest = $self->adaptor->fetch_by_stable_id($self->stable_id);
+ return $latest;
+}
+
+
+=head2 is_latest
+
+ Arg[1] : (optional) Boolean $is_latest
+ Example : if ($arch_id->is_latest) {
+ print "Version ".$arch_id->version." is the latest version
+ of ".$arch_id->stable_id."\n";
+ }
+ Description : Indicates whether this is the latest version of this stable ID.
+ Can also be used as a setter if we know this is the latest
+ version.
+ Return type : Boolean (TRUE if yes, FALSE if no)
+ Exceptions : none
+ Caller : Bio::EnsEMBL::DBSQL::ArchiveStableIdAdaptor->fetch_by_stable_id, general
+ Status : At Risk
+ : under development
+
+=cut
+
+sub is_latest {
+ my $self = shift;
+ $self->{'is_latest'} = shift if (@_);
+ return ($self->{'is_latest'} || $self->is_current);
+}
+
+
+#
# getter/setters for attributes
+#
sub stable_id {
my $self = shift;
@@ -342,6 +458,12 @@ sub stable_id {
return $self->{'stable_id'};
}
+sub version {
+ my $self = shift;
+ $self->{'version'} = shift if (@_);
+ return $self->{'version'};
+}
+
sub db_name {
my $self = shift;
$self->{'db_name'} = shift if (@_);
@@ -360,53 +482,24 @@ sub assembly {
return $self->{'assembly'};
}
-sub adaptor {
- my $self = shift;
- $self->{'adaptor'} = shift if (@_);
- return $self->{'adaptor'};
-}
-
sub type {
my $self = shift;
$self->{'type'} = shift if (@_);
return $self->{'type'};
}
-sub successors {
+sub adaptor {
my $self = shift;
- $self->{'successors'} = \@_;
- return $self->{'successors'};
+ $self->{'adaptor'} = shift if (@_);
+ return $self->{'adaptor'};
}
-
-# lazy loading
-
-sub version {
+sub successors {
my $self = shift;
- if( @_ ) {
- $self->{'version'} = shift;
-
- } else {
- if( ! defined $self->{'version'} ) {
- if( defined $self->{'db_name'} && defined $self->{'adaptor'} ) {
- # lazy loading
- $self->{'adaptor'}->_lookup_version( $self );
- }
- }
- }
- return $self->{'version'};
-}
-
-
-# deprecated methods (changed to more descriptive names)
-
-sub get_translation_archive_id {
- my $self = shift;
-
- deprecate("Use get_all_translation_archive_ids() instead");
-
- return $self->get_all_translation_archive_ids;
+ $self->{'successors'} = \@_;
+ return $self->{'successors'};
}
1;
+
--
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