Inheritance diagram for Bio::EnsEMBL::DBSQL::DnaAlignFeatureAdaptor:

Public Member Functions
protected List	_tables ()

protected	_left_join ()

protected List	_columns ()

public void	store ()

public void	remove ()

protected Listref	_objs_from_sth ()

public List	list_dbIDs ()

Public Member Functions inherited from Bio::EnsEMBL::DBSQL::BaseAlignFeatureAdaptor
public Listref	fetch_all_by_Slice_and_hcoverage ()

public Listref	fetch_all_by_Slice_and_external_db ()

public Listref	fetch_all_by_Slice_and_pid ()

public Listref	fetch_all_by_hit_name ()

public Listref	fetch_all_by_hit_name_unversioned ()

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

$dafa = $registry->get_adaptor( 'Human', 'Core', 'DnaAlignFeature' );
 
my @features = @{ $dafa->fetch_all_by_Slice($slice) };
 
$dafa->store(@features);

Description

This is an adaptor responsible for the retrieval and storage of
DnaDnaAlignFeatures from the database. This adaptor inherits most of its
functionality from the BaseAlignFeatureAdaptor and BaseFeatureAdaptor
superclasses.

Definition at line 25 of file DnaAlignFeatureAdaptor.pm.

Member Function Documentation

◆ _columns()

protected List Bio::EnsEMBL::DBSQL::DnaAlignFeatureAdaptor::_columns ( )

  Args       : none
  Example    :

@columns = $self->_columns

  Description: PROTECTED implementation of abstract superclass method.  
               Returns a list of columns that are needed for object creation.
  Returntype : list of strings
  Exceptions : none
  Caller     : Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::generic_fetch
  Status     : Stable

Code:

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◆ _left_join()

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

Undocumented method

Code:

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◆ _objs_from_sth()

protected Listref Bio::EnsEMBL::DBSQL::DnaAlignFeatureAdaptor::_objs_from_sth ( )

  Arg [1]    : DBI statement handle $sth
               an exectuted DBI statement handle generated by selecting 
               the columns specified by _columns() from the table specified 
               by _table()
  Example    :

@dna_dna_align_feats = $self->_obj_from_hashref

  Description: PROTECTED implementation of superclass abstract method. 
               Creates DnaDnaAlignFeature objects from a DBI hashref
  Returntype : listref of Bio::EnsEMBL::DnaDnaAlignFeatures
  Exceptions : none
  Caller     : Bio::EnsEMBL::BaseFeatureAdaptor::generic_fetch
  Status     : Stable

Code:

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sub _objs_from_sth {
  my ( $self, $sth, $mapper, $dest_slice ) = @_;
 
  #
  # This code is ugly because an attempt has been made to remove as many
  # function calls as possible for speed purposes.  Thus many caches and
  # a fair bit of gymnastics is used.
  #
 
  # In case of userdata we need the features on the dest_slice.  In case
  # of get_all_supporting_features dest_slice is not provided.
  my $sa = (   $dest_slice
             ? $dest_slice->adaptor()
             : $self->db()->get_SliceAdaptor() );
  my $aa = $self->db->get_AnalysisAdaptor();
 
  my @features;
  my %analysis_hash;
  my %slice_hash;
  my %sr_name_hash;
  my %sr_cs_hash;
 
  my ( $dna_align_feature_id, $seq_region_id,
       $analysis_id,          $seq_region_start,
       $seq_region_end,       $seq_region_strand,
       $hit_start,            $hit_end,
       $hit_name,             $hit_strand,
       $cigar_line,           $evalue,
       $perc_ident,           $score,
       $external_db_id,       $hcoverage,
       $align_type,
       $external_db_name,     $external_display_db_name );
 
  $sth->bind_columns( \( $dna_align_feature_id, $seq_region_id,
                         $analysis_id,          $seq_region_start,
                         $seq_region_end,       $seq_region_strand,
                         $hit_start,            $hit_end,
                         $hit_name,             $hit_strand,
                         $cigar_line,           $evalue,
                         $perc_ident,           $score,
                         $external_db_id,       $hcoverage,
                         $align_type,
                         $external_db_name, $external_display_db_name )
  );
 
  my $dest_slice_start;
  my $dest_slice_end;
  my $dest_slice_strand;
  my $dest_slice_length;
  my $dest_slice_cs;
  my $dest_slice_sr_name;
  my $dest_slice_sr_id;
  my $asma;
 
  if ($dest_slice) {
    $dest_slice_start   = $dest_slice->start();
    $dest_slice_end     = $dest_slice->end();
    $dest_slice_strand  = $dest_slice->strand();
    $dest_slice_length  = $dest_slice->length();
    $dest_slice_cs      = $dest_slice->coord_system();
    $dest_slice_sr_name = $dest_slice->seq_region_name();
    $dest_slice_sr_id   = $dest_slice->get_seq_region_id();
    $asma               = $self->db->get_AssemblyMapperAdaptor();
  }
 
