Raw content of Bio::EnsEMBL::UnmappedObject
<![CDATA[=head1 LICENSE
Copyright (c) 1999-2009 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
/info/about/code_licence.html
=head1 CONTACT
Please email comments or questions to the public Ensembl
developers list at <ensembl-dev@ebi.ac.uk>.
Questions may also be sent to the Ensembl help desk at
<helpdesk@ensembl.org>.
=cut
=head1 NAME
Bio:EnsEMBL::UnmappedObject - A object representing why a particular entity
was NOT mapped to the ensembl.
=head1 SYNOPSIS
use Bio::EnsEMBL::UnmappedObject;
my $uo = Bio::EnsEMBL::UnmappedObject->new(
-type => 'xref',
-analysis => $analysis,
-external_db_id => 4100,
-identifier => "Q12345",
-query_score => 45.5,
-target_score => 29.2,
-ensembl_id => 122346,
-ensembl_type => "Translation",
-summary => "match failed for exonerate",
-full_desc => "match failed for the xref exonerate run "
. "as match was below threshold of 90"
);
=head1 DESCRIPTION
UnmappedObjects represent entities NOT mapped to ensembl. Therefore this
should help users to find out why certain accessions etc can not be
found.
=head1 METHODS
=cut
package Bio::EnsEMBL::UnmappedObject;
use strict;
use warnings;
use Bio::EnsEMBL::Utils::Argument qw(rearrange);
use Bio::EnsEMBL::Utils::Exception qw(throw);
use Bio::EnsEMBL::Storable;
use vars qw(@ISA);
@ISA = qw(Bio::EnsEMBL::Storable);
=head2 new
Arg [TYPE] : the type of mapping i.e. 'xref','cDNA'
Arg [ANALYSIS] : Analysis object.
Arg [EXTERNAL_DB_ID] : id for the external db id this identifier is from
Arg [IDENTIFIER] : name of the identifier i.e. accession
Arg [QUERY_SCORE] : (optional) The query score
Arg [TARGET_SCORE] : (optional) The target score
Arg [SUMMARY] : The summary reason for not mapping.
Arg [FULL_DESC] : The Full description of why it did not map.
Arg [ENSEMBL_ID] : (optional) internal ensembl id for the best match
Arg [ENSEMBL_OBJECT_TYPE] : (optional) the type of object for the best match
Example : see SYNOPSIS
Returntype : Bio::EnsEMBL::UnmappedObject
Exceptions : If any of the none optional args are missing
Caller : general
Status : At Risk
=cut
sub new {
my $caller = shift;
#allow constructor to be called as class or object method
my $class = ref($caller) || $caller;
my ($dbID, $unmapped_reason_id, $type, $analysis, $ex_db_id, $identifier,
$query_score, $target_score, $summary, $full_desc,
$ensembl_id, $ensembl_object_type, $adaptor ) =
rearrange([qw(UNMAPPED_OBJECT_ID UNMAPPED_REASON_ID TYPE ANALYSIS
EXTERNAL_DB_ID IDENTIFIER QUERY_SCORE TARGET_SCORE
SUMMARY FULL_DESC ENSEMBL_ID ENSEMBL_OBJECT_TYPE ADAPTOR)], @_);
my $self = $class->SUPER::new(@_);
if(defined($analysis)) {
if(!ref($analysis) || !$analysis->isa('Bio::EnsEMBL::Analysis')) {
throw('-ANALYSIS argument must be a Bio::EnsEMBL::Analysis not '.
