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

List of all members.


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::_default_where_clause ( ) [inherited]
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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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::_list_dbIDs ( ) [inherited]

Undocumented method

Code:
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protected Bio::EnsEMBL::DBSQL::BaseAdaptor::_straight_join ( ) [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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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

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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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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
 
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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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Reimplemented in Bio::EnsEMBL::DBSQL::AnalysisAdaptor, Bio::EnsEMBL::DBSQL::AssemblyExceptionFeatureAdaptor, Bio::EnsEMBL::DBSQL::AssemblyMapperAdaptor, Bio::EnsEMBL::DBSQL::AssemblySliceAdaptor, Bio::EnsEMBL::DBSQL::AttributeAdaptor, Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor, Bio::EnsEMBL::DBSQL::CoordSystemAdaptor, Bio::EnsEMBL::DBSQL::DensityFeatureAdaptor, Bio::EnsEMBL::DBSQL::DensityTypeAdaptor, Bio::EnsEMBL::DBSQL::GOTermAdaptor, Bio::EnsEMBL::DBSQL::MetaCoordContainer, Bio::EnsEMBL::DBSQL::MiscSetAdaptor, Bio::EnsEMBL::DBSQL::SequenceAdaptor, Bio::EnsEMBL::DBSQL::SliceAdaptor, Bio::EnsEMBL::DBSQL::SOTermAdaptor, Bio::EnsEMBL::DBSQL::StrainSliceAdaptor, Bio::EnsEMBL::DBSQL::UnmappedObjectAdaptor, and Bio::EnsEMBL::External::BlastAdaptor.

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
 
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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
 
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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: