Bio::EnsEMBL::Analysis Class Reference

Inheritance diagram for Bio::EnsEMBL::Analysis:

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

Detailed Description

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 36 of file Analysis.pm.

Member Function Documentation

compare()

public Int Bio::EnsEMBL::Analysis::compare

(

)

  Arg  1     : Bio::EnsEMBL::Analysis $ana
               The analysis to compare to
  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:

created()

public String Bio::EnsEMBL::Analysis::created

(

)

  Arg [1]    : string $created
  Description: get/set for attribute created time.
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

db()

public String Bio::EnsEMBL::Analysis::db

(

)

  Arg [1]    : string $db
  Description: get/set for the attribute db
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

db_file()

public String Bio::EnsEMBL::Analysis::db_file

(

)

  Arg [1]    : string $db_file
  Description: get/set for attribute db_file
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

db_version()

public String Bio::EnsEMBL::Analysis::db_version

(

)

  Arg [1]    : string $db_version
  Description: get/set for attribute db_version
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

description()

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:

display_label()

public String Bio::EnsEMBL::Analysis::display_label

(

)

  Arg [1]    : string $display_label
  Description: get/set for attribute display_label
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

displayable()

public String Bio::EnsEMBL::Analysis::displayable

(

)

  Arg [1]    : string $displayable
  Description: get/set for attribute displayable
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

gff_feature()

public String Bio::EnsEMBL::Analysis::gff_feature

(

)

  Arg [1]    : string $gff_feature
  Description: get/set for attribute gff_feature
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

gff_source()

public String Bio::EnsEMBL::Analysis::gff_source

(

)

  Arg [1]    : string $gff_source
  Description: get/set for attribute gff_source
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

has_database()

public Int Bio::EnsEMBL::Analysis::has_database

(

)

  Args       : 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:

logic_name()

public String Bio::EnsEMBL::Analysis::logic_name

(

)

  Arg [1]    : string $logic_name
  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:

module()

public String Bio::EnsEMBL::Analysis::module

(

)

  Arg [1]    : string $module
  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:

module_version()

public String Bio::EnsEMBL::Analysis::module_version

(

)

  Arg [1]    : string $module_version
  Description: get/set for attribute module_version
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

new()

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:

parameters()

public String Bio::EnsEMBL::Analysis::parameters

(

)

  Arg [1]    : string $parameters
  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:

program()

public String Bio::EnsEMBL::Analysis::program

(

)

  Arg [1]    : string $program
  Description: get/set for attribute program
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

program_file()

public String Bio::EnsEMBL::Analysis::program_file

(

)

  Arg [1]    : string $program_file
  Description: get/set for attribute program_file
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

program_version()

public String Bio::EnsEMBL::Analysis::program_version

(

)

  Arg [1]    : string $program_version
  Description: get/set for attribute program_version
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

web_data()

public String Bio::EnsEMBL::Analysis::web_data

(

)

  Arg [1]    : string $web_data
  Description: get/set for attribute web_data
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

---

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

• ensembl/modules/Bio/EnsEMBL/Analysis.pm