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Bio::EnsEMBL::DBSQL::AnalysisAdaptor Class Reference
Inheritance diagram for Bio::EnsEMBL::DBSQL::AnalysisAdaptor:

List of all members.


Class Summary

Synopsis

  use Bio::EnsEMBL::Registry;

  Bio::EnsEMBL::Registry-\>load_registry_from_db(
    -host =\> 'ensembldb.ensembl.org',
    -user =\> 'anonymous'
  );

  $analysis_adaptor =
    Bio::EnsEMBL::Registry-\>get_adaptor( "human", "core", "analysis" );

  my $analysis = $analysis_adaptor-\>fetch_by_logic_name('genscan');

Description

  Module to encapsulate all db access for persistent class Analysis.
  There should be just one per application and database connection.
 

Definition at line 29 of file AnalysisAdaptor.pm.

Available Methods

protected _columns ()
protected _default_where_clause ()
protected _final_clause ()
protected _left_join ()
protected _list_dbIDs ()
protected Bio::EnsEMBL::Analysis _objFromHashref ()
protected _objs_from_sth ()
protected _straight_join ()
protected _tables ()
public Listref bind_param_generic_fetch ()
public
Bio::EnsEMBL::DBSQL::DBAdaptor 
db ()
public
Bio::EnsEMBL::DBSQL::DBConnection 
dbc ()
public dump_data ()
public Int exists ()
public List feature_classes ()
public Listref fetch_all ()
public Listref fetch_all_by_dbID_list ()
public Listref fetch_all_by_feature_class ()
public Bio::EnsEMBL::Analysis fetch_by_dbID ()
public Bio::EnsEMBL::Analysis fetch_by_logic_name ()
public Listref generic_fetch ()
public get_dumped_data ()
public Boolean is_multispecies ()
public Scalar last_insert_id ()
public
Bio::EnsEMBL::DBSQL::AnalysisAdaptor 
new ()
public DBI::StatementHandle prepare ()
public void remove ()
public Int species_id ()
public Int store ()
public Int update ()

Method Documentation

protected Bio::EnsEMBL::DBSQL::BaseAdaptor::_default_where_clause ( ) [inherited]
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::Analysis Bio::EnsEMBL::DBSQL::AnalysisAdaptor::_objFromHashref ( )
  Arg [1]    : hashref $rowHash
  Description: Private helper function generates an Analysis object from a 
               mysql row hash reference.
  Returntype : Bio::EnsEMBL::Analysis
  Exceptions : none
  Caller     : Bio::EnsEMBL::DBSQL::AnalsisAdaptor::fetch_* methods
  Status     : Stable
 
Code:
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protected Bio::EnsEMBL::DBSQL::BaseAdaptor::_straight_join ( ) [inherited]

Undocumented method

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

Undocumented method

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public Int Bio::EnsEMBL::DBSQL::AnalysisAdaptor::exists ( )
  Arg [1]    : Bio::EnsEMBL::Analysis $anal
  Example    : if($adaptor->exists($anal)) #do something
  Description: Tests whether this Analysis already exists in the database
               by checking first if the adaptor and dbID are set and
               secondly by whether it is in this adaptors internal cache.
               Note that this will not actually check the database and will
               not find and analysis which were recently added by other
               processes.  You are better off simply trying to store an
               analysis which will reliably ensure that it is not stored twice
               in the database.
  Returntype : int dbID if analysis is found, otherwise returns undef
  Exceptions : thrown if $anal arg is not an analysis object
  Caller     : store
  Status     : Stable
 
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public List Bio::EnsEMBL::DBSQL::AnalysisAdaptor::feature_classes ( )
  Arg [1]    : NONE
  Example    : my @fclasses = $analysis_adaptor->feature_classes;
  Description: Returns a list of the different classes of Ensembl feature 
               object that have an analysis
  Returntype : List of feature classes
  Exceptions : none
  Caller     : general
  Status     : Stable
 
