Inheritance diagram for Bio::EnsEMBL::DBSQL::MiscFeatureAdaptor:

Public Member Functions
public Listref	fetch_all_by_Slice_and_set_code ()

public Listref	fetch_all_by_attribute_type_value ()

public Listref	fetch_by_attribute_set_value ()

protected	_tables ()

protected	_columns ()

protected	_default_where_clause ()

protected	_left_join ()

protected	_final_clause ()

protected	_objs_from_sth ()

public List	list_dbIDs ()

public void	store ()

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

$mfa = $database_adaptor->get_MiscFeatureAdaptor();
 
# retrieve a misc feature by its dbID
my $misc_feat = $mfa->fetch_by_dbID(1234);
 
# retrieve all misc features in a given region
my @misc_feats = @{ $mfa->fetch_all_by_Slice($slice) };
 
# retrieve all misc features in a given region with a given set code
my @misc_clones =
  @{ $mfa->fetch_all_by_Slice_and_set_code('cloneset') };
 
# store some misc features in the database
$mfa->store(@misc_features);

Description

This is an adaptor for the retrieval and storage of MiscFeatures.
Misc Features are extremely generic features that can be added with
minimal effort to the database.  Currently misc features are used to
describe the locations of clone sets and tiling path information,
but arbitrary features can be stored.  Misc features are grouped
into sets and can be fetched according to their grouping using the
fetch_all_by_Slice_and_set_code and fetch_all_by_set_code methods.
MiscFeatures may belong to more than one set.

Definition at line 40 of file MiscFeatureAdaptor.pm.

Member Function Documentation

◆ _columns()

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

Undocumented method

Code:

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◆ _default_where_clause()

protected Bio::EnsEMBL::DBSQL::MiscFeatureAdaptor::_default_where_clause ( )

Undocumented method

Code:

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◆ _final_clause()

protected Bio::EnsEMBL::DBSQL::MiscFeatureAdaptor::_final_clause ( )

Undocumented method

Code:

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◆ _left_join()

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

Undocumented method

Code:

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◆ _objs_from_sth()

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

Undocumented method

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 $msa = $self->db()->get_MiscSetAdaptor();
 
  my @features;
  my %ms_hash;
  my %slice_hash;
  my %sr_name_hash;
  my %sr_cs_hash;
 
  my(
     $misc_feature_id, $seq_region_id, $seq_region_start,
     $seq_region_end, $seq_region_strand,
     $attrib_value, $attrib_type_code, $misc_set_id,
     $attrib_type_name, $attrib_type_description );
 
  $sth->bind_columns( \$misc_feature_id, \$seq_region_id, \$seq_region_start,
                      \$seq_region_end, \$seq_region_strand,
                      \$attrib_value, \$attrib_type_code,\$misc_set_id,
                      \$attrib_type_name, \$attrib_type_description );
 
  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();
  }
 
  my $current = -1;
  my $throw_away = -1;
  my $feat;
  my $feat_misc_sets;
  my $feat_attribs;
  my $seen_attribs;
 
  FEATURE: while($sth->fetch()) {
    #if this feature is not being used, skip all rows related to it
    next if($throw_away == $misc_feature_id);
 
    if ($current == $misc_feature_id) {
      #still working on building up attributes and sets for current feature
 
      #if there is a misc_set, add it to the current feature
      if ($misc_set_id) {
        my $misc_set = $ms_hash{$misc_set_id} ||=
          $msa->fetch_by_dbID($misc_set_id);
        if ( ! exists $feat_misc_sets->{$misc_set->{'code'}} ) {
          $feat->add_MiscSet( $misc_set );
          $feat_misc_sets->{$misc_set->{'code'}} = $misc_set;
        }
      }
 
      #if there is a new attribute add it to the current feature
      if ($attrib_value && $attrib_type_code && !$seen_attribs->{"$attrib_type_code:$attrib_value"}) {
        my $attrib = Bio::EnsEMBL::Attribute->new
          ( -CODE => $attrib_type_code,
            -NAME => $attrib_type_name,
            -DESC => $attrib_type_description,
            -VALUE => $attrib_value
          );
  
  
        $feat_attribs ||= [];
        push @$feat_attribs, $attrib;
        $seen_attribs->{"$attrib_type_code:$attrib_value"} = 1;
      }
 
    } else {
      if ($feat) {
        #start working on a new feature, discard references to last one
        $feat = {};
        $feat_attribs = [];
        $feat_misc_sets = {};
        $seen_attribs = {};
      }
 
