Inheritance diagram for Bio::EnsEMBL::Map::DBSQL::DitagFeatureAdaptor:

Class Summary

Synopsis

  my $dfa = $db-\>get_DitagFeatureAdaptor;
  my $ditagFeatures = $dfa-\>fetch_all_by_Slice( $slice, "SME005" );

  foreach my $ditagFeature (@$ditagFeatures) {
    print $ditagFeature-\>ditag_id . " "
      . $ditagFeature-\>slice . " "
      . $ditagFeature-\>start . "-"
      . $ditagFeature-\>end . " "
      . $ditagFeature-\>strand;
  }

Description

Provides database interaction for the Bio::EnsEMBL::Map::DitagFeature
object

Definition at line 30 of file DitagFeatureAdaptor.pm.

Available Methods
protected	_columns ()
protected	_default_where_clause ()
protected Listref	_fetch ()
protected	_final_clause ()
protected	_left_join ()
protected	_list_dbIDs ()
protected	_objs_from_sth ()
protected	_straight_join ()
protected	_tables ()
public void	batch_store ()
public Listref	bind_param_generic_fetch ()
public Bio::EnsEMBL::DBSQL::DBAdaptor	db ()
public Bio::EnsEMBL::DBSQL::DBConnection	dbc ()
public	dump_data ()
public Listref	fetch_all ()
public Listref	fetch_all_by_dbID_list ()
public Listref	fetch_all_by_ditagID ()
public Listref	fetch_all_by_Slice ()
public Listref	fetch_all_by_type ()
public Bio::EnsEMBL::Map::DitagFeature	fetch_by_dbID ()
public Array	fetch_pairs_by_Slice ()
public Listref	generic_fetch ()
public	get_dumped_data ()
public Boolean	is_multispecies ()
public Scalar	last_insert_id ()
public List	list_dbIDs ()
public Bio::EnsEMBL::DBSQL::BaseAdaptor	new ()
public DBI::StatementHandle	prepare ()
public String	sequence ()
public Int	species_id ()
public void	store ()
public Boolean	update ()

Method Documentation

protected Bio::EnsEMBL::DBSQL::BaseAdaptor::_columns ( ) [inherited]

Undocumented method

Code:

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protected Bio::EnsEMBL::DBSQL::BaseAdaptor::_default_where_clause ( ) [inherited]

Undocumented method

Code:

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Reimplemented in Bio::EnsEMBL::DBSQL::MiscFeatureAdaptor, Bio::EnsEMBL::DBSQL::RepeatFeatureAdaptor, Bio::EnsEMBL::Map::DBSQL::MarkerFeatureAdaptor, and Bio::EnsEMBL::Map::DBSQL::QtlFeatureAdaptor.

protected Listref Bio::EnsEMBL::Map::DBSQL::DitagFeatureAdaptor::_fetch ( )

  Arg [1]    : statement handler
  Arg [2]    : (optional) target-slice for the feature
  Description: generic sql-fetch function for the DitagFeature fetch methods
  Returntype : listref of Bio::EnsEMBL::Map::DitagFeatures
  Caller     : private
  Status     : At Risk

Code:

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sub _fetch {
  my ($self, $sth, $dest_slice) = @_;

  my ( $tag_id, $mothertag_id, $seqreg, $seqstart, $seqend, $strand, $analysis_id, $hit_start,
       $hit_end, $hit_strand, $cigar_line, $ditag_side, $ditag_pair_id, $tag_count );
  $sth->bind_columns( \$tag_id,        \$mothertag_id, \$seqreg,
                      \$seqstart,      \$seqend,       \$strand,
                      \$analysis_id,   \$hit_start,    \$hit_end,
                      \$hit_strand,    \$cigar_line,   \$ditag_side,
                      \$ditag_pair_id, \$tag_count );

  my @ditag_features;
  my $dest_slice_start;
  my $dest_slice_end;
  my $dest_slice_strand;
  if($dest_slice) {
    $dest_slice_start   = $dest_slice->start();
    $dest_slice_end     = $dest_slice->end();
    $dest_slice_strand  = $dest_slice->strand();
  }

  while ( $sth->fetch ) {
    my $analysis_obj = $self->db->get_AnalysisAdaptor->fetch_by_dbID($analysis_id);
    my $slice        = $self->db->get_SliceAdaptor->fetch_by_seq_region_id($seqreg);

    if($dest_slice) {
      if($dest_slice_start != 1 || $dest_slice_strand != 1) {
        if($dest_slice_strand == 1) {
          $seqstart    = $seqstart  - $dest_slice_start + 1;
          $seqend      = $seqend    - $dest_slice_start + 1;
        } else {
          my $tmp_seq_region_start = $seqstart;
          $seqstart    = $dest_slice_end - $seqend + 1;
          $seqend      = $dest_slice_end - $tmp_seq_region_start + 1;
          $strand     *= -1;
        }
    $slice = $dest_slice;
      }
    }

    push @ditag_features,
      Bio::EnsEMBL::Map::DitagFeature->new( -dbid          => $tag_id,
                                            -slice         => $slice,
                                            -start         => $seqstart,
                                            -end           => $seqend,
                                            -strand        => $strand, 
                                            -analysis      => $analysis_obj,
                                            -hit_start     => $hit_start,
                                            -hit_end       => $hit_end,
                                            -hit_strand    => $hit_strand,
                                            -ditag_id      => $mothertag_id,
                                            -cigar_line    => $cigar_line,
                                            -ditag_side    => $ditag_side,
                        -ditag_pair_id => $ditag_pair_id,
                        -ditag         => undef,
                        -tag_count     => $tag_count,
                                            -adaptor       => $self,
                                            );
  }

  return \@ditag_features;
}

protected Bio::EnsEMBL::DBSQL::BaseAdaptor::_final_clause ( ) [inherited]

Undocumented method

Code:

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Reimplemented in Bio::EnsEMBL::DBSQL::ExonAdaptor, Bio::EnsEMBL::DBSQL::MiscFeatureAdaptor, and Bio::EnsEMBL::DBSQL::PredictionExonAdaptor.

protected Bio::EnsEMBL::DBSQL::BaseAdaptor::_left_join ( ) [inherited]

Undocumented method

Code:

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Reimplemented in Bio::EnsEMBL::DBSQL::DnaAlignFeatureAdaptor, Bio::EnsEMBL::DBSQL::GeneAdaptor, Bio::EnsEMBL::DBSQL::MiscFeatureAdaptor, Bio::EnsEMBL::DBSQL::ProteinAlignFeatureAdaptor, Bio::EnsEMBL::DBSQL::SplicingEventAdaptor, Bio::EnsEMBL::DBSQL::TranscriptAdaptor, Bio::EnsEMBL::DBSQL::UnmappedObjectAdaptor, Bio::EnsEMBL::Map::DBSQL::MarkerFeatureAdaptor, and Bio::EnsEMBL::Map::DBSQL::QtlFeatureAdaptor.

protected Bio::EnsEMBL::DBSQL::BaseAdaptor::_list_dbIDs ( ) [inherited]

Undocumented method

Code:

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protected Bio::EnsEMBL::DBSQL::BaseAdaptor::_objs_from_sth ( ) [inherited]

Undocumented method

Code:

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protected Bio::EnsEMBL::DBSQL::BaseAdaptor::_straight_join ( ) [inherited]

Undocumented method

Code:

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protected Bio::EnsEMBL::DBSQL::BaseAdaptor::_tables ( ) [inherited]

Undocumented method

Code:

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public void Bio::EnsEMBL::Map::DBSQL::DitagFeatureAdaptor::batch_store ( )

  Arg [1]    : (Array ref of) Bio::EnsEMBL::Map::DitagFeatures
  Arg [2]    : bool have_dbIDs
  Example    : $ditagfeature_adaptor->batch_store(\@ditag_features);
  Description: Stores a list of ditagFeatures in this database.
               DitagFeatures are expected to have no dbID yet unless flag "have_dbIDs" is true.
               They are inserted in one combined INSERT for better performance.
  Returntype : none
  Exceptions : thrown if not all data needed for storing is given for the
               ditag features
  Caller     : general
  Status     : At Risk

Code:

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sub batch_store {
  my ( $self, $ditag_features, $have_dbIDs ) = @_;

  my @good_ditag_features;
  my ($sql, $sqladd);
  my $inserts = 0;

  if ( ref $ditag_features eq 'ARRAY' ) {
    if ( scalar(@$ditag_features) == 0 ) {
      throw( "Must call store with ditag_feature or list ref of ditag_features." );
    }
  } elsif ($ditag_features) {
    my @ditag_features;
    push @ditag_features, $ditag_features;
    $ditag_features = \@ditag_features;
  } else {
    throw( "Must call store with ditag_feature or list ref of ditag_features." );
  }

  my $db = $self->db() or throw "Couldn t get database connection.";

