Inheritance diagram for Bio::EnsEMBL::DBSQL::ProteinAlignFeatureAdaptor:

Public Member Functions
public void	store ()

protected Listref	_objs_from_sth ()

protected	_tables ()

protected	_columns ()

protected	_left_join ()

public Listref	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

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

Definition at line 18 of file ProteinAlignFeatureAdaptor.pm.

Member Function Documentation

◆ _columns()

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

Undocumented method

Code:

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◆ _left_join()

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

Undocumented method

Code:

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◆ _objs_from_sth()

protected Listref Bio::EnsEMBL::DBSQL::ProteinAlignFeatureAdaptor::_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::ProteinAlignFeatures
  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.
  #
 
  my $sa = $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 (
    $protein_align_feature_id, $seq_region_id,  $seq_region_start,
    $seq_region_end,           $analysis_id,    $seq_region_strand,
    $hit_start,                $hit_end,        $hit_name,
    $cigar_line,               $evalue,         $perc_ident,
    $score,                    $external_db_id, $hcoverage, $align_type,
    $external_db_name,         $external_display_db_name );
 
  $sth->bind_columns(\(
           $protein_align_feature_id, $seq_region_id,  $seq_region_start,
           $seq_region_end,           $analysis_id,    $seq_region_strand,
           $hit_start,                $hit_end,        $hit_name,
           $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 ProteinAlignFeature.
    push(
      @features,
      $self->_create_feature_fast(
        'Bio::EnsEMBL::DnaPepAlignFeature', {
          'slice'        => $slice,
          'start'        => $seq_region_start,
          'end'          => $seq_region_end,
          'strand'       => $seq_region_strand,
          'hseqname'     => $hit_name,
          'hstart'       => $hit_start,
          'hend'         => $hit_end,
          'hstrand'      => 1,                  # dna_pep_align features
                                                # are always hstrand 1
          'score'        => $score,
          'p_value'      => $evalue,
          'percent_id'   => $perc_ident,
          'cigar_string' => $cigar_line,
          'analysis'     => $analysis,
          'adaptor'      => $self,
          'dbID'           => $protein_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
        } ) );
 
  }
 
  return \@features;
}

◆ _tables()

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

Undocumented method

Code:

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◆ list_dbIDs()

public Listref Bio::EnsEMBL::DBSQL::ProteinAlignFeatureAdaptor::list_dbIDs ( )

  Arg [1]    : none
  Example    :

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

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

Code:

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◆ store()

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

  Arg [1]    : list of Bio::EnsEMBL::DnaPepAlignFeature @feats
  Example    :

$protein_align_feature_adaptor->store(@feats);

  Description: stores a list of ProteinAlignFeatures 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 associated 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 $slice_adaptor = $db->get_SliceAdaptor();
  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_name, cigar_line,
                             analysis_id, score, evalue, perc_ident, external_db_id, hcoverage, align_type)
     VALUES (?,?,?,?,?,?,?,?,?,?, ?, ?, ?, ?,?)");
 
 FEATURE: foreach my $feat ( @feats ) {
   if( !ref $feat || !$feat->isa("Bio::EnsEMBL::DnaPepAlignFeature") ) {
     throw("feature must be a Bio::EnsEMBL::DnaPepAlignFeature,"
           . " not a [".ref($feat)."].");
   }
 
   if($feat->is_stored($db)) {
     warning("PepDnaAlignFeature [".$feat->dbID."] is already stored" .
             " in this database.");
     next FEATURE;
   }
 
   #sanity check the hstart and hend
   my $hstart  = $feat->hstart();
   my $hend    = $feat->hend();
   $self->_check_start_end_strand($hstart,$hend,1,$feat->hslice);
 
   my $cigar_string = $feat->cigar_string();
   if(!$cigar_string) {
     $cigar_string = $feat->length() . 'M';
     warning("DnaPepAlignFeature does not define a cigar_string.\n" .
             "Assuming ungapped block with cigar_string=$cigar_string\n");
   }
 
   my $hseqname = $feat->hseqname();
   if(!$hseqname) {
     throw("DnaPepAlignFeature 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 $slice = $feat->slice();
   if(!defined($slice) || !($slice->isa("Bio::EnsEMBL::Slice") or $slice->isa('Bio::EnsEMBL::LRGSlice')) ) {
     throw("A slice must be attached to the features to be stored.");
   }
 
   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);
   $sth->bind_param(5,$feat->hstart,SQL_INTEGER);
   $sth->bind_param(6,$feat->hend,SQL_INTEGER);
   $sth->bind_param(7,$feat->hseqname,SQL_VARCHAR);
   $sth->bind_param(8,$feat->cigar_string,SQL_LONGVARCHAR);
   $sth->bind_param(9,$feat->analysis->dbID,SQL_INTEGER);
   $sth->bind_param(10,$feat->score,SQL_DOUBLE);
   $sth->bind_param(11,$feat->p_value,SQL_DOUBLE);
   $sth->bind_param(12,$feat->percent_id,SQL_REAL);
   $sth->bind_param(13,$feat->external_db_id,SQL_INTEGER);
   $sth->bind_param(14,$feat->hcoverage,SQL_DOUBLE);
   $sth->bind_param(15,$feat->align_type,SQL_VARCHAR);
 
   $sth->execute();
   my $dbId = $self->last_insert_id("${tablename}_id", undef, $tablename);
   $original->dbID($dbId);
   $original->adaptor($self);
 }
 
 $sth->finish();
}

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

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

Public Member Functions

Detailed Description

Synopsis

Member Function Documentation

◆ _columns()

◆ _left_join()

◆ _objs_from_sth()

◆ _tables()

◆ list_dbIDs()

◆ store()