Archive Ensembl HomeArchive Ensembl Home
Bio::EnsEMBL::Analysis Class Reference
Inheritance diagram for Bio::EnsEMBL::Analysis:

List of all members.


Class Summary

Synopsis

    my $obj = new Bio::EnsEMBL::Analysis(
      -id              =\> $id,
      -logic_name      =\> 'SWIRBlast',
      -db              =\> $db,
      -db_version      =\> $db_version,
      -db_file         =\> $db_file,
      -program         =\> $program,
      -program_version =\> $program_version,
      -program_file    =\> $program_file,
      -gff_source      =\> $gff_source,
      -gff_feature     =\> $gff_feature,
      -module          =\> $module,
      -module_version  =\> $module_version,
      -parameters      =\> $parameters,
      -created         =\> $created,
      -description     =\> 'some warm words about this analysis',
      -display_label   =\> 'UNIprot alignment',
      -displayable     =\> '1',
      -web_data        =\> 'web metadata info'
    );

Description

Object to store details of an analysis run.
 

Definition at line 37 of file Analysis.pm.

Available Methods

public
Bio::EnsEMBL::DBSQL::BaseAdaptor 
adaptor ()
public Int compare ()
public String created ()
public String db ()
public String db_file ()
public String db_version ()
public Int dbID ()
public String description ()
public String display_label ()
public String displayable ()
public get_all_DAS_Features ()
public String gff_feature ()
public String gff_source ()
public Int has_database ()
public Boolean is_stored ()
public String logic_name ()
public String module ()
public String module_version ()
public Bio::EnsEMBL::Analysis new ()
public Bio::EnsEMBL::Analysis new_fast ()
public String parameters ()
public String program ()
public String program_file ()
public String program_version ()
public String web_data ()

Method Documentation

public Bio::EnsEMBL::DBSQL::BaseAdaptor Bio::EnsEMBL::Storable::adaptor ( ) [inherited]
  Arg [1]    : Bio::EnsEMBL::DBSQL::BaseAdaptor $adaptor
  Example    : none
  Description: get/set for this objects Adaptor
  Returntype : Bio::EnsEMBL::DBSQL::BaseAdaptor
  Exceptions : none
  Caller     : general, set from adaptor on store
  Status     : Stable
 
Code:
click to view
public Int Bio::EnsEMBL::Analysis::compare ( )
  Arg  1     : Bio::EnsEMBL::Analysis $ana
               The analysis to compare to
  Example    : none
  Description: returns 1 if this analysis is special case of given analysis
               returns 0 if they are equal
	       returns -1 if they are completely different
  Returntype : int -1,0,1
  Exceptions : none
  Caller     : unknown
  Status     : Stable
 
Code:
click to view
public String Bio::EnsEMBL::Analysis::created ( )
  Arg [1]    : string $created
  Example    : none
  Description: get/set for attribute created time.
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
click to view
public String Bio::EnsEMBL::Analysis::db ( )
  Arg [1]    : string $db
  Example    : none
  Description: get/set for the attribute db
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
click to view
public String Bio::EnsEMBL::Analysis::db_file ( )
  Arg [1]    : string $db_file
  Example    : none
  Description: get/set for attribute db_file
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
click to view
public String Bio::EnsEMBL::Analysis::db_version ( )
  Arg [1]    : string $db_version
  Example    : none
  Description: get/set for attribute db_version
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
click to view
public Int Bio::EnsEMBL::Storable::dbID ( ) [inherited]
  Arg [1]    : int $dbID
  Example    : none
  Description: getter/setter for the database internal id
  Returntype : int
  Exceptions : none
  Caller     : general, set from adaptor on store
  Status     : Stable
 
Code:
click to view

Reimplemented in Bio::EnsEMBL::Map::Ditag, and Bio::EnsEMBL::Map::DitagFeature.

public String Bio::EnsEMBL::Analysis::description ( )
  Arg [1]    : string $description
  Example    : none
  Description: get/set for attribute description
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
click to view
public String Bio::EnsEMBL::Analysis::display_label ( )
  Arg [1]    : string $display_label
  Example    : none
  Description: get/set for attribute display_label
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
click to view
public String Bio::EnsEMBL::Analysis::displayable ( )
  Arg [1]    : string $displayable
  Example    : none
  Description: get/set for attribute displayable
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
click to view
public Bio::EnsEMBL::Storable::get_all_DAS_Features ( ) [inherited]

Undocumented method

Code:
click to view

Reimplemented in Bio::EnsEMBL::Gene, Bio::EnsEMBL::Transcript, and Bio::EnsEMBL::Translation.

public String Bio::EnsEMBL::Analysis::gff_feature ( )
  Arg [1]    : string $gff_feature
  Example    : none
  Description: get/set for attribute gff_feature
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
click to view
public String Bio::EnsEMBL::Analysis::gff_source ( )
  Arg [1]    : string $gff_source
  Example    : none
  Description: get/set for attribute gff_source
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
click to view
public Int Bio::EnsEMBL::Analysis::has_database ( )
  Args       : none
  Example    : none
  Description: tests if the db attribute is set, returns 1 if so,
               0 if not.
  Returntype : int 0,1
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
click to view
public Boolean Bio::EnsEMBL::Storable::is_stored ( ) [inherited]
  Arg [1]    : Bio::EnsEMBL::DBSQL::DBConnection 
             : or Bio::EnsEMBL::DBSQL::DBAdaptor
  Example    : do_something if($object->is_stored($db));
  Description: Returns true if this object is stored in the provided database.
               This works under the assumption that if the adaptor and dbID are
               set and the database of the adaptor shares the port, dbname and
               hostname with the provided database, this object is stored in
               that database.
  Returntype : 1 or 0
  Exceptions : throw if dbID is set but adaptor is not
               throw if adaptor is set but dbID is not
               throw if incorrect argument is passed
  Caller     : store methods
  Status     : Stable
 
Code:
click to view
public String Bio::EnsEMBL::Analysis::logic_name ( )
  Arg [1]    : string $logic_name
  Example    : none
  Description: Get/set method for the logic_name, the name under 
               which this typical analysis is known.
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
click to view
public String Bio::EnsEMBL::Analysis::module ( )
  Arg [1]    : string $module
  Example    : none
  Description: get/set for attribute module. Usually a RunnableDB perl 
               module that executes this analysis job. 
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
click to view
public String Bio::EnsEMBL::Analysis::module_version ( )
  Arg [1]    : string $module_version
  Example    : none
  Description: get/set for attribute module_version
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
click to view
public Bio::EnsEMBL::Analysis Bio::EnsEMBL::Analysis::new ( )
  Arg [..]   :  Takes a set of named arguments
  Example    : $analysis = new Bio::EnsEMBL::Analysis::Analysis(
                                -id              => $id,
                                -logic_name      => 'SWIRBlast',
                                -db              => $db,
                                -db_version      => $db_version,
                                -db_file         => $db_file,
                                -program         => $program,
                                -program_version => $program_version,
                                -program_file    => $program_file,
                                -gff_source      => $gff_source,
                                -gff_feature     => $gff_feature,
                                -module          => $module,
                                -module_version  => $module_version,
                                -parameters      => $parameters,
                                -created         => $created );
  Description: Creates a new Analysis object
  Returntype : Bio::EnsEMBL::Analysis
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
click to view

Reimplemented from Bio::EnsEMBL::Storable.

public Bio::EnsEMBL::Analysis Bio::EnsEMBL::Analysis::new_fast ( )
  Arg [1]    : HashRef $hashref
               Value to bless
  Description: Bless a hash into this object type
  Exceptions : none
  Returntype : Bio::EnsEMBL::Analysis
  Caller     : general, subclass constructors
 
Code:
click to view
public String Bio::EnsEMBL::Analysis::parameters ( )
  Arg [1]    : string $parameters
  Example    : none
  Description: get/set for attribute parameters. This should be evaluated
               by the module if given or the program that is specified.
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
click to view
public String Bio::EnsEMBL::Analysis::program ( )
  Arg [1]    : string $program
  Example    : none
  Description: get/set for attribute program
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
click to view
public String Bio::EnsEMBL::Analysis::program_file ( )
  Arg [1]    : string $program_file
  Example    : none
  Description: get/set for attribute program_file
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
click to view
public String Bio::EnsEMBL::Analysis::program_version ( )
  Arg [1]    : string $program_version
  Example    : none
  Description: get/set for attribute program_version
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
click to view
public String Bio::EnsEMBL::Analysis::web_data ( )
  Arg [1]    : string $web_data
  Example    : none
  Description: get/set for attribute web_data
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
click to view

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