      $current = $misc_feature_id;
      #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();
      }
 
      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
        if(!defined($seq_region_id)) {
          $throw_away = $misc_feature_id;
          next FEATURE;
        }
 
        #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 ($dest_slice) {
        my $seq_region_len = $dest_slice->seq_region_length();
 
        if ($dest_slice_strand == 1) { # Positive strand
          $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 cicular chromosomes.
 
            if ($seq_region_start > $seq_region_end) {
            # Looking at a feature overlapping the chromsome 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   += $seq_region_len;
              }
            }
          }           ## end if ($dest_slice->is_circular...)
        } else {    # Negative strand
            
          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
        if ($seq_region_end < 1 || $seq_region_start > $dest_slice_length ||
            $dest_slice_sr_id != $seq_region_id) {
          #flag this feature as one to throw away
          $throw_away = $misc_feature_id;
          next FEATURE;
        }
 
        $slice = $dest_slice;
      }
 
 
      if ($attrib_value && $attrib_type_code) {
        my $attrib = Bio::EnsEMBL::Attribute->new
          ( -CODE => $attrib_type_code,
            -NAME => $attrib_type_name,
            -DESC => $attrib_type_description,
            -VALUE => $attrib_value
          );
        $feat_attribs = [$attrib];
        $seen_attribs->{"$attrib_type_code:$attrib_value"} = 1;
      }
 
      $feat =
        $self->_create_feature_fast( 'Bio::EnsEMBL::MiscFeature', {
                                       'start'   => $seq_region_start,
                                       'end'     => $seq_region_end,
                                       'strand'  => $seq_region_strand,
                                       'slice'   => $slice,
                                       'adaptor' => $self,
                                       'dbID'    => $misc_feature_id,
                                       'attributes' => $feat_attribs ||= []
                                     } );
 
      push @features, $feat;
 
      if ($misc_set_id) {
        #get the misc_set object
        my $misc_set = $ms_hash{$misc_set_id} ||=
          $msa->fetch_by_dbID($misc_set_id);
        if ( ! exists $feat_misc_sets->{$misc_set->{'code'}} ) {
          $feat->add_MiscSet( $misc_set );
          $feat_misc_sets->{$misc_set->{'code'}} = $misc_set;
        }
      }
    }
  }
 
  return \@features;
}

◆ _tables()

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

Undocumented method

Code:

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◆ fetch_all_by_attribute_type_value()

public Listref Bio::EnsEMBL::DBSQL::MiscFeatureAdaptor::fetch_all_by_attribute_type_value ( )

  Arg [1]    : string $attrib_type_code
               The code of the attribute type to fetch features for
  Arg [2]    : (optional) string $attrib_value
               The value of the attribute to fetch features for
  Example    :

#get all misc features that have an embl accession
@feats = @{$mfa->fetch_all_by_attrib_type_value('embl_acc')};
#get the misc feature with synonym 'AL014121'
($feat)=@{$mfa->fetch_all_by_attrib_type_value('synonym','AL014121');

  Description: Retrieves MiscFeatures which have a particular attribute.
               If the attribute value argument is also provided only
               features which have the attribute AND a particular value
               are returned.  The features are returned in their native
               coordinate system (i.e. the coordinate system that they
               are stored in).
  Returntype : listref of Bio::EnsEMBL::MiscFeatures
  Exceptions : throw if attrib_type code arg is not provided
  Caller     : general
  Status     : Stable

Code:

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◆ fetch_all_by_Slice_and_set_code()

public Listref Bio::EnsEMBL::DBSQL::MiscFeatureAdaptor::fetch_all_by_Slice_and_set_code ( )

  Arg [1]    : Bio::EnsEMBL::Slice $slice
               A slice representing the region to fetch from
  Arg [2...] : string $set_code
               The code of the set to retrieve features from
  Example    :

@feats = @{$mfa->fetch_all_by_Slice_and_set_code('cloneset')};

  Description: Retrieves a set of MiscFeatures which have a particular set code
               and which lie in a particular region.  All features with the
               provide set code and which overlap the given slice are returned.
  Returntype : listref of Bio::EnsEMBL::MiscFeatures
  Exceptions : throw if set_code is not provided
               warning if no set for provided set code exists
  Caller     : general
  Status     : Stable

Code:

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◆ fetch_by_attribute_set_value()

public Listref Bio::EnsEMBL::DBSQL::MiscFeatureAdaptor::fetch_by_attribute_set_value ( )

