/ 
Bio-EnsEMBL-112.0_55
River stage zero No dependents
/ Bio::EnsEMBL::Analysis

LICENSE

Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute Copyright [2016-2024] EMBL-European Bioinformatics Institute

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at

http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.

CONTACT

Please email comments or questions to the public Ensembl
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Questions may also be sent to the Ensembl help desk at
<http://www.ensembl.org/Help/Contact>.

NAME

Bio::EnsEMBL::Analysis.pm - Stores details of an analysis run

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.

METHODS

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

db

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

db_version

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

db_file

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

program

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

program_version

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

program_file

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

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

module_version

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

gff_source

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

gff_feature

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

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

created

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

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

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

description

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

display_label

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

displayable

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

web_data

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

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