diff variant_effect_predictor/Bio/EnsEMBL/DBEntry.pm @ 0:2bc9b66ada89 draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/EnsEMBL/DBEntry.pm	Thu Apr 11 06:29:17 2013 -0400
@@ -0,0 +1,715 @@
+=head1 LICENSE
+
+  Copyright (c) 1999-2012 The European Bioinformatics Institute and
+  Genome Research Limited.  All rights reserved.
+
+  This software is distributed under a modified Apache license.
+  For license details, please see
+
+    http://www.ensembl.org/info/about/code_licence.html
+
+=head1 CONTACT
+
+  Please email comments or questions to the public Ensembl
+  developers list at <[e-mail]>.
+
+  Questions may also be sent to the Ensembl help desk at
+  <[e-mail]>.
+
+=cut
+
+=head1 NAME
+
+Bio::EnsEMBL::DBEntry -
+Object representing an external reference (xref)
+
+=head1 DESCRIPTION
+
+This object holds information about external references (xrefs) to
+Ensembl objects.
+
+=head1 METHODS
+
+=cut
+
+package Bio::EnsEMBL::DBEntry;
+
+use strict;
+use warnings;
+no warnings qw(uninitialized);
+
+use Bio::EnsEMBL::Storable;
+use Bio::Annotation::DBLink;
+
+use Bio::EnsEMBL::Utils::Argument qw(rearrange);
+use Bio::EnsEMBL::Utils::Exception qw(deprecate);
+use Scalar::Util qw(weaken isweak);
+
+our @ISA = qw(Bio::EnsEMBL::Storable Bio::Annotation::DBLink);
+
+
+=head2 new_fast
+
+  Arg [1]    : Hashref $hashref - hash reference to bless as new DBEntry object
+  Description: A very quick constructor that requires internal knowledge of
+               the class. This is used in speed critical sections of the code
+               where many objects need to be created quickly.
+  Returntype : Bio::EnsEMBL::DBEntry
+  Exceptions : none
+  Caller     : general
+  Status     : Stable
+
+=cut
+
+sub new_fast {
+  my $class = shift;
+  my $hashref = shift;
+  my $self = bless $hashref, $class;
+  weaken($self->{adaptor})  if ( ! isweak($self->{adaptor}) );
+  return $self;
+}
+
+
+=head2 new
+
+  Args [...] : list of named parameters 
+  Example    : my $dbentry = new Bio::EnsEMBL::DBEntry(
+                    -adaptor => $adaptor,
+                    -primary_id => $pid,
+                    -version => $version,
+                    -dbname  => $dbname,
+                    -release => $release,
+                    -display_id => $did,
+                    -description => $description,
+                    -priority => $priority,
+                    -db_display_name => $db_display_name,
+                    -info_type => $info_type,
+                    -info_text => $info_text,
+                    -type => $type,
+                    -secondary_db_name => $secondary_db_name,
+                    -secondary_db_table => $secondary_db_table
+		    -linkage_annotation => $object_xref_text);
+  Description: Creates a new DBEntry object
+  Returntype : Bio::EnsEMBL::DBEntry
+  Exceptions : none
+  Caller     : Bio::EnsEMBL::DBEntryAdaptor
+  Status     : At Risk
+               Due to 'PRIORITY',
+              'INFO_TYPE', 'INFO_TEXT', ''DB_DISPLAY_NAME', 'TYPE',
+              'SECONDARY_DB_NAME', 'SECONDARY_DB_TABLE'
+               being under development - if you don't use any of these the
+               method can be considered Stable
+
+=cut
+
+sub new {
+  my ($class, @args) = @_;
+  
+  my $self = bless {},$class;
+
+  my ( $adaptor, $dbID, $primary_id, $version,
+       $dbname, $release, $display_id, $description,
+       $priority,
+       $db_display_name, $info_type, $info_text, $type,
+       $secondary_db_name, $secondary_db_table, $link_annotation, $analysis) =
+    rearrange ( ['ADAPTOR','DBID','PRIMARY_ID','VERSION',
+                 'DBNAME','RELEASE','DISPLAY_ID','DESCRIPTION',
+		 'PRIORITY',
+		 'DB_DISPLAY_NAME', 'INFO_TYPE', 'INFO_TEXT', 'TYPE',
+                 'SECONDARY_DB_NAME', 'SECONDARY_DB_TABLE', 'LINKAGE_ANNOTATION', 'ANALYSIS'], @args );
+
+  $self->adaptor($adaptor);
+  $self->{'dbID'}    = $dbID;
+
+  if( defined $primary_id ) { $self->primary_id( $primary_id ) }
+  if( defined $version ) { $self->version( $version ) } else
+    { $self->version( 0 ); }
+  if( defined $dbname ) { $self->dbname( $dbname ) }
+  if( defined $release) { $self->release( $release ) }
+  if( defined $display_id) { $self->display_id( $display_id ) }
+  if( defined $description) { $self->description($description) }
+  if( defined $priority) { $self->priority($priority) }
+  if( defined $db_display_name) { $self->db_display_name($db_display_name) }
+  if( defined $info_type) { $self->info_type($info_type) }
+  if( defined $info_text) { $self->info_text($info_text) }
+  if( defined $type) { $self->type($type) }
+  if( defined $secondary_db_name) { $self->secondary_db_name($secondary_db_name) }
+  if( defined $secondary_db_table) { $self->secondary_db_table($secondary_db_table) }
+
+  $self->linkage_annotation($link_annotation) if defined $link_annotation;
+  $self->analysis($analysis) if defined $analysis;
+
+
+  return $self;
+}
+
+
+=head2 primary_id
+
+  Arg [1]    : (optional) String $arg - value to set
+  Example    : none
+  Description: Getter/setter for attribute 'primary_id'.
+               This is the object's primary id in the external database.
+  Returntype : String
+  Exceptions : none
+  Caller     : general
+  Status     : Stable
+
+=cut
+
+sub primary_id {
+  my ( $self, $arg ) = @_;
+  if( defined $arg ) {
+    $self->{primary_id} = $arg;
+  } 
+  return $self->{primary_id};
+}
+
+
+=head2 display_id
+
+  Arg [1]    : (optional) String $arg - value to set
+  Example    : none
+  Description: Getter/setter for attribute 'display_id'.
+               The object's preferred display name. This can be the same
+               as primary_id or ensembl-specific.
+  Returntype : String
+  Exceptions : none
+  Caller     : general
+  Status     : Stable
+
+=cut
+
+sub display_id{
+   my ( $self, $arg ) = @_;
+   if( defined $arg ) {
+       $self->{display_id} = $arg;
+   } 
+   return $self->{display_id};
+}
+
+
+=head2 optional_id
+
+  Args       : none
+  Example    : none
+  Description: Additional getter for attribute 'display_id'.
+               The object's preferred display name.
+               Only include for BioPerl interface compliance, please use
+               $self->display_id().
+  Returntype : String
+  Exceptions : none
+  Caller     : general
+  Status     : Stable
+
+=cut
+
+sub optional_id {
+  my $self = shift;
+  return $self->display_id;
+}
+
+
+=head2 dbname
+
+  Arg [1]    : (optional) String $arg - value to set
+  Example    : none
+  Description: Getter/setter for attribute 'dbname'.
+               The name of the external database.
+  Returntype : String
+  Exceptions : none
+  Caller     : general
+  Status     : Stable
+
+=cut
+
+sub dbname {
+  my ( $self, $arg ) = @_;
+  if( defined $arg ) {
+    $self->{dbname} = $arg;
+  } 
+  return $self->{dbname};
+}
+
+
+=head2 database
+
+  Args       : none
+  Example    : none
+  Description: Additional getter for attribute 'dbname'.
+               The name of the external database.
+               Only include for BioPerl interface compliance, please use
+               $self->dbname().
+  Returntype : String
+  Exceptions : none
+  Caller     : general
+  Status     : Stable
+
+=cut
+
+sub database {
+  my $self = shift;
+  return $self->dbname();
+}
+
+
+=head2 release
+
+  Arg [1]    : (optional) String $arg - value to set
+  Example    : none
+  Description: Getter/setter for attribute 'release'.
+               The external database release name.
+  Returntype : String
+  Exceptions : none
+  Caller     : general
+  Status     : Stable
+
+=cut
+
+sub release {
+  my ( $self, $arg ) = @_;
+  if( defined $arg ) {
+    $self->{release} = $arg;
+  } 
+  return $self->{release};
+}
+
+
+=head2 version
+
+  Arg [1]    : (optional) String $arg - value to set
+  Example    : none
+  Description: Getter/setter for attribute 'version'.
+               The object's version in the external database.
+  Returntype : String
+  Exceptions : none
+  Caller     : general
+  Status     : Stable
+
+=cut
+
+sub version {
+  my ( $self, $arg ) = @_;
+  if( defined $arg ) {
+    $self->{version} = $arg;
+  } 
+  return $self->{version};
+}
+
+
+=head2 description
+
+  Arg [1]    : (optional) String $arg - value to set
+  Example    : none
+  Description: Getter/setter for attribute 'description'.
