Bio::EnsEMBL::Utils::Converter Class Reference

Inheritance diagram for Bio::EnsEMBL::Utils::Converter:

Public Member Functions
public L	new ()
protected	_initialize ()
protected	_guess_module ()
public An	convert ()
protected	_convert_single ()
protected	_load_module ()

Detailed Description

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

Definition at line 33 of file Converter.pm.

Member Function Documentation

_convert_single()

protected Bio::EnsEMBL::Utils::Converter::_convert_single

(

)

Undocumented method

Code:

_guess_module()

protected Bio::EnsEMBL::Utils::Converter::_guess_module

(

)

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

Code:

_initialize()

protected Bio::EnsEMBL::Utils::Converter::_initialize

(

)

Undocumented method

Code:

_load_module()

protected Bio::EnsEMBL::Utils::Converter::_load_module

(

)

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

Code:

convert()

public An Bio::EnsEMBL::Utils::Converter::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

Code:

new()

public L Bio::EnsEMBL::Utils::Converter::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 : 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.

Code:

---

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

• ensembl/modules/Bio/EnsEMBL/Utils/Converter.pm