$analysis);
}
}
else{
throw('-ANALYSIS argument must be given');
}
$self->{'analysis'} = $analysis;
$self->{'dbID'} = $dbID if (defined($dbID));
$self->{'description'} = $full_desc || throw('FULL_DESC must be given');
$self->{'summary'} = $summary || throw('SUMMARY must be given');
$self->{'type'} = $type || throw('TYPE must be given');
$self->{'external_db_id'} = $ex_db_id;
if (lc($type) eq "xref") {
throw('EXTERNAL_DB_ID must be given') if ! defined $ex_db_id;
}
$self->{'identifier'} = $identifier || throw('IDENTIFIER must be given');
$self->{'query_score'} = $query_score if(defined($query_score));
$self->{'target_score'} = $target_score if(defined($target_score));
$self->{'ensembl_id'} = $ensembl_id if(defined($ensembl_id));
$self->{'ensembl_object_type'} = $ensembl_object_type
if(defined($ensembl_object_type));
$self->{'unmapped_reason_id'} = $unmapped_reason_id
if(defined($unmapped_reason_id));
$self->{'adaptor'} = $adaptor if(defined($adaptor));
return $self;
}
=head2 new_fast
Arg [...] : none
Example : $feature = Bio::EnsEMBL::UnmappedObject->new_fast();
Description: Creates a new Unmapped Object.
Returntype : Bio::EnsEMBL::UnmappedObject
Exceptions : none
Caller : general
Status : At Risk
=cut
sub new_fast{
my $caller = shift;
#allow constructor to be called as class or object method
my $class = ref($caller) || $caller;
my $self = $class->SUPER::new(@_);
return $self;
}
=head2 description
Arg [1] : (optional) * to be set to
Example : print $unmappedObject->description."\n";
Description : Basic getter/setter for description
ReturnType : String
Exceptions : none
Caller : general
Status : At Risk
=cut
sub description{
my $self = shift;
if(@_) {
my $des = shift;
$self->{'description'} = $des;
}
return $self->{'description'};
}
=head2 summary
Arg [1] : (optional) summary to be set to
Example : print $unmappedObject->summary."\n";
Description : Basic getter/setter for summary
ReturnType : String
Exceptions : none
Caller : general
Status : At Risk
=cut
sub summary{
my $self = shift;
if(@_) {
my $des = shift;
$self->{'summary'} = $des;
}
return $self->{'summary'};
}
=head2 type
Arg [1] : (optional) type to be set to
Example : print $unmappedObject->type."\n";
Description : Basic getter/setter for type
ReturnType : String
Exceptions : none
Caller : general
Status : At Risk
=cut
sub type{
my $self = shift;
if(@_) {
my $arg = shift;
$self->{'type'} = $arg;
}
return $self->{'type'};
}
=head2 adaptor
Arg [1] : (optional) UnmappedObjectadaptor to be set to
Example : my $adap = $unmappedObject->adaptor."\n";
Description : Basic getter/setter for adaptor
ReturnType : UnamppedObjectAdaptor
Exceptions : none
Caller : general
Status : At Risk
=cut
sub adaptor{
my $self = shift;
if(@_) {
my $arg = shift;
$self->{'adaptor'} = $arg;
}
return $self->{'adaptor'};
}
=head2 ensembl_object_type
Arg [1] : (optional) ensembl object type to be set to
Example : print $unmappedObject->ensembl_object_type."\n";
Description : Basic getter/setter for ensembl object type
ReturnType : String
Exceptions : none
Caller : general
Status : At Risk
=cut
sub ensembl_object_type{
my $self = shift;
if(@_) {
my $arg = shift;
$self->{'ensembl_object_type'} = $arg;
}
return $self->{'ensembl_object_type'};
}
=head2 ensembl_id
Arg [1] : (optional) ensembl id to be set to
Example : print $unmappedObject->ensembl_id."\n";
Description : Basic getter/setter for ensembl id
ReturnType : String
Exceptions : none
Caller : general
Status : At Risk
=cut
sub ensembl_id{
my $self = shift;
if(@_) {
my $arg = shift;
$self->{'ensembl_id'} = $arg;
}
return $self->{'ensembl_id'};
}
=head2 external_db_id
Arg [1] : (optional) external_db_id to be set to
Example : print $unmappedObject->external_db_id."\n";
Description : Basic getter/setter for external_db_id
ReturnType : int
Exceptions : none
Caller : general
Status : At Risk
=cut
sub external_db_id{
my $self = shift;
if(@_) {
my $arg = shift;
$self->{'external_db_id'} = $arg;
}
return $self->{'external_db_id'};
}
=head2 external_db_name
Example : print $unmappedObject->external_db_name()."\n";
Description : Basic getter for external_db_name
ReturnType : int
Exceptions : none
Caller : general
Status : At Risk
=cut
sub external_db_name{
my $self = shift;
my $handle = $self->{'adaptor'};
if(defined($handle) and defined($self->{'external_db_id'})){
my $sth = $handle->prepare("select db_name from external_db where external_db_id = ".$self->{'external_db_id'});
$sth->execute();
my $name;
$sth->bind_columns(\$name);
$sth->fetch();
return $name;
}
return "";
}
sub stable_id{
my ($self) = shift;
my $handle = $self->{'adaptor'};
if(defined($handle)){
my $sql = "select stable_id from ".lc($self->{'ensembl_object_type'})."_stable_id where ".