+               The object's description, from the xref table
+  Returntype : String
+  Exceptions : none
+  Caller     : general
+  Status     : Stable
+
+=cut
+
+sub description {
+  my ( $self, $arg ) = @_;
+
+  if ( defined($arg) ) { $self->{'description'} = $arg }
+
+  return $self->{description};
+}
+
+=head2 analysis
+
+  Arg [1]    : Bio::EnsEMBL::Analysis $analysis
+  Example    : none
+  Description: get/set for attribute analysis
+  Returntype : Bio::EnsEMBL::Analysis
+  Exceptions : none
+  Caller     : general
+  Status     : Stable
+
+=cut
+
+sub analysis {
+   my $self = shift;
+  $self->{analysis} = shift if( @_ );
+  return $self->{analysis};
+}
+
+=head2 comment
+
+  Args       : none
+  Example    : none
+  Description: Additional getter for attribute 'description'.
+               The object's description.
+               Only include for BioPerl interface compliance, please use
+               $self->description().
+  Returntype : String
+  Exceptions : none
+  Caller     : general
+  Status     : Stable
+
+=cut
+
+sub comment {
+  my $self = shift;
+  return $self->description();
+}
+
+
+=head2 priority
+
+  Arg [1]    : int $priority
+  Example    : none
+  Priority   : Getter/setter for attribute 'priority'. Note this
+               is the priority from the external_db table.
+  Returntype : String
+  Exceptions : none
+  Caller     : general
+  Status     : At Risk
+             : due to it being under development
+
+=cut
+
+sub priority {
+  my ( $self, $arg ) = @_;
+  if( defined $arg ) {
+    $self->{priority} = $arg;
+  } 
+  return $self->{priority};
+}
+
+
+=head2 db_display_name
+
+  Arg [1]    : String $db_display_name
+  Example    : none
+  Description: Getter/setter for attribute 'db_display_name'.
+               The preferred display name for the external database. Has
+               "Projected " prepended if info_type='PROJECTION'.
+  Returntype : String
+  Exceptions : none
+  Caller     : general
+
+=cut
+
+sub db_display_name {
+  my ( $self, $arg ) = @_;
+  if( defined $arg ) {
+    $self->{db_display_name} = $arg;
+  }
+
+  my $name;
+  if ($self->{info_type} && $self->{info_type} eq "PROJECTION") {
+    $name = "Projected " . $self->{db_display_name};
+  } else {
+    $name =  $self->{db_display_name};
+  }
+
+  return $name;
+}
+
+
+=head2 info_type
+
+  Arg [1]    : String $info_type
+  Example    : none
+  Description: Getter/setter for attribute 'info_type'.
+  Returntype : String
+  Exceptions : none
+  Caller     : general
+
+=cut
+
+sub info_type {
+  my ( $self, $arg ) = @_;
+  if( defined $arg ) {
+    $self->{info_type} = $arg;
+  }
+  return $self->{info_type};
+ }
+
+
+=head2 info_text
+
+  Arg [1]    : String $info_text
+  Example    : none
+  Description: Getter/setter for attribute 'info_text'.
+  Returntype : String
+  Exceptions : none
+  Caller     : general
+
+=cut
+
+sub info_text {
+  my ( $self, $arg ) = @_;
+  if( defined $arg ) {
+    $self->{info_text} = $arg;
+  } 
+  return $self->{info_text};
+}
+
+=head2 linkage_annotation
+
+  Arg [1]    : String $object_xref_text
+  Example    : none
+  Description: Getter/setter for attribute 'linkage_annotation'.
+  Returntype : String
+  Exceptions : none
+  Caller     : general
+
+=cut
+
+sub linkage_annotation {
+  my ( $self, $arg ) = @_;
+
+  $self->{linkage_annotation} = $arg if defined $arg;
+  
+  return $self->{linkage_annotation};
+}
+
+
+=head2 type
+
+  Arg [1]    : String $type
+  Example    : none
+  Description: Getter/setter for attribute 'type'.
+  Returntype : String
+  Exceptions : none
+  Caller     : general
+
+=cut
+
+sub type {
+  my ( $self, $arg ) = @_;
+  if( defined $arg ) {
+    $self->{type} = $arg;
+  }
+  return $self->{type};
+}
+
+=head2 secondary_db_name
+
+  Arg [1]    : String $secondary_db_name
+  Description: Getter/setter for attribute 'secondary_db_name'.
+  Returntype : String
+  Exceptions : none
+  Caller     : general
+
+=cut
+
+sub secondary_db_name {
+  my ( $self, $arg ) = @_;
+  if( defined $arg ) {
+    $self->{secondary_db_name} = $arg;
+  }
+  return $self->{secondary_db_name};
+}
+
+
+=head2 secondary_db_table
+
+  Arg [1]    : String $secondary_db_table
+  Description: Getter/setter for attribute 'secondary_db_table'.
+  Returns    : String
+  Exceptions : none
+  Caller     : general
+
+=cut
+
+sub secondary_db_table {
+  my ( $self, $arg ) = @_;
+  if( defined $arg ) {
+    $self->{secondary_db_table} = $arg;
+  }
+  return $self->{secondary_db_table};
+}
+
+
+=head2 add_synonym
+
+  Arg [1]    : String $arg - synonym to add
+  Description: Add a synonym for the external object.
