Inheritance diagram for Bio::EnsEMBL::DBSQL::UnmappedObjectAdaptor:

Public Member Functions
public Bio::EnsEMBL::DBSQL::UnmappedObjectAdaptor	new ()

protected	_tables ()

protected	_columns ()

protected	_left_join ()

public List	list_dbIDs ()

public List	list_unmapped_reasons ()

protected	_objs_from_sth ()

public void	store ()

public Array	fetch_all_by_type ()

public Array	fetch_all_by_analysis ()

public Array	fetch_by_identifier ()

public Array	fetch_all_by_object_type_id ()

Public Member Functions inherited from Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor
public Bio::EnsEMBL::BaseFeatureAdaptor	new ()

public Boolean	start_equals_end ()

public void	clear_cache ()

protected	_clear_slice_feature_cache ()

protected Bio::EnsEMBL::Utils::Cache	_slice_feature_cache ()

public Listref	fetch_all_by_Slice ()

public Bio::EnsEMBL::Utils::Iterator	fetch_Iterator_by_Slice_method ()

public Bio::EnsEMBL::Utils::Iterator	fetch_Iterator_by_Slice ()

public Listref	fetch_all_by_Slice_and_score ()

public Listref	fetch_all_by_Slice_constraint ()

public Listref	fetch_all_by_logic_name ()

public Listref	fetch_all_by_stable_id_list ()

protected	_create_feature ()

protected	_create_feature_fast ()

public Int	count_by_Slice_constraint ()

protected ArrayRef	_get_and_filter_Slice_projections ()

protected ArrayRef	_generate_feature_bounds ()

protected Listref	_get_by_Slice ()

protected	_slice_fetch ()

public	get_seq_region_id_external ()

public	get_seq_region_id_internal ()

protected	_pre_store ()

protected	_pre_store_userdata ()

protected	_check_start_end_strand ()

protected	_remap ()

protected	_seq_region_boundary_from_db ()

public void	store ()

public void	remove ()

public void	remove_by_Slice ()

protected	_max_feature_length ()

protected	_list_seq_region_ids ()

public	remove_by_analysis_id ()

public	remove_by_feature_id ()

public Bio::EnsEMBL::Feature	fetch_nearest_by_Feature ()

public Listref	fetch_all_by_outward_search ()

public Listref	fetch_all_nearest_by_Feature ()

public Listref	select_nearest ()

protected Int	_compute_nearest_end ()

protected Int	_compute_prime_distance ()

protected Int	_compute_midpoint ()

protected	_discard_excess_features_from_matrix ()

Public Member Functions inherited from Bio::EnsEMBL::DBSQL::BaseAdaptor
public Bio::EnsEMBL::DBSQL::BaseAdaptor	new ()

public DBI::StatementHandle	prepare ()

public Bio::EnsEMBL::DBSQL::DBAdaptor	db ()

public Bio::EnsEMBL::DBSQL::DBConnection	dbc ()

public Boolean	is_multispecies ()

public Int	species_id ()

protected	_list_dbIDs ()

protected	_straight_join ()

protected	_can_straight_join ()

public Listref	bind_param_generic_fetch ()

protected	_bind_param_generic_fetch ()

public String	generate_in_constraint ()

public Listref	generic_fetch ()

public Int	generic_count ()

protected	_generate_sql ()

public Bio::EnsEMBL::Feature	fetch_by_dbID ()

protected	_uncached_fetch_by_dbID ()

public Listref	fetch_all_by_dbID_list ()

protected	_uncached_fetch_all_by_dbID_list ()

protected ArrayRef	_uncached_fetch_all_by_id_list ()

public	fetch_all ()

public Scalar	last_insert_id ()

public	insert_ignore_clause ()

protected Bio::EnsEMBL::DBSQL::Support::BaseCache	_id_cache ()

protected Boolean	_no_id_cache ()

public Boolean	ignore_cache_override ()

public Int	schema_version ()

protected	_tables ()

protected	_columns ()

protected	_default_where_clause ()

protected	_left_join ()

protected	_final_clause ()

protected	_objs_from_sth ()

protected	_build_id_cache ()

protected	_logic_name_to_constraint ()

Detailed Description

Synopsis

my $uoa = $database_adaptor->get_UnmappedObjectAdaptor();
 
my $missed = @{ $uoa->fetch_all_by_type('xref') };

Description

Unmapped ObjectAdaptor - An adaptor responsible for the creation,
editing, retrieval of Unmapped Objects. These being the Objects that
where not mapped in a specific process i.e. xref, cDNA, Markers.

Definition at line 25 of file UnmappedObjectAdaptor.pm.

Member Function Documentation

◆ _columns()

protected Bio::EnsEMBL::DBSQL::UnmappedObjectAdaptor::_columns ( )

Undocumented method

Code:

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◆ _left_join()

protected Bio::EnsEMBL::DBSQL::UnmappedObjectAdaptor::_left_join ( )

Undocumented method

Code:

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◆ _objs_from_sth()

protected Bio::EnsEMBL::DBSQL::UnmappedObjectAdaptor::_objs_from_sth ( )

Undocumented method

Code:

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◆ _tables()

protected Bio::EnsEMBL::DBSQL::UnmappedObjectAdaptor::_tables ( )

Undocumented method

Code:

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◆ fetch_all_by_analysis()

public Array Bio::EnsEMBL::DBSQL::UnmappedObjectAdaptor::fetch_all_by_analysis ( )

  Arg [1]  : Bio:EnsEMBL::Analysis object
  Arg [2]  : (optional) string database name
  Example  :

@unmapped_object = @{$uoa->fetch_all_by_analysis($analysis)};

  Description : Retrieves all the unmapped object for a particular
                analysis type with the the option of a particular
                database type.
  Returntype  : array ref of Bio::EnsEMBL::UnmappedObject
  Exceptions  : thorws if first argument is not an anaylisi object
  Caller      : general
  Status      : At Risk

Code:

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◆ fetch_all_by_object_type_id()

public Array Bio::EnsEMBL::DBSQL::UnmappedObjectAdaptor::fetch_all_by_object_type_id ( )

  Arg [1]  : string - The object type of the ensembl object e.g. Gene
  Arg [2]  : int    - The internal dbID of the ensembl object
  Example  :

my @unmapped_objects = @{$uoa->fetch_all_by_object_type_id('Gene', 12341)};

  Description : Retrieves the unmapped objects for a particular ensembl object
                This is a base method which should be called by wrapper methods
                defining the correct object type e.g. $uoa->fetch_all_by_Gene($gene)
  Returntype  : array ref of Bio::EnsEMBL::UnmappedObject objects
  Exceptions  : Throws if arguments are not defined
  Caller      : general
  Status      : At Risk

Code:

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◆ fetch_all_by_type()

public Array Bio::EnsEMBL::DBSQL::UnmappedObjectAdaptor::fetch_all_by_type ( )

  Arg [1]  : string type. The type of unmapped objects
  Example  :

@unmapped_object = @{$uoa->fetch_all_by_type('xref')};

  Description : Retrieves all the unmapped object for a particular
                type. e.g. 'xref','cDNA', 'marker'
  Returntype  : Array ref of Bio::EnsEMBL::UnmappedObject
  Exceptions  : none
  Caller      : general
  Status      : At Risk

Code:

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◆ fetch_by_identifier()

public Array Bio::EnsEMBL::DBSQL::UnmappedObjectAdaptor::fetch_by_identifier ( )

  Arg [1]  : string type. The type of unmapped objects
  Arg [2]  : (optional) string database name
  Example  :

@unmapped_object = @{$uoa->fetch_by_identifier('Q123345')};

  Description : Retrieves the unmapped object for a particular
                identifier/accession
  Returntype  : array ref of Bio::EnsEMBL::UnmappedObject
  Exceptions  : none
  Caller      : general
  Status      : At Risk

Code:

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◆ list_dbIDs()

public List Bio::EnsEMBL::DBSQL::UnmappedObjectAdaptor::list_dbIDs ( )

  Arg [1]    : none
  Example    :

@unmapped_object_ids = @{$unmapped_object_adaptor->list_dbIDs()};

  Description: Gets an array of internal ids for all unmapped_objects in the current db
  Returntype : list of ints
  Exceptions : none
  Caller     : ?
  Status     : Stable

Code:

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◆ list_unmapped_reasons()

public List Bio::EnsEMBL::DBSQL::UnmappedObjectAdaptor::list_unmapped_reasons ( )

  Arg [1]    : none
  Example    :

@unmapped_object_reason+ids =

@{$unmapped_object_adaptor->list_unmapped_reasons()};

  Description: Gets an array of internal ids for all unmapped_objects in the current db
  Returntype : list of ints
  Exceptions : none
  Caller     : ?
  Status     : Stable

Code:

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◆ new()

public Bio::EnsEMBL::DBSQL::UnmappedObjectAdaptor Bio::EnsEMBL::DBSQL::UnmappedObjectAdaptor::new ( )

  Arg [1]    : list of args @args
               Superclass constructor arguments
  Example    :

none

  Description: Constructor which just initializes internal cache structures
  Returntype : Bio::EnsEMBL::DBSQL::UnmappedObjectAdaptor
  Exceptions : none
  Caller     : implementing subclass constructors
  Status     : At Risk

Code:

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◆ store()

public void Bio::EnsEMBL::DBSQL::UnmappedObjectAdaptor::store ( )

  Arg [1]    : list of Bio::EnsEMBL::UnmappedObjects @uo
               the unmapped objects to store in the database
  Example    :

$ou_adaptor->store(@uo);

  Description: Stores a list of unmapped objects in the database
  Returntype : none
  Exceptions : thrown if no Analysis, or no list of objects to store. 
  Caller     : general
  Status     : Stable

Code:

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sub store{
  my ($self,@uos) = @_;
 
  if( scalar(@uos) == 0 ) {
    throw("Must call store with list of UnmappedObjects");
  }
 
 
  my $db = $self->db();
  my $analysis_adaptor = $db->get_AnalysisAdaptor();
 
  my $sth_reason = $self->prepare
    ("INSERT INTO unmapped_reason (summary_description, full_description)".
     " VALUES (?,?)");
 
  my $sth_unmapped_object = $self->prepare
    ("INSERT INTO unmapped_object (type, analysis_id, external_db_id,
              identifier, unmapped_reason_id, query_score, target_score,
              ensembl_id, ensembl_object_type)".
        " VALUES (?,?,?,?,?,?,?,?,?)");
 
  my $sth_fetch_reason =
    $self->prepare(
      "SELECT 
        unmapped_reason_id
      FROM 
        unmapped_reason
      WHERE
        full_description = ? 
        " );
 
  FEATURE: foreach my $uo ( @uos ) {
 
    if( !ref $uo || !$uo->isa("Bio::EnsEMBL::UnmappedObject") ) {
      throw("UnmappedObject must be an Ensembl UnmappedObject, " .
            "not a [".ref($uo)."]");
    }
    if($uo->is_stored($db)){
      next;
    } 
    
    my $analysis = $uo->analysis();
    throw("UnmappedObject must have an analysis object.".$uo->analysis."\n") if(!defined($analysis));
 
    my $analysis_id;
    if($analysis->is_stored($db)) {
      $analysis_id = $analysis->dbID();
    } 
    else {
      $analysis_id = $db->get_AnalysisAdaptor->store($analysis);
    }
    
 
 
    # Check if unmapped reason is cached
    # Check if it has been added since the cache was created
    # Try to store it
 
    if(!defined($desc_to_id{$uo->{'description'}})){
      $sth_reason->bind_param(1,$uo->{'summary'},SQL_VARCHAR);
      $sth_reason->bind_param(2,$uo->{'description'},SQL_VARCHAR);
      
      if(! eval{ $sth_reason->execute(); 1 }){    
        # DBI Trace possible here?
        warning($@); #
        my $msg;
        $msg .= "INSERT INTO unmapped_reason (summary_description, full_description) VALUES (";
        $msg .=  $uo->{'summary'} .','. $uo->{'description'}. ')';
        # Temporary fix for naughty cross-dependency regulation code.
        use Data::Dumper;
        warning("Query: \n$msg");
        print STDERR "UnmappedObject: \n";
        print STDERR Dumper $uo;
 
        $sth_fetch_reason->execute($uo->{'description'});
        
        my $unmapped_reasons = $sth_fetch_reason->fetchrow_arrayref();
        if(! defined($unmapped_reasons)){
          my $msg = $uo->{'description'}. " unable to store. Check MySQL schema, maybe PK not big enough?";
          throw($msg);
        }
        if(scalar @$unmapped_reasons != 1){
          throw("Multiple results for this description");
        }
        $uo->{'unmapped_reason_id'} = $unmapped_reasons->[0];
 
      }    
      else{
        # print 'Last mohican: '.$self->last_insert_id ."\n";
        $uo->{'unmapped_reason_id'} = $self->last_insert_id;
      }
    }
    else{
      $uo->{'unmapped_reason_id'} = $desc_to_id{$uo->{'description'}};
    }
    $sth_unmapped_object->bind_param(1,$uo->{'type'},SQL_VARCHAR);
    $sth_unmapped_object->bind_param(2,$uo->analysis->dbID,SQL_INTEGER);
    $sth_unmapped_object->bind_param(3,$uo->{'external_db_id'},SQL_INTEGER);
    $sth_unmapped_object->bind_param(4,$uo->{'identifier'},SQL_VARCHAR);
    $sth_unmapped_object->bind_param(5,$uo->{'unmapped_reason_id'},SQL_VARCHAR);
    $sth_unmapped_object->bind_param(6,$uo->{'query_score'},SQL_DOUBLE);
    $sth_unmapped_object->bind_param(7,$uo->{'target_score'},SQL_DOUBLE);
    $sth_unmapped_object->bind_param(8,$uo->{'ensembl_id'},SQL_INTEGER);
    $sth_unmapped_object->bind_param(9,$uo->{'ensembl_object_type'},SQL_VARCHAR);
    $sth_unmapped_object->execute();
    $uo->dbID($self->last_insert_id('unmapped_object_id', undef, 'unmapped_object'));
  }
  $sth_reason->finish();      
  return;
}

The documentation for this class was generated from the following file:

ensembl/modules/Bio/EnsEMBL/DBSQL/UnmappedObjectAdaptor.pm

Public Member Functions

Detailed Description

Synopsis

Description

Member Function Documentation

◆ _columns()

◆ _left_join()

◆ _objs_from_sth()

◆ _tables()

◆ fetch_all_by_analysis()

◆ fetch_all_by_object_type_id()

◆ fetch_all_by_type()

◆ fetch_by_identifier()

◆ list_dbIDs()

◆ list_unmapped_reasons()

◆ new()

◆ store()