view variant_effect_predictor/Bio/EnsEMBL/Utils/IO/Serializer.pm @ 0:1f6dce3d34e0

Uploaded

=pod

=head1 LICENSE

  Copyright (c) 1999-2012 The European Bioinformatics Institute and
  Genome Research Limited.  All rights reserved.

  This software is distributed under a modified Apache license.
  For license details, please see

  http://www.ensembl.org/info/about/code_licence.html

=head1 NAME

Serializer - An abstract serializer for turning EnsEMBL data into other formats

=head1 AUTHOR

Kieron Taylor, 2011 - [e-mail]

=head1 SYNOPSIS

my $serializer = new Serializer( $filehandle );
$serializer->print_feature_list( \@list_of_features );

=head1 DESCRIPTION

Subclass this class to create a format-specific serializer.
Be sure to implement print_feature at the bare minimum

=cut

package Bio::EnsEMBL::Utils::IO::Serializer;
use strict;
use warnings;
use Bio::EnsEMBL::Utils::Exception;
use Bio::EnsEMBL::Utils::SeqDumper;


=head2 new

	Constructor
	Arg [1]    : Optional File handle
	Returntype : Bio::EnsEMBL::Utils::IO::Serializer

=cut

sub new {
	my $class = shift;
	my $self = {
		'filehandle' => shift,
		'achieved_something' => 0,
	};
	bless $self, $class;
	if (!defined ($self->{'filehandle'})) {
		# no file handle, let the handle point to a copy of STDOUT instead
		open $self->{'filehandle'}, ">&STDOUT";
		$self->{'stdout'} = 1;
	}
	return $self;
}

=head2 DESTROY

	Destructor
	Description: Restores default state of the STDOUT filehandle as it is a copy
	             and may not flush correctly.
=cut

sub DESTROY {
	my $self = shift;
	if ($self->{'stdout'}) {
		close $self->{'filehandle'};
	}
}

=head2 print_metadata 
	
	Arg [1]    : String
	Description: Pipes a custom string into the filehandle that the serializer is using

=cut

sub print_metadata {
	my $self = shift;
	my $text = shift;
	my $fh = $self->{'filehandle'};
	print $fh "\n".$text."\n";
}

=head2 print_main_header

	Arg [1]    : Data for header, depends on serializer
	Description: Printing the header text or metadata required for this file format,
	             Re-implement in the serializer.
	Returntype : None
=cut

sub print_main_header {
	my $self = shift;
	warning("No writer for headers in this format. Nothing done" );
}

=head2 printed_something
    Description: Check if serializer has printed any useful data. Not accurate with FASTA
                 due to non-reporting dumper.
    Returntype : Boolean
=cut

sub printed_something {
	my $self = shift;
	if ($self->{'achieved_something'}) { return 1;}
	else {return 0;}
}

=head2 formatted_write

   Arg [1]    : Line format, see Perldoc of formline()
   Arg [2]    : Array of arguments to suit the line format in Arg [1]
   Description: Writes data to the filehandle and rigidly formats it.
                Refer to Perldoc on formline() to specify valid formats.
                Useful for fixed-width file formats.
                Suicides in the event of file system issues.
   Example    : my $FORMAT = '^<<<<<<<<<<<<<<<<<<<|<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<\n';
                $serializer->formatted_write($FORMAT,@text_fields);
   Returntype : None
=cut

sub formatted_write {
  my ($self, $FORMAT, @values) = @_;
  my $fh = $self->{'filehandle'};
  
  #while the last value still contains something
  while(defined($values[-1]) and $values[-1] ne '') {
    formline($FORMAT, @values);
    print $fh $^A or die "Failed write to filehandle";
    $^A = '';
  }
}

1;