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public Listref Bio::EnsEMBL::DBSQL::AnalysisAdaptor::fetch_all ( )
  Args       : none
  Example    : my @analysis = @{$analysis_adaptor->fetch_all()};
  Description: fetches all of the Analysis objects from the database and caches
               them internally.
  Returntype : listref of Bio::EnsEMBL::Analysis retrieved from the database
  Exceptions : none
  Caller     : AnalysisAdaptor::new
  Status     : Stable
 
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::DBSQL::AnalysisAdaptor::fetch_all_by_feature_class ( )
  Arg [1]    : string $feature_cless - The name of the feature class
  Example    : my @analyses = @{$analysis_adaptor->fetch_all_by_feature_class('Gene');
  Description: Returns all analyses that correspond to a given 
               feature class; see feature_classes method for a list.
  Returntype : Listref of Bio::EnsEMBL::Analysis
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
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public Bio::EnsEMBL::Analysis Bio::EnsEMBL::DBSQL::AnalysisAdaptor::fetch_by_dbID ( )
  Arg [1]    : int $internal_analysis_id - the database id of the analysis 
               record to retrieve
  Example    : my $analysis = $analysis_adaptor->fetch_by_dbID(1);
  Description: Retrieves an Analysis object from the database via its internal
               id.
  Returntype : Bio::EnsEMBL::Analysis
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
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Reimplemented from Bio::EnsEMBL::DBSQL::BaseAdaptor.

public Bio::EnsEMBL::Analysis Bio::EnsEMBL::DBSQL::AnalysisAdaptor::fetch_by_logic_name ( )
  Arg [1]    : string $logic_name the logic name of the analysis to retrieve
  Example    : my $analysis = $a_adaptor->fetch_by_logic_name('Eponine');
  Description: Retrieves an analysis object from the database using its unique
               logic name.
  Returntype : Bio::EnsEMBL::Analysis
  Exceptions : none
  Caller     : general
  Status     : Stable
 
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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 Bio::EnsEMBL::DBSQL::AnalysisAdaptor Bio::EnsEMBL::DBSQL::AnalysisAdaptor::new ( )
  Args       : Bio::EnsEMBL::DBSQL::DBAdaptor
  Example    : my $aa = new Bio::EnsEMBL::DBSQL::AnalysisAdaptor();
  Description: Creates a new Bio::EnsEMBL::DBSQL::AnalysisAdaptor object and
               internally loads and caches all the Analysis objects from the 
               database.
  Returntype : Bio::EnsEMBL::DBSQL::AnalysisAdaptor
  Exceptions : none
  Caller     : Bio::EnsEMBL::DBSQL::DBAdaptor
  Status     : Stable
 
Code:
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Reimplemented from Bio::EnsEMBL::DBSQL::BaseAdaptor.

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 void Bio::EnsEMBL::DBSQL::AnalysisAdaptor::remove ( )
  Arg [1]    : Bio::EnsEMBL::Analysis $anal
  Example    : $adaptor->remove($anal)
  Description: Removes this analysis from the database.  This is not really
               safe to execute in a multi process environment, so programs
               should not remove analysis while out on the farm.
  Returntype : none
  Exceptions : thrown if $anal arg is not an analysis object
  Caller     : ?
  Status     : Stable
 
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 Int Bio::EnsEMBL::DBSQL::AnalysisAdaptor::store ( )
  Arg [1]    : Bio:EnsEMBL::Analysis $analysis
  Example    : $analysis_adaptor->store($analysis);
  Description: Stores $analysis in db.  If the analysis is already stored in
               the database its dbID and adaptor are updated, but the analysis
               is not stored a second time.
               Sets created date if not already set. Sets dbID and adaptor
               inside $analysis. Returns dbID.
  Returntype : int - dbID of stored analysis
  Exceptions : throw on incorrect argument
               throw if analysis argument does not have a logic name
  Caller     : general
  Status     : Stable
 
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public Int Bio::EnsEMBL::DBSQL::AnalysisAdaptor::update ( )
  Arg [1]    : Bio::EnsEMBL::Analysis $anal
  Example    : $adaptor->update($anal)
  Description: Updates this analysis in the database
  Returntype : int 1 if update is performed, undef if it is not
  Exceptions : throw if arg is not an analysis object
  Caller     : ?
  Status     : Stable
 
Code:
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The documentation for this class was generated from the following file: