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

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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