  #check whether it s a DitagFeature object and is not stored already
  foreach my $ditag_feature (@$ditag_features) {

    if ( !ref $ditag_feature || !$ditag_feature->isa("Bio::EnsEMBL::Map::DitagFeature") ) {
      throw(   "Object must be an Ensembl DitagFeature, "
             . "not a " . ref($ditag_feature) );
    }
    if(!$ditag_feature->ditag_id or !($self->db->get_DitagAdaptor->fetch_by_dbID($ditag_feature->ditag_id))){
      throw("DitagFeature must be supplied with the id of a corresponding Ditag object.");
    }

    if(!$ditag_feature->ditag or !$ditag_feature->ditag->isa("Bio::EnsEMBL::Map::Ditag")){
      throw("DitagFeature must be linked to a valid Ditag object.");
    }
    if ( $ditag_feature->is_stored($db) ) {
      warning(   "DitagFeature " . $ditag_feature->dbID
                 . " is already stored in this database." );
      next;
    }
    push(@good_ditag_features, $ditag_feature);
  }
  $ditag_features = undef;

  #create batch INSERT
  if($have_dbIDs){
    $sql = "INSERT INTO ditag_feature ( ditag_feature_id, ditag_id, seq_region_id, seq_region_start, ".
           "seq_region_end, seq_region_strand, analysis_id, hit_start, hit_end, ".
           "hit_strand, cigar_line, ditag_side, ditag_pair_id ) VALUES ";
    foreach my $ditag_feature (@good_ditag_features) {
      $sqladd = "";
      if($inserts){ $sqladd = ", " }
      $sqladd .= "(". $ditag_feature->ditag_feature_id.", ".$ditag_feature->ditag_id.", ".
             ($ditag_feature->slice->get_seq_region_id).", ". $ditag_feature->start.", ".
         $ditag_feature->end.", '".$ditag_feature->strand."', ".$ditag_feature->analysis->dbID.", ".
                 $ditag_feature->hit_start.", ".$ditag_feature->hit_end.", '".$ditag_feature->hit_strand.
         "', '".$ditag_feature->cigar_line."', '".$ditag_feature->ditag_side."', ".
         $ditag_feature->ditag_pair_id.")";
      $sql .= $sqladd;
      $inserts++;
    }
  }
  else{
    $sql = "INSERT INTO ditag_feature ( ditag_id, seq_region_id, seq_region_start, ".
           "seq_region_end, seq_region_strand, analysis_id, hit_start, hit_end, ".
           "hit_strand, cigar_line, ditag_side, ditag_pair_id ) VALUES ";
    foreach my $ditag_feature (@good_ditag_features) {
      $sqladd = "";
      if($inserts){ $sqladd = ", " }
      $sqladd .= "(". $ditag_feature->ditag_id.", ".($ditag_feature->slice->get_seq_region_id).", ".
             $ditag_feature->start.", ".$ditag_feature->end.", '".$ditag_feature->strand."', ".
         $ditag_feature->analysis->dbID.", ".$ditag_feature->hit_start.", ".$ditag_feature->hit_end.
         ", '".$ditag_feature->hit_strand."', '".$ditag_feature->cigar_line."', '".
         $ditag_feature->ditag_side."', ".$ditag_feature->ditag_pair_id.")";
      $sql .= $sqladd;
      $inserts++;
    }
  }

  #STORE
  if($inserts){
    print STDERR "\nHave $inserts Features.\n";
    eval{
      $db->dbc->do($sql);
    };
    if($@){
      warning("Problem inserting ditag feature batch!".$@."\n");
    }
  }
  else{
    warn "Nothing stored!";
  }

}

public Listref Bio::EnsEMBL::DBSQL::BaseAdaptor::bind_param_generic_fetch ( ) [inherited]

 Arg [1]   : (optional)  scalar $param
              This is the parameter to bind
 Arg [2]   : (optional) int $sql_type
              Type of the parameter (from DBI (:sql_types))
 Example   :  $adaptor->bind_param_generic_fetch($stable_id,SQL_VARCHAR);
              $adaptor->generic_fetch();
 Description:  When using parameters for the query, will call the bind_param to avoid
               some security issues. If there are no arguments, will return the bind_parameters
 ReturnType : listref
 Exceptions:  if called with one argument

Code:

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public Bio::EnsEMBL::DBSQL::DBAdaptor Bio::EnsEMBL::DBSQL::BaseAdaptor::db ( ) [inherited]

  Arg [1]    : (optional) Bio::EnsEMBL::DBSQL::DBAdaptor $obj 
               the database this adaptor is using.
  Example    : $db = $adaptor->db();
  Description: Getter/Setter for the DatabaseConnection that this adaptor is 
               using.
  Returntype : Bio::EnsEMBL::DBSQL::DBAdaptor
  Exceptions : none
  Caller     : Adaptors inherited from BaseAdaptor
  Status     : Stable

Code:

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public Bio::EnsEMBL::DBSQL::DBConnection Bio::EnsEMBL::DBSQL::BaseAdaptor::dbc ( ) [inherited]

  Arg [1]    : (optional) Bio::EnsEMBL::DBSQL::DBConnection $obj 
               the database this adaptor is using.
  Example    : $db = $adaptor->db();
  Description: Getter/Setter for the DatabaseConnection that this adaptor is 
               using.
  Returntype : Bio::EnsEMBL::DBSQL::DBConnection
  Exceptions : none
  Caller     : Adaptors inherited from BaseAdaptor
  Status     : Stable

Code:

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public Bio::EnsEMBL::DBSQL::BaseAdaptor::dump_data ( ) [inherited]

Undocumented method

Code:

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public Listref Bio::EnsEMBL::Map::DBSQL::DitagFeatureAdaptor::fetch_all ( )

  Arg [1]    : none
  Example    : @all_tags = @{$ditagfeature_adaptor->fetch_all};
  Description: Retrieves all ditagFeatures from the database;
               Usually not a good idea, use fetch_all_by_Slice instead.
  Returntype : listref of Bio::EnsEMBL::Map::DitagFeature
  Caller     : general
  Status     : At Risk

Code:

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Reimplemented from Bio::EnsEMBL::DBSQL::BaseAdaptor.

public Listref Bio::EnsEMBL::DBSQL::BaseAdaptor::fetch_all_by_dbID_list ( ) [inherited]

  Arg [1]    : listref of integers $id_list
               The unique database identifiers for the features to
               be obtained.
  Arg [2]    : optional - Bio::EnsEMBL::Slice to map features onto.
  Example    : @feats = @{$adaptor->fetch_all_by_dbID_list([1234, 2131, 982]))};
  Description: Returns the features created from the database
               defined by the the IDs in contained in the provided
               ID list $id_list.  The features will be returned
               in their native coordinate system.  That is, the
               coordinate system in which they are stored in the
               database.  In order to convert the features to a
               particular coordinate system use the transfer() or
               transform() method.  If none of the features are
               found in the database a reference to an empty list is
               returned.
  Returntype : listref of Bio::EnsEMBL::Features
  Exceptions : thrown if $id arg is not provided
               does not exist
  Caller     : general
  Status     : Stable

Code:

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Reimplemented in Bio::EnsEMBL::DBSQL::OntologyTermAdaptor.

public Listref Bio::EnsEMBL::Map::DBSQL::DitagFeatureAdaptor::fetch_all_by_ditagID ( )

  Arg [1]    : ditag dbID
  Arg [2]    : (optional) ditag-pair dbID
  Arg [3]    : (optional) analysis ID
  Example    : @my_tags = @{$ditagfeature_adaptor->fetch_all_by_ditag_id($my_id)};
  Description: Retrieves all ditagFeatures from the database linking to a specific ditag-id
  Returntype : listref of Bio::EnsEMBL::Map::DitagFeature
  Caller     : general
  Status     : At Risk

Code:

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public Listref Bio::EnsEMBL::Map::DBSQL::DitagFeatureAdaptor::fetch_all_by_Slice ( )

  Arg [1]    : Bio::EnsEMBL::Slice
  Arg [2]    : (optional) ditag type name (specific library) or an aray ref with multiple type names
  Arg [3]    : (optional) analysis logic_name
  Example    : $tags = $ditagfeature_adaptor->fetch_all_by_Slice($slice, "SME005");
  Description: Retrieves ditagFeatures from the database overlapping a specific region
               and (optional) of a specific ditag type or analysis.
               Start & end locations are returned in slice coordinates, now.
  Returntype : listref of Bio::EnsEMBL::Map::DitagFeatures
  Caller     : general
  Status     : At Risk

Code:

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public Listref Bio::EnsEMBL::Map::DBSQL::DitagFeatureAdaptor::fetch_all_by_type ( )

  Arg [1]    : ditag type
  Example    : @my_tags = @{$ditagfeature_adaptor->fetch_all_by_type($type)};
  Description: Retrieves all ditagFeatures from the database linking to a specific ditag-type
  Returntype : listref of Bio::EnsEMBL::Map::DitagFeature
  Caller     : general
  Status     : At Risk

Code:

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public Bio::EnsEMBL::Map::DitagFeature Bio::EnsEMBL::Map::DBSQL::DitagFeatureAdaptor::fetch_by_dbID ( )

  Arg [1]    : ditagFeature dbID
  Example    : @my_tags = @{$ditagfeature_adaptor->fetch_by_dbID($my_id)};
  Description: Retrieves a ditagFeature from the database.
  Returntype : Bio::EnsEMBL::Map::DitagFeature
  Caller     : general
  Status     : At Risk

Code:

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Reimplemented from Bio::EnsEMBL::DBSQL::BaseAdaptor.

public Array Bio::EnsEMBL::Map::DBSQL::DitagFeatureAdaptor::fetch_pairs_by_Slice ( )

  Arg [1]    : Bio::EnsEMBL::Slice
  Arg [2]    : (optional) ditag type (specific library)
  Arg [3]    : (optional) analysis logic_name
  Example    : my $ditagfeatures = $dfa->fetch_pairs_by_Slice($slice);
               foreach my $ditagfeature (@$ditagfeatures){
                 $minstart   = $$ditagfeature2{'start'};
                 $maxend     = $$ditagfeature2{'end'};
                 $bothstrand = $$ditagfeature2{'strand'};
                 $tag_count  = $$ditagfeature2{'tag_count'};
                 print "$minstart, $maxend, $bothstrand, $tag_count\\n";
               }
  Description: Retrieves ditagFeature information in pairs from the database overlapping a specific region
               and (optional) of a specific ditag type or analysis. The absotute start and end points are
               fetched.
               Slices should be SMALL!
  Returntype : array ref with hash ref of artifical DitagFeature object
  Caller     : general
  Status     : At Risk

Code:

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public Listref Bio::EnsEMBL::DBSQL::BaseAdaptor::generic_fetch ( ) [inherited]

  Arg [1]    : (optional) string $constraint
               An SQL query constraint (i.e. part of the WHERE clause)
  Arg [2]    : (optional) Bio::EnsEMBL::AssemblyMapper $mapper
               A mapper object used to remap features
               as they are retrieved from the database
  Arg [3]    : (optional) Bio::EnsEMBL::Slice $slice
               A slice that features should be remapped to
  Example    : $fts = $a->generic_fetch('contig_id in (1234, 1235)', 'Swall');
  Description: Performs a database fetch and returns feature objects in
               contig coordinates.
  Returntype : listref of Bio::EnsEMBL::SeqFeature in contig coordinates
  Exceptions : none
  Caller     : BaseFeatureAdaptor, ProxyDnaAlignFeatureAdaptor::generic_fetch
  Status     : Stable

Code:

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sub generic_fetch {
  my ($self, $constraint, $mapper, $slice) = @_;

  my @tabs = $self->_tables();

  my $extra_default_where;

  # Hack for feature types that needs to be restricted to species_id (in
  # coord_system).
  if (    $self->is_multispecies()
       && $self->isa('Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor')
       && !$self->isa('Bio::EnsEMBL::DBSQL::UnmappedObjectAdaptor') )
  {
    # We do a check to see if there is already seq_region
    # and coord_system defined to ensure we get the right
    # alias.  We then do the extra query irrespectively of
    # what has already been specified by the user.
    my %thash = map { $_->[0] => $_->[1] } @tabs;

    my $sr_alias =
      ( exists( $thash{seq_region} ) ? $thash{seq_region} : 'sr' );
    my $cs_alias =
      ( exists( $thash{coord_system} ) ? $thash{coord_system} : 'cs' );

    if ( !exists( $thash{seq_region} ) ) {
      push( @tabs, [ 'seq_region', $sr_alias ] );
    }
    if ( !exists( $thash{coord_system} ) ) {
      push( @tabs, [ 'coord_system', $cs_alias ] );
    }

    $extra_default_where = sprintf(
                      '%s.seq_region_id = %s.seq_region_id '
                        . 'AND %s.coord_system_id = %s.coord_system_id '
                        . 'AND %s.species_id = ?',
                      $tabs[0]->[1], $sr_alias, $sr_alias,
                      $cs_alias,     $cs_alias );

    $self->bind_param_generic_fetch( $self->species_id(), SQL_INTEGER );
  } ## end if ( $self->is_multispecies...)

  my $columns = join(', ', $self->_columns());

  my $db = $self->db();

  #
  # Construct a left join statement if one was defined, and remove the
  # left-joined table from the table list
  #
  my @left_join_list = $self->_left_join();
  my $left_join_prefix = '';
  my $left_join = '';
  my @tables;
  if(@left_join_list) {
    my %left_join_hash = map { $_->[0] => $_->[1] } @left_join_list;
    while(my $t = shift @tabs) {
        my $t_alias = $t->[0] . " " . $t->[1];
      if( exists $left_join_hash{ $t->[0] } || exists $left_join_hash{$t_alias}) {
        my $condition = $left_join_hash{ $t->[0] };
        $condition ||= $left_join_hash{$t_alias};
        my $syn = $t->[1];
        $left_join .=
          "\n  LEFT JOIN " . $t->[0] . " $syn ON $condition ) ";
        $left_join_prefix .= '(';
      } else {
        push @tables, $t;
      }
    }
  } else {
    @tables = @tabs;
  }

  my $straight_join = '';

  if($self->_straight_join()) {
    $straight_join = "STRAIGHT_JOIN";
  }

  #construct a nice table string like 'table1 t1, table2 t2'
  my $tablenames = join(', ', map({ join(' ', @$_) } @tables));

  my $sql =
      "SELECT $straight_join $columns\n"
    . "FROM $left_join_prefix ($tablenames) $left_join";

  my $default_where = $self->_default_where_clause();
  my $final_clause = $self->_final_clause;

  if ($extra_default_where) {
    if ($default_where) {
      $default_where .= "\n AND $extra_default_where";
    } else {
      $default_where = $extra_default_where;
    }
  }

  #append a where clause if it was defined
  if ($constraint) {
    $sql .= "\n WHERE $constraint ";
    if ($default_where) {
      $sql .= " AND\n       $default_where ";
    }
  } elsif ($default_where) {
    $sql .= "\n WHERE $default_where ";
  }

  #append additional clauses which may have been defined
  $sql .= "\n$final_clause";


  # FOR DEBUG:
  #printf(STDERR "SQL:\n%s\n", $sql);
  
  
  my $sth = $db->dbc->prepare($sql);
  my $bind_parameters = $self->bind_param_generic_fetch();
  if (defined $bind_parameters){
      #if we have bind the parameters, call the DBI to bind them
      my $i = 1;
      foreach my $param (@{$bind_parameters}){
        $sth->bind_param($i,$param->[0],$param->[1]);
        $i++;
      }
      #after binding parameters, undef for future queries
      $self->{'_bind_param_generic_fetch'} = ();
  }
  eval { $sth->execute() };
  if ($@) {
    throw("Detected an error whilst executing SQL '${sql}': $@");
  }

  my $res = $self->_objs_from_sth($sth, $mapper, $slice);
  $sth->finish();
  return $res;
}

Reimplemented in Bio::EnsEMBL::DBSQL::DataFileAdaptor.

public Bio::EnsEMBL::DBSQL::BaseAdaptor::get_dumped_data ( ) [inherited]

Undocumented method

Code:

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public Boolean Bio::EnsEMBL::DBSQL::BaseAdaptor::is_multispecies ( ) [inherited]

  Arg [1]    : (optional) boolean $arg
  Example    : if ($adaptor->is_multispecies()) { }
  Description: Getter/Setter for the is_multispecies boolean of
               to use for this adaptor.
  Returntype : boolean
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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public Scalar Bio::EnsEMBL::DBSQL::BaseAdaptor::last_insert_id ( ) [inherited]

  Arg [1]     : (optional) $field the name of the field the inserted ID was pushed 
                into
  Arg [2]     : (optional) HashRef used to pass extra attributes through to the 
                DBD driver
  Description : Delegating method which uses DBI to extract the last inserted 
                identifier. If using MySQL we just call the DBI method 
                DBI::last_insert_id() since MySQL ignores any extra
                arguments. See DBI for more information about this 
                delegated method. 
  Example     : my $id = $self->last_insert_id('my_id'); my $other_id = $self->last_insert_id();
  Returntype  : Scalar or undef

Code:

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public List Bio::EnsEMBL::Map::DBSQL::DitagFeatureAdaptor::list_dbIDs ( )

  Args       : None
  Example    : my @feature_ids = @{$dfa->list_dbIDs()};
  Description: Gets an array of internal IDs for all DitagFeature objects in
               the current database.
  Arg[1]     : <optional> int. not 0 for the ids to be sorted by the seq_region.
  Returntype : List of ints
  Exceptions : None
  Status     : Stable

Code:

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public Bio::EnsEMBL::DBSQL::BaseAdaptor Bio::EnsEMBL::DBSQL::BaseAdaptor::new ( ) [inherited]