+  Returntype : none
+  Exceptions : none
+  Caller     : general
+  Status     : Stable
+
+=cut
+
+
+sub add_synonym {
+  my ( $self, $arg ) = @_;
+  if( defined $arg ) {
+    push( @{$self->{synonyms}}, $arg );
+  }
+}
+
+
+=head2 get_all_synonyms
+
+  Args      : none
+  Example    : my @synonyms = @{ $db_entry->get_all_synonyms };
+  Description: Get a list of synonyms known for this object.
+               Synonyms are lazy-loaded if required.
+  Returntype : listref of strings. May be empty.
+  Exceptions : none
+  Caller     : general
+  Status     : Stable
+
+=cut
+
+sub get_all_synonyms {
+
+  my $self = shift;
+
+  # lazy-load synonyms if required
+  if (!$self->{synonyms} && $self->adaptor()) {
+    $self->{synonyms} = $self->adaptor()->fetch_all_synonyms($self->dbID());
+  }
+
+  return $self->{synonyms};
+}
+
+
+=head2 get_all_dependents
+
+  Args[1]    : (optional) Bio::EnsEMBL::Gene, Transcript or Translation object
+  Example    : my @dependents = @{ $db_entry->get_all_dependents };
+  Description: Get a list of DBEntrys that are depenednet on the DBEntry.
+               if an ensembl gene transcript or translation is given then only
+               the ones on that object will be given
+  Returntype : listref of DBEntrys. May be empty.
+  Exceptions : none
+  Caller     : general
+  Status     : UnStable
+
+=cut
+
+sub get_all_dependents {
+  my $self = shift;
+  my $ensembl_object = shift;
+
+  return  $self->adaptor()->get_all_dependents($self->dbID(), $ensembl_object);
+}
+
+=head2 get_all_masters
+
+  Args[1]    : (optional) Bio::EnsEMBL::Gene, Transcript or Translation object
+  Example    : my @masters = @{ $db_entry->get_all_masters };
+  Description: Get a list of DBEntrys that are the masters of the DBEntry.
+               if an ensembl gene transcript or translation is given then only
+               the ones on that object will be given.
+  Returntype : listref of DBEntrys. May be empty.
+  Exceptions : none
+  Caller     : general
+  Status     : UnStable
+
+=cut
+
+sub get_all_masters {
+  my $self = shift;
+  my $ensembl_object = shift;
+
+  return  $self->adaptor()->get_all_masters($self->dbID(), $ensembl_object);
+}
+
+
+=head2 flush_synonyms
+
+  Args       : none
+  Description: Remove all synonyms from this object.
+  Returntype : none
+  Exceptions : none
+  Caller     : general
+  Status     : Stable
+
+=cut
+
+sub flush_synonyms {
+  my $self = shift;
+  $self->{synonyms} = [];
+}
+
+
+=head2 status
+
+  Arg [1]    : (optional) String $arg - value to set
+  Description: Getter/setter for attribute 'status'.
+  Returntype : String
+  Exceptions : none
+  Caller     : general
+  Status     : Stable
+
+=cut
+
+
+sub status{
+  my ( $self, $arg ) = @_;
+  if( defined $arg ) {
+     $self->{status} = $arg;
+  } 
+  return $self->{status};
+}
+
+=head2 ensembl_object_type
+
+  Arg [1]    : (optional) String $arg - value to set
+  Description: Getter/setter for attribute ensembl_object_type.
+  Returntype : String
+  Exceptions : none
+  Caller     : general
+  Status     : Stable
+
+=cut
+
+
+sub ensembl_object_type{
+  my ( $self, $arg ) = @_;
+  if( defined $arg ) {
+     $self->{ensembl_object_type} = $arg;
+  } 
+  return $self->{ensembl_object_type};
+}
+
+=head2 ensembl_id
+
+  Arg [1]    : (optional) String $arg - value to set
+  Description: Getter/setter for attribute ensembl_id.
+  Returntype : String
+  Exceptions : none
+  Caller     : general
+  Status     : Stable
+
+=cut
+
+
+sub ensembl_id{
+  my ( $self, $arg ) = @_;
+  if( defined $arg ) {
+     $self->{ensembl_id} = $arg;
+  } 
+  return $self->{ensembl_id};
+}
+
+
+
+=head1 DEPRECATED METHODS
+
+=cut
+
+=head2 get_synonyms
+
+  DEPRECATED use get_all_synonyms instead
+
+=cut
+
+sub get_synonyms {
+  my $self = shift;
+
+  deprecate("get_synonyms has been renamed get_all_synonyms.");
+  return $self->get_all_synonyms;
+}
+
+1;
+