Included libraries | Package variables | General documentation | Methods |
WebCvs | Raw content |
alive | No description | Code |
approval_authority | No description | Code |
get_all_GroupVersions | No description | Code |
get_all_ccds_ids | No description | Code |
get_current_GroupVersion | No description | Code |
new | No description | Code |
organization | No description | Code |
organization_id | No description | Code |
transcript_ncbi_id | No description | Code |
transcript_stable_id | No description | Code |
transcript_version | No description | Code |
translation_ncbi_id | No description | Code |
translation_stable_id | No description | Code |
translation_version | No description | Code |
alive | description | prev | next | Top |
my $self = shift; $self->{'alive'} = shift if ( @_ ); return $self->{'alive'};}
approval_authority | description | prev | next | Top |
my $self = shift; $self->{'approval_authority'} = shift if ( @_ ); return $self->{'approval_authority'}; } 1;}
get_all_GroupVersions | description | prev | next | Top |
my $self = shift; if( ! exists $self->{'_groupversion_array'} ) { if( defined $self->adaptor() ) { my $gva = $self->adaptor()->db()->get_GroupVersionAdaptor(); my $groupversions = $gva->fetch_all_by_accession( $self->transcript_stable_id, $self->transcript_version ); $self->{'_groupversion_array'} = $groupversions; } } return $self->{'_groupversion_array'};}
get_all_ccds_ids | description | prev | next | Top |
my $self = shift; if( ! exists $self->{'_ccds_id'} ) { if( defined $self->adaptor() ) { my $gva = $self->adaptor()->db()->get_GroupVersionAdaptor(); my @gv = @{$gva->fetch_all_by_accession($self->transcript_stable_id, $self->transcript_version)}; my @ccds_id; foreach my $gv (@gv){ push @ccds_id, $gv->get_ccds_id; } $self->{'_ccds_id'} =\@ ccds_id; } } return $self->{'_ccds_id'};}
get_current_GroupVersion | description | prev | next | Top |
my $self = shift; my $build_number = shift; throw("Require ncbi_build_number for get_current_GroupVersion") unless ($build_number); #need build number as an accession can have >1 current gv if it is on multiple builds}
if( ! exists $self->{'_groupversion_array'} ) { if( defined $self->adaptor() ) { my $gva = $self->adaptor()->db()->get_GroupVersionAdaptor(); my $groupversions = $gva->fetch_all_current_by_accession( $self->transcript_stable_id, $self->transcript_version, $build_number ); $self->{'_groupversion_array'} = $groupversions; } } return $self->{'_groupversion_array'}; } #sub get_all_statuses { #do we only want current status? or status on a certain build?
# my $self = shift;
# if( ! exists $self->{'_status'} ) {
#
# my @status;
# my @status_id = @{$self->adaptor->fetch_all_status_id($self->transcript_stable_id, $self->transcript_version)};
#
# if( defined $self->adaptor() ) {
# my $csa = $self->adaptor()->db()->get_CcdsStatusAdaptor();
#
# foreach my $stat_id (@status_id){
# push @status, $csa->fetch_by_status_id($stat_id)->ccds_status;
# }
# }
# $self->{'_status'} = \@status;
# }
# return $self->{'_status'};
#}
#
#
#sub get_all_Locations { #could bring back multiple sets of locations...
# my $self = shift;
# if( ! exists $self->{'_locations'} ) {
#
# print "in here\n";
#
# if( defined $self->adaptor() ) {
# my $gva = $self->adaptor()->db()->get_GroupVersionAdaptor();
# my @gv = @{$gva->fetch_all_by_accession($self->transcript_stable_id, $self->transcript_version)};
# my @locations;
# foreach my $gv (@gv){
# print $gv->dbID."\n";
# my @loc = @{$gv->get_all_Locations};
# foreach my $l (@loc){
# print $l->exon_start." - ".$l->exon_end."\n";
# }
# push @locations, [@{$gv->get_all_Locations}];
# }
# $self->{'_locations'} = \@locations;
# }
# }
# return $self->{'_locations'};
#
#
#
#
new | description | prev | next | Top |
my($class,@args) = @_; my $self = bless {},$class; my ($dbid, $transcript_stable_id, $transcript_version, $transcript_ncbi_id, $translation_stable_id, $translation_version, $translation_ncbi_id, $organization_id, $alive, $organization, $approval_authority, $adaptor) = rearrange([qw(DBID TRANSCRIPT_STABLE_ID TRANSCRIPT_VERSION TRANSCRIPT_NCBI_ID TRANSLATION_STABLE_ID TRANSLATION_VERSION TRANSLATION_NCBI_ID ORGANIZATION_ID ALIVE ORGANIZATION APPROVAL_AUTHORITY ADAPTOR )],@args); $self->dbID ( $dbid ); $self->transcript_stable_id ( $transcript_stable_id ); $self->transcript_version ( $transcript_version ); $self->transcript_ncbi_id ( $transcript_ncbi_id ); $self->translation_stable_id ( $translation_stable_id ); $self->translation_version ( $translation_version ); $self->translation_ncbi_id ( $translation_ncbi_id ); $self->organization_id ( $organization_id ); $self->alive ( $alive ); $self->organization ( $organization ); $self->approval_authority ( $approval_authority ); $self->adaptor ( $adaptor ); return $self;}
organization | description | prev | next | Top |
my $self = shift; $self->{'name'} = shift if ( @_ ); return $self->{'name'};}
organization_id | description | prev | next | Top |
my $self = shift; $self->{'organization_uid'} = shift if ( @_ ); return $self->{'organization_uid'};}
transcript_ncbi_id | description | prev | next | Top |
my $self = shift; $self->{'nuc_gi'} = shift if ( @_ ); return $self->{'nuc_gi'};}
transcript_stable_id | description | prev | next | Top |
my $self = shift; $self->{'nuc_acc'} = shift if ( @_ ); return $self->{'nuc_acc'};}
transcript_version | description | prev | next | Top |
my $self = shift; $self->{'nuc_version'} = shift if ( @_ ); return $self->{'nuc_version'};}
translation_ncbi_id | description | prev | next | Top |
my $self = shift; $self->{'prot_gi'} = shift if ( @_ ); return $self->{'prot_gi'};}
translation_stable_id | description | prev | next | Top |
my $self = shift; $self->{'prot_acc'} = shift if ( @_ ); return $self->{'prot_acc'};}
translation_version | description | prev | next | Top |
my $self = shift; $self->{'prot_version'} = shift if ( @_ ); return $self->{'prot_version'};}