  Arg [1]    : Bio::EnsEMBL::DBSQL::DBConnection $dbobj
  Example    : $adaptor = new AdaptorInheritedFromBaseAdaptor($dbobj);
  Description: Creates a new BaseAdaptor object.  The intent is that this
               constructor would be called by an inherited superclass either
               automatically or through $self->SUPER::new in an overridden 
               new method.
  Returntype : Bio::EnsEMBL::DBSQL::BaseAdaptor
  Exceptions : none
  Caller     : Bio::EnsEMBL::DBSQL::DBConnection
  Status     : Stable

Code:

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public DBI::StatementHandle Bio::EnsEMBL::DBSQL::BaseAdaptor::prepare ( ) [inherited]

  Arg [1]    : string $string
               a SQL query to be prepared by this adaptors database
  Example    : $sth = $adaptor->prepare("select yadda from blabla")
  Description: provides a DBI statement handle from the adaptor. A convenience
               function so you dont have to write $adaptor->db->prepare all the
               time
  Returntype : DBI::StatementHandle
  Exceptions : none
  Caller     : Adaptors inherited from BaseAdaptor
  Status     : Stable

Code:

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Reimplemented in Bio::EnsEMBL::DBSQL::SliceAdaptor, and Bio::EnsEMBL::External::BlastAdaptor.

public String Bio::EnsEMBL::Map::DBSQL::DitagFeatureAdaptor::sequence ( )

  Arg [1]    : dbID of DitagFeature
  Example    : $ditagfeature_adaptor->get_sequence($ditagFeature->dbID)
  Description: get the part of the sequence of a ditag,
               that is actully aligned to the genome.
  Returntype : string
  Exceptions : thrown if not all data needed for storing is populated in the
               ditag features
  Caller     : Bio::EnsEMBL::Map::DitagFeature
  Status     : At Risk

Code:

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public Int Bio::EnsEMBL::DBSQL::BaseAdaptor::species_id ( ) [inherited]

  Arg [1]    : (optional) int $species_id
               The internal ID of the species in a multi-species database.
  Example    : $db = $adaptor->db();
  Description: Getter/Setter for the internal ID of the species in a
               multi-species database.  The default species ID is 1.
  Returntype : Integer
  Exceptions : none
  Caller     : Adaptors inherited from BaseAdaptor
  Status     : Stable

Code:

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public void Bio::EnsEMBL::Map::DBSQL::DitagFeatureAdaptor::store ( )

  Arg [1]    : (Array ref of) Bio::EnsEMBL::Map::DitagFeature
  Example    : $ditagfeature_adaptor->store(@ditag_features);
  Description: Stores a single ditagFeature or
               a list of ditagFeatures in this database.
  Returntype : none
  Exceptions : thrown if not all data needed for storing is populated in the
               ditag features
  Caller     : general
  Status     : At Risk

Code:

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sub store {
  my ( $self, $ditag_features ) = @_;

  if ( ref $ditag_features eq 'ARRAY' ) {
    if ( scalar(@$ditag_features) == 0 ) {
      throw( "Must call store with ditag_feature or list ref of ditags_features" );
    }
  } elsif ($ditag_features) {
    my @ditag_features;
    push @ditag_features, $ditag_features;
    $ditag_features = \@ditag_features;
  } else {
    throw( "Must call store with ditag_feature or list ref of ditag_features." );
  }

  my $db = $self->db() or throw "Couldn t get database connection.";

  my $sth1 = $self->prepare( "INSERT INTO ditag_feature( ditag_id, seq_region_id, seq_region_start, 
                              seq_region_end, seq_region_strand, analysis_id, hit_start, hit_end, 
                              hit_strand, cigar_line, ditag_side, ditag_pair_id ) 
                              VALUES( ?,?,?,?,?,?,?,?,?,?,?,? )" );
  my $sth2 = $self->prepare( "INSERT INTO ditag_feature( ditag_feature_ID, ditag_id, seq_region_id, 
                              seq_region_start, seq_region_end, seq_region_strand, analysis_id, hit_start, 
                              hit_end, hit_strand, cigar_line, ditag_side, ditag_pair_id ) 
                              VALUES( ?,?,?,?,?,?,?,?,?,?,?,?,? )" );
#  my $sth3 = $self->prepare( "SELECT COUNT(*) FROM ditag_feature 
#                              WHERE ditag_id = ?" );

TAG:
  foreach my $ditag_feature (@$ditag_features) {

    if ( !ref $ditag_feature || !$ditag_feature->isa("Bio::EnsEMBL::Map::DitagFeature") ) {
      throw(   "Object must be an Ensembl DitagFeature, "
             . "not a " . ref($ditag_feature) );
    }
    if ( $ditag_feature->is_stored($db) ) {
      warning(   "DitagFeature " . $ditag_feature->dbID .
                 " is already stored in this database,".
                 " maybe you need to use the update() method?" );
      next TAG;
    }
    if(!$ditag_feature->ditag_id or !($self->db->get_DitagAdaptor->fetch_by_dbID($ditag_feature->ditag_id))){
      throw("DitagFeature must be supplied with the id of a corresponding Ditag object.");
    }
    if(!$ditag_feature->ditag or !$ditag_feature->ditag->isa("Bio::EnsEMBL::Map::Ditag")){
      throw("DitagFeature must be linked to a valid Ditag object.");
    }


#    #check if more than x tags with this ditag id exist
#    $sth3->execute( $ditag_feature->ditag_id );
#    my ($num) = $sth3->fetchrow_array();
#    if ( ($num) and ($num > 1) ) {
#      warning( "There are already at least 2 DitagFeatures relating to Ditag ".
#                 $ditag->ditag_id." stored in this database." );
#      if ( $num > 4 ) {
#        warning( "not storing" );
#        next TAG;
#      }
#    }

    if ( $ditag_feature->dbID ) {
      $sth2->bind_param( 1,  $ditag_feature->dbID,                      SQL_INTEGER );
      $sth2->bind_param( 2,  $ditag_feature->ditag_id,                  SQL_INTEGER );
      $sth2->bind_param( 3, ($ditag_feature->slice->get_seq_region_id), SQL_INTEGER );
      $sth2->bind_param( 4,  $ditag_feature->start,                     SQL_INTEGER );
      $sth2->bind_param( 5,  $ditag_feature->end,                       SQL_INTEGER );
      $sth2->bind_param( 6,  $ditag_feature->strand,                    SQL_VARCHAR );
      $sth2->bind_param( 7,  $ditag_feature->analysis->dbID,            SQL_INTEGER );
      $sth2->bind_param( 8,  $ditag_feature->hit_start,                 SQL_INTEGER );
      $sth2->bind_param( 9,  $ditag_feature->hit_end,                   SQL_INTEGER );
      $sth2->bind_param( 10, $ditag_feature->hit_strand,                SQL_VARCHAR );
      $sth2->bind_param( 11, $ditag_feature->cigar_line,                SQL_VARCHAR );
      $sth2->bind_param( 12, $ditag_feature->ditag_side,                SQL_VARCHAR );
      $sth2->bind_param( 13, $ditag_feature->ditag_pair_id,             SQL_VARCHAR );
      $sth2->execute();
    }
    else{
      $sth1->bind_param( 1,  $ditag_feature->ditag_id,                  SQL_INTEGER );
      $sth1->bind_param( 2, ($ditag_feature->slice->get_seq_region_id), SQL_INTEGER );
      $sth1->bind_param( 3,  $ditag_feature->start,                     SQL_INTEGER );
      $sth1->bind_param( 4,  $ditag_feature->end,                       SQL_INTEGER );
      $sth1->bind_param( 5,  $ditag_feature->strand,                    SQL_VARCHAR );
      $sth1->bind_param( 6,  $ditag_feature->analysis->dbID,            SQL_INTEGER );
      $sth1->bind_param( 7,  $ditag_feature->hit_start,                 SQL_INTEGER );
      $sth1->bind_param( 8,  $ditag_feature->hit_end,                   SQL_INTEGER );
      $sth1->bind_param( 9,  $ditag_feature->hit_strand,                SQL_VARCHAR );
      $sth1->bind_param( 10, $ditag_feature->cigar_line,                SQL_VARCHAR );
      $sth1->bind_param( 11, $ditag_feature->ditag_side,                SQL_VARCHAR );
      $sth1->bind_param( 12, $ditag_feature->ditag_pair_id,             SQL_VARCHAR );
      $sth1->execute();
      my $dbID = $sth1->{'mysql_insertid'};
      $ditag_feature->dbID($dbID);
      $ditag_feature->adaptor($self);
    }

  }
}

public Boolean Bio::EnsEMBL::Map::DBSQL::DitagFeatureAdaptor::update ( )

  Arg [1]    : ditagFeature to update
  Description: update an existing ditagFeature with new values
  Returntype : 1 on success
  Status     : At Risk

Code:

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

Bio/EnsEMBL/Map/DBSQL/DitagFeatureAdaptor.pm

Class Summary

Synopsis

Description

Available Methods

Method Documentation