From 00e7cc8cb2d3c26800cdb2a19385991f13ffe3f8 Mon Sep 17 00:00:00 2001
From: Kieron Taylor <ktaylor@ebi.ac.uk>
Date: Thu, 12 Jan 2012 11:50:17 +0000
Subject: [PATCH] Added header override, to prevent default printing. Useful in
case of very custom header functions.
---
modules/Bio/EnsEMBL/Utils/IO/FASTASerializer.pm | 13 ++++++++++---
1 file changed, 10 insertions(+), 3 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Utils/IO/FASTASerializer.pm b/modules/Bio/EnsEMBL/Utils/IO/FASTASerializer.pm
index 0e32545fab..576858a829 100644
--- a/modules/Bio/EnsEMBL/Utils/IO/FASTASerializer.pm
+++ b/modules/Bio/EnsEMBL/Utils/IO/FASTASerializer.pm
@@ -35,6 +35,8 @@ Bio::EnsEMBL::Utils::IO::FASTASerializer
return ">Custom header";
}
);
+ $serializer->print_metadata($slice);
+ $serializer->print_Slice($slice,"no duplicate headers please");
=head1 DESCRIPTION
@@ -123,9 +125,13 @@ sub print_metadata {
=head2 print_slice
Arg [1] : Bio::EnsEMBL::Slice or other Bio::PrimarySeqI compliant object
- Description: Serialises the slice into FASTA format. Buffering is used
+ Arg [2] : Optional Boolean - override the default serialisation of a header
+ Description: Serializes the slice into FASTA format. Buffering is used
While other Bioperl PrimarySeqI implementations can be used,
a custom header function will be required to accommodate it.
+
+ Add an override as second argument if more control is needed
+ over when and how custom headers are written.
Returntype : None
=cut
@@ -133,9 +139,10 @@ sub print_metadata {
sub print_Slice {
my $self = shift;
my $slice = shift;
+ my $override = shift;
my $fh = $self->{'filehandle'};
- # Insert header line
- $self->print_metadata($slice);
+ # Default print header, override
+ $self->print_metadata($slice) unless $override;
# set buffer size
my $chunk_size = $self->{'chunk_factor'} * $self->{'line_width'};
--
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