  FEATURE: while($sth->fetch()) {
 
    #get the analysis object
    my $analysis = $analysis_hash{$analysis_id} ||= $aa->fetch_by_dbID($analysis_id);
    $analysis_hash{$analysis_id} = $analysis;
 
    #need to get the internal_seq_region, if present
    $seq_region_id = $self->get_seq_region_id_internal($seq_region_id);
    my $slice = $slice_hash{"ID:".$seq_region_id};
 
    if (!$slice) {
      $slice                            = $sa->fetch_by_seq_region_id($seq_region_id);
      $slice_hash{"ID:".$seq_region_id} = $slice;
      $sr_name_hash{$seq_region_id}     = $slice->seq_region_name();
      $sr_cs_hash{$seq_region_id}       = $slice->coord_system();
    }
 
    #obtain a mapper if none was defined, but a dest_seq_region was
    if(!$mapper && $dest_slice && !$dest_slice_cs->equals($slice->coord_system)) {
      $mapper = $asma->fetch_by_CoordSystems($dest_slice_cs, $slice->coord_system);
    }
 
    my $sr_name = $sr_name_hash{$seq_region_id};
    my $sr_cs   = $sr_cs_hash{$seq_region_id};
 
    #
    # remap the feature coordinates to another coord system
    # if a mapper was provided
    #
 
    if ($mapper) {
 
      if (defined $dest_slice && $mapper->isa('Bio::EnsEMBL::ChainedAssemblyMapper') ) {
        ($seq_region_id, $seq_region_start, $seq_region_end, $seq_region_strand) =
         $mapper->map($sr_name, $seq_region_start, $seq_region_end, $seq_region_strand, $sr_cs, 1, $dest_slice);
 
      } else {
        ($seq_region_id, $seq_region_start, $seq_region_end, $seq_region_strand) =
         $mapper->fastmap($sr_name, $seq_region_start, $seq_region_end, $seq_region_strand, $sr_cs);
      }
 
      #skip features that map to gaps or coord system boundaries
      next FEATURE if (!defined($seq_region_id));
 
      #get a slice in the coord system we just mapped to
      $slice = $slice_hash{"ID:".$seq_region_id} ||= $sa->fetch_by_seq_region_id($seq_region_id);
    }
 
    #
    # If a destination slice was provided convert the coords.
    #
    if (defined($dest_slice)) {
      my $seq_region_len = $dest_slice->seq_region_length();
 
      if ( $dest_slice_strand == 1 ) {
        $seq_region_start = $seq_region_start - $dest_slice_start + 1;
        $seq_region_end   = $seq_region_end - $dest_slice_start + 1;
 
        if ( $dest_slice->is_circular ) {
        # Handle circular chromosomes.
 
          if ( $seq_region_start > $seq_region_end ) {
            # Looking at a feature overlapping the chromosome origin.
 
            if ( $seq_region_end > $dest_slice_start ) {
              # Looking at the region in the beginning of the chromosome
              $seq_region_start -= $seq_region_len;
            }
            if ( $seq_region_end < 0 ) {
              $seq_region_end += $seq_region_len;
            }
          } else {
            if ($dest_slice_start > $dest_slice_end && $seq_region_end < 0) {
              # Looking at the region overlapping the chromosome
              # origin and a feature which is at the beginning of the
              # chromosome.
              $seq_region_start += $seq_region_len;
              $seq_region_end   += $seq_region_len;
            }
          }
        }
      } else {
 
        my $start = $dest_slice_end - $seq_region_end + 1;
        my $end = $dest_slice_end - $seq_region_start + 1;
 
        if ($dest_slice->is_circular()) {
 
          if ($dest_slice_start > $dest_slice_end) {
            # slice spans origin or replication
 
            if ($seq_region_start >= $dest_slice_start) {
              $end += $seq_region_len;
              $start += $seq_region_len if $seq_region_end > $dest_slice_start;
 
            } elsif ($seq_region_start <= $dest_slice_end) {
              # do nothing
            } elsif ($seq_region_end >= $dest_slice_start) {
              $start += $seq_region_len;
              $end += $seq_region_len;
 
            } elsif ($seq_region_end <= $dest_slice_end) {
              $end += $seq_region_len if $end < 0;
 
            } elsif ($seq_region_start > $seq_region_end) {
              $end += $seq_region_len;
            }
 
          } else {
 
            if ($seq_region_start <= $dest_slice_end and $seq_region_end >= $dest_slice_start) {
              # do nothing
            } elsif ($seq_region_start > $seq_region_end) {
              if ($seq_region_start <= $dest_slice_end) {
                $start -= $seq_region_len;
              } elsif ($seq_region_end >= $dest_slice_start) {
                $end += $seq_region_len;
              }
            }
          }
        }
 
        $seq_region_start = $start;
        $seq_region_end = $end;
        $seq_region_strand *= -1;
 
      } ## end else [ if ( $dest_slice_strand...)]
 
      # Throw away features off the end of the requested slice or on
      # different seq_region.
      if ($seq_region_end < 1
          || $seq_region_start > $dest_slice_length
          || ($dest_slice_sr_id != $seq_region_id)) {
        next FEATURE;
      }
      $slice = $dest_slice;
    }
 
    # Finally, create the new DnaAlignFeature.
    push( @features,
          $self->_create_feature_fast(
             'Bio::EnsEMBL::DnaDnaAlignFeature', {
               'slice'           => $slice,
               'start'           => $seq_region_start,
               'end'             => $seq_region_end,
               'strand'          => $seq_region_strand,
               'hseqname'        => $hit_name,
               'hstart'          => $hit_start,
               'hend'            => $hit_end,
               'hstrand'         => $hit_strand,
               'score'           => $score,
               'p_value'         => $evalue,
               'percent_id'      => $perc_ident,
               'cigar_string'    => $cigar_line,
               'analysis'        => $analysis,
               'adaptor'         => $self,
               'dbID'            => $dna_align_feature_id,
               'external_db_id'  => $external_db_id,
               'hcoverage'       => $hcoverage,
               'align_type'      => $align_type,
               'dbname'          => $external_db_name,
               'db_display_name' => $external_display_db_name
             } ) );
 
  } ## end while ( $sth->fetch() )
 
  return \@features;
} ## end sub _objs_from_sth

◆ _tables()

protected List Bio::EnsEMBL::DBSQL::DnaAlignFeatureAdaptor::_tables ( )

  Args       : none
  Example    :

@tabs = $self->_tables

  Description: PROTECTED implementation of the abstract method inherited from
               BaseFeatureAdaptor.  Returns list of [tablename, alias] pairs
  Returntype : list of listrefs of strings
  Exceptions : none
  Caller     : Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::generic_fetch
  Status     : Stable

Code:

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◆ list_dbIDs()

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

  Arg [1]    : none
  Example    :

@feature_ids = @{$dna_align_feature_adaptor->list_dbIDs()};

  Description: Gets an array of internal ids for all dna align features in 
               the current db
  Arg[1]     : <optional> int. not 0 for the ids to be sorted by the seq_region.
  Returntype : list of ints
  Exceptions : none
  Caller     : ?
  Status     : Stable

Code:

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◆ remove()

public void Bio::EnsEMBL::DBSQL::DnaAlignFeatureAdaptor::remove ( )

  Arg [1]    : A feature $feature 
  Example    :

$feature_adaptor->remove($feature);

  Description: This removes a feature from the database.  The table the
               feature is removed from is defined by the abstract method
               _tablename, and the primary key of the table is assumed
               to be _tablename() . '_id'.  The feature argument must 
               be an object implementing the dbID method, and for the
               feature to be removed from the database a dbID value must
               be returned.
  Returntype : none
  Exceptions : thrown if $feature arg does not implement dbID(), or if
               $feature->dbID is not a true value
  Caller     : general
  Status     : Stable

Code:

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◆ store()

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

  Arg [1]    : list of Bio::EnsEMBL::DnaAlignFeatures @feats
               the features to store in the database
  Example    :

$dna_align_feature_adaptor->store(@features);

  Description: Stores a list of DnaAlignFeatures in the database
  Returntype : none
  Exceptions : throw if any of the provided features cannot be stored
               which may occur if:
                   The feature does not have an associate Slice
                   The feature does not have an associated analysis
                   The Slice the feature is associated with is on a seq_region
                   unknown to this database
               A warning is given if:
                   The feature has already been stored in this db
  Caller     : Pipeline
  Status     : Stable

Code:

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sub store {
  my ( $self, @feats ) = @_;
 
  throw("Must call store with features") if ( scalar(@feats) == 0 );
 
  my @tabs = $self->_tables;
  my ($tablename) = @{ $tabs[0] };
 
  my $db               = $self->db();
  my $analysis_adaptor = $db->get_AnalysisAdaptor();
 
  my $sth = $self->prepare(
    "INSERT INTO $tablename (seq_region_id, seq_region_start,
                             seq_region_end, seq_region_strand,
                             hit_start, hit_end, hit_strand, hit_name,
                             cigar_line, analysis_id, score, evalue,
                             perc_ident, external_db_id, hcoverage, align_type)
     VALUES (?,?,?,?,?,?,?,?,?,?,?,?,?,?,?,?)"    # 16 arguments, external_data removed and align_type added
  );
 
FEATURE:
  foreach my $feat (@feats) {
    if ( !ref $feat || !$feat->isa("Bio::EnsEMBL::DnaDnaAlignFeature") )
    {
      throw("feature must be a Bio::EnsEMBL::DnaDnaAlignFeature, not a [". ref($feat). "]." );
    }
 
    if ( $feat->is_stored($db) ) {
      warning( "DnaDnaAlignFeature [".$feat->dbID()."] is already stored in this database." );
      next FEATURE;
    }
 
    my $hstart  = $feat->hstart();
    my $hend    = $feat->hend();
    my $hstrand = $feat->hstrand();
    $self->_check_start_end_strand( $hstart, $hend, $hstrand, $feat->hslice );
 
    my $cigar_string = $feat->cigar_string();
    if ( !$cigar_string ) {
      $cigar_string = $feat->length() . 'M';
      warning( "DnaDnaAlignFeature does not define a cigar_string.\n"
          . "Assuming ungapped block with cigar_line=$cigar_string ." );
    }
    my $align_type = $feat->align_type();
 
    my $hseqname = $feat->hseqname();
    if ( !$hseqname ) {
      throw("DnaDnaAlignFeature must define an hseqname.");
    }
 
    if ( !defined( $feat->analysis ) ) {
      throw(
        "An analysis must be attached to the features to be stored.");
    }
 
    #store the analysis if it has not been stored yet
    if ( !$feat->analysis->is_stored($db) ) {
      $analysis_adaptor->store( $feat->analysis() );
    }
 
    my $original = $feat;
    my $seq_region_id;
    ( $feat, $seq_region_id ) = $self->_pre_store($feat);
    
    $sth->bind_param( 1,  $seq_region_id,        SQL_INTEGER );
    $sth->bind_param( 2,  $feat->start,          SQL_INTEGER );
    $sth->bind_param( 3,  $feat->end,            SQL_INTEGER );
    $sth->bind_param( 4,  $feat->strand,         SQL_TINYINT );
    $sth->bind_param( 5,  $hstart,               SQL_INTEGER );
    $sth->bind_param( 6,  $hend,                 SQL_INTEGER );
    $sth->bind_param( 7,  $hstrand,              SQL_TINYINT );
    $sth->bind_param( 8,  $hseqname,             SQL_VARCHAR );
    $sth->bind_param( 9,  $cigar_string,         SQL_LONGVARCHAR );
    $sth->bind_param( 10, $feat->analysis->dbID, SQL_INTEGER );
    $sth->bind_param( 11, $feat->score,          SQL_DOUBLE );
    $sth->bind_param( 12, $feat->p_value,        SQL_DOUBLE );
    $sth->bind_param( 13, $feat->percent_id,     SQL_FLOAT );
    $sth->bind_param( 14, $feat->external_db_id, SQL_INTEGER );
    $sth->bind_param( 15, $feat->hcoverage,      SQL_DOUBLE );
    $sth->bind_param( 16, $feat->align_type,     SQL_VARCHAR);
    $sth->execute();
 
    my $dbId = $self->last_insert_id("${tablename}_id", undef, $tablename);
 
    # store attributes if there are any
    my $attr_adaptor = $db->get_AttributeAdaptor();
    $attr_adaptor->store_on_DnaDnaAlignFeature($dbId, $feat->get_all_Attributes);
 
    $original->dbID( $dbId );
    $original->adaptor($self);
  } ## end foreach my $feat (@feats)
 
  $sth->finish();
} ## end sub store

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

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

Public Member Functions

Detailed Description

Synopsis

Description

Member Function Documentation

◆ _columns()

◆ _left_join()

◆ _objs_from_sth()

◆ _tables()

◆ list_dbIDs()

◆ remove()

◆ store()