  Arg [1]    : string $attrib_type_code
               The code of the attribute type to fetch features for
  Arg [2]    : (optional) string $attrib_value
               The value of the attribute to fetch features for
  Arg [3]    : (optional) string $misc_set
               The name of the set to which the feature belongs
  Example    :

$feat = $mfa->fetch_by_attribute_set_value('clone', 'RP11-411G9', 'tilepath');

@section autotoc_md8 Get the clone belonging to the tilepath

  Description: Retrieves MiscFeatures which have a particular attribute.
               If the attribute value argument is also provided only
               features which have the attribute AND a particular value
               are returned.  The features are returned in their native
               coordinate system (i.e. the coordinate system that they
               are stored in).
  Returntype : listref of Bio::EnsEMBL::MiscFeatures
  Exceptions : throw if attrib_type code arg is not provided
  Caller     : general
  Status     : Stable

Code:

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◆ list_dbIDs()

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

  Arg [1]    : none
  Example    :

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

  Description: Gets an array of internal ids for all misc_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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◆ store()

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

  Arg [1]    : list of Bio::EnsEMBL::MiscFeatures @misc_features
  Example    :

$misc_feature_adaptor->store(@misc_features);

  Description: Stores a list of MiscFeatures in this database.  The stored
               features will have their 
  Returntype : none
  Exceptions : throw on invalid arguments
               warning if misc feature is already stored in this database
               throw if start/end/strand attribs are not valid
  Caller     : general
  Status     : Stable

Code:

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sub store {
  my $self = shift;
  my @misc_features = @_;
 
  my $db = $self->db();
 
  my $feature_sth = $self->prepare(
    q{INSERT INTO misc_feature (
        seq_region_id,
        seq_region_start,
        seq_region_end,
        seq_region_strand
      ) VALUES (?, ?, ?, ?)
    });
 
  my $insert_ignore = $self->insert_ignore_clause();
  my $feature_set_sth = $self->prepare(
    qq{${insert_ignore} INTO misc_feature_misc_set (
         misc_feature_id,
         misc_set_id
       ) VALUES (?, ?)
      });
 
  my $msa = $db->get_MiscSetAdaptor();
  my $aa  = $db->get_AttributeAdaptor();
 
 FEATURE:
  foreach my $mf (@misc_features) {
    if(!ref($mf) || !$mf->isa('Bio::EnsEMBL::MiscFeature')) {
      throw("List of MiscFeature arguments expeceted");
    }
 
    if($mf->is_stored($db)) {
      warning("MiscFeature [" .$mf->dbID."] is already stored in database.");
      next FEATURE;
    }
 
    # do some checking of the start/end and convert to seq_region coords
    my $original = $mf;
    my $seq_region_id;
    ($mf, $seq_region_id) = $self->_pre_store($mf);
 
    # store the actual MiscFeature
    $feature_sth->bind_param(1,$seq_region_id,SQL_INTEGER);
    $feature_sth->bind_param(2,$mf->start,SQL_INTEGER);
    $feature_sth->bind_param(3,$mf->end,SQL_INTEGER);
    $feature_sth->bind_param(4,$mf->strand,SQL_TINYINT);
    $feature_sth->execute();
 
    my $dbID = $self->last_insert_id('misc_feature_id', undef, 'misc_feature');
 
    $mf->dbID($dbID);
    $mf->adaptor($self);
 
    # store all the attributes
    my $attribs = $mf->get_all_Attributes();
    $aa->store_on_MiscFeature($mf, $attribs);
 
    # store all the sets that have not been stored yet
    my $sets = $mf->get_all_MiscSets();
    foreach my $set (@$sets) {
      $msa->store($set) if(!$set->is_stored($db));
 
      # update the misc_feat_misc_set table to store the set relationship
      $feature_set_sth->bind_param(1,$dbID,SQL_INTEGER);
      $feature_set_sth->bind_param(2,$set->dbID,SQL_INTEGER);
 
      $feature_set_sth->execute();
    }
  }
 
  return;
}

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

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

Public Member Functions

Detailed Description

Synopsis

Description

Member Function Documentation

◆ _columns()

◆ _default_where_clause()

◆ _final_clause()

◆ _left_join()

◆ _objs_from_sth()

◆ _tables()

◆ fetch_all_by_attribute_type_value()

◆ fetch_all_by_Slice_and_set_code()

◆ fetch_by_attribute_set_value()

◆ list_dbIDs()

◆ store()