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
  developers list at <http://lists.ensembl.org/mailman/listinfo/dev>.

  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

cpanm Bio::EnsEMBL::CDS

perl -MCPAN -e shell
install Bio::EnsEMBL::CDS