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Bio-EnsEMBL-113.0.0
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/ Bio::EnsEMBL::Utils::Converter

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>.

AUTHOR

Juguang Xiao <juguang@tll.org.sg>

NAME

Bio::EnsEMBL::Utils::Converter, a converter factory

SYNOPSIS

my $converter = Bio::EnsEMBL::Utils::Converter->new(
  -in  => 'Bio::SeqFeature::Generic',
  -out => 'Bio::EnsEMBL::SimpleFeature'
);

my ( $fearture1, $feature2 );
my $ens_simple_features =
  $converter->convert( [ $feature1, $feature2 ] );
my @ens_simple_features = @{$ens_simple_features};

DESCRIPTION

Module to converter the business objects between EnsEMBL and any other projects, currently BioPerl.

What the ready conversions are,

Bio::SeqFeature::Generic <-> Bio::EnsEMBL::SeqFeature, Bio::EnsEMBL::SimpleFeature
Bio::SeqFeature::FeaturePair <-> Bio::EnsEMBL::SeqFeature, Bio::EnsEMBL::RepeatFeature
Bio::Search::HSP::GenericHSP -> Bio::EnsEMBL::BaseAlignFeature's submodules
Bio::Tools::Prediction::Gene -> Bio::EnsEMBL::PredictionTranscript
Bio::Tools::Prediction::Exon -> Bio::EnsEMBL::Exon
Bio::Pipeline::Analysis -> Bio::EnsEMBL::Analysis

METHODS

new

Title   : new
Usage   : 
      my $converter = Bio::EnsEMBL::Utils::Converter->new(
          -in => 'Bio::SeqFeature::Generic',
           -out => 'Bio::EnsEMBL::SimpleFeature'
       );

Function: constructor for converter object
Returns : L<Bio::EnsEMBL::Utils::Converter>
Args    : 
  in - the module name of the input.
  out - the module name of the output.
  analysis - a Bio::EnsEMBL::Analysis object, if converting other objects to EnsEMBL features.
  contig - a Bio::EnsEMBL::RawContig object, if converting other objects to EnsEMBL features.

_guess_module

Usage   : $module = $class->_guess_module(
  'Bio::EnsEMBL::SimpleFeature',
  'Bio::EnsEMBL::Generic'
);

convert

Title   : convert
Usage   : my $array_ref = $converter->convert(\@input);
Function: does the actual conversion
Returns : an array ref of converted objects
Args    : an array ref of converting objects

_load_module

This method is copied from Bio::Root::Root