lc($self->{'ensembl_object_type'})."_id = ".
$self->{'ensembl_id'};
my $sth = $handle->prepare($sql);
$sth->execute();
my $name;
$sth->bind_columns(\$name);
$sth->fetch();
return $name;
}
return "";
}
# my $adaptor;
# if($self->{'ensembl_object_type'} eq "Transcript"){
# $adaptor= $self->adaptor->db->get_TranscriptAdaptor();
# }
# elsif($self->{'ensembl_object_type'} eq "Translation"){
# $adaptor= $self->adaptor->db->get_TranslationAdaptor();
# }
# elsif($self->{'ensembl_object_type'} eq "Gene"){
# $adaptor= $self->adaptor->db->get_GeneAdaptor();
# }
# else{
# return undef;
# }
# my $object = $adaptor->fetch_by_dbID($self->{'ensembl_id'});
# if(defined($object)){
# return $object->stable_id;
# }
# else{
# return undef;
# }
#}
=head2 identifier
Arg [1] : (optional) identifier to be set to
Example : print $unmappedObject->identifier."\n";
Description : Basic getter/setter for identifier
ReturnType : String
Exceptions : none
Caller : general
Status : At Risk
=cut
sub identifier{
my $self = shift;
if(@_) {
my $arg = shift;
$self->{'identifier'} = $arg;
}
return $self->{'identifier'};
}
=head2 query_score
Arg [1] : (optional) query_score to be set to
Example : print $unmappedObject->query_score."\n";
Description : Basic getter/setter for query_score
ReturnType : float
Exceptions : none
Caller : general
Status : At Risk
=cut
sub query_score{
my $self = shift;
if(@_) {
my $arg = shift;
$self->{'query_score'} = $arg;
}
return $self->{'query_score'};
}
=head2 target_score
Arg [1] : (optional) target_score to be set to
Example : print $unmappedObject->target_score."\n";
Description : Basic getter/setter for target_score
ReturnType : float
Exceptions : none
Caller : general
Status : At Risk
=cut
sub target_score{
my $self = shift;
if(@_) {
my $arg = shift;
$self->{'target_score'} = $arg;
}
return $self->{'target_score'};
}
=head2 unmapped_reason_id
Arg [1] : (optional) unmapped_reason_id to be set to
Example : print $unmappedObject->unmapped_reason_id."\n";
Description : Basic getter/setter for unmapped_reason_id
ReturnType : int
Exceptions : none
Caller : general
Status : At Risk
=cut
sub unmapped_reason_id{
my $self = shift;
if(@_) {
my $arg = shift;
$self->{'unmapped_reason_id'} = $arg;
}
return $self->{'unmapped_reason_id'};
}
=head2 analysis
Arg [1] : (optional) analysis to be set to
Example : print $unmappedObject->analysis->logic_name."\n";
Description : Basic getter/setter for analysis
ReturnType : Bio::EnsEMBL::Analysis
Exceptions : none
Caller : general
Status : At Risk
=cut
sub analysis {
my $self = shift;
if(@_) {
my $an = shift;
if(defined($an) && (!ref($an) || !$an->isa('Bio::EnsEMBL::Analysis'))) {
throw('analysis argument must be a Bio::EnsEMBL::Analysis');
}
$self->{'analysis'} = $an;
}
return $self->{'analysis'};
}
1;
]]>