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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/EnsEMBL/Utils/IO/Serializer.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,141 @@
+=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;