From 5cc85aa2b4267335d5aa382377832baf10fd9023 Mon Sep 17 00:00:00 2001
From: Kieron Taylor <ktaylor@ebi.ac.uk>
Date: Mon, 20 Aug 2012 09:54:25 +0000
Subject: [PATCH] Tidying up.
---
.../Bio/EnsEMBL/Utils/IO/FASTASerializer.pm | 59 ++++++++++---------
1 file changed, 30 insertions(+), 29 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Utils/IO/FASTASerializer.pm b/modules/Bio/EnsEMBL/Utils/IO/FASTASerializer.pm
index db77457aa3..fb9334ebfb 100644
--- a/modules/Bio/EnsEMBL/Utils/IO/FASTASerializer.pm
+++ b/modules/Bio/EnsEMBL/Utils/IO/FASTASerializer.pm
@@ -30,10 +30,10 @@ Bio::EnsEMBL::Utils::IO::FASTASerializer
$serializer->print_Seq($slice);
$serializer = Bio::EnsEMBL::Utils::IO::FASTASerializer->new($filehandle,
- sub {
- my $slice = shift;
- return "Custom header";
- }
+ sub {
+ my $slice = shift;
+ return "Custom header";
+ }
);
=head1 DESCRIPTION
@@ -63,17 +63,17 @@ use base qw(Bio::EnsEMBL::Utils::IO::Serializer);
=head2 new
- Arg [1] : Filehandle (optional)
- Arg [2] : CODEREF subroutine for writing custom headers
- Arg [3] : [optional] Chunking size (integer)
- Arg [4] : [optional] Line width (integer)
- Example : $dumper = Bio::EnsEMBL::Utils::IO::FASTASerializer->new($filehandle,$header_function,1000,60);
+ Arg [1] : Filehandle (optional)
+ Arg [2] : CODEREF subroutine for writing custom headers
+ Arg [3] : [optional] Chunking size (integer)
+ Arg [4] : [optional] Line width (integer)
+ Example : $dumper = Bio::EnsEMBL::Utils::IO::FASTASerializer->new($filehandle,$header_function,1000,60);
Description: Constructor
- Allows the specification of a custom function for rendering
- header lines.
+ Allows the specification of a custom function for rendering
+ header lines.
Returntype : Bio::EnsEMBL::Utils::IO::FASTASerializer;
Exceptions : none
- Caller : general
+ Caller : general
=cut
@@ -92,7 +92,6 @@ sub new {
$self->{'chunk_factor'} = ($chunk_factor)? $chunk_factor : 1000;
# gives a 60kb buffer by default, increase for higher database and disk efficiency.
- # TODO: Check this error trap works as intended
if ( defined($self->{'header_function'}) ) {
if (ref($self->{'header_function'}) ne "CODE") {
throw("Custom header function must be an anonymous subroutine when instantiating FASTASerializer");}
@@ -123,11 +122,11 @@ sub new {
=head2 print_metadata
- Arg [1] : Bio::EnsEMBL::Slice
+ Arg [1] : Bio::EnsEMBL::Slice
Description: Printing header lines into FASTA files. Usually handled
- internally to the serializer.
+ internally to the serializer.
Returntype : None
- Caller : print_Seq
+ Caller : print_Seq
=cut
sub print_metadata {
@@ -141,11 +140,11 @@ sub print_metadata {
=head2 print_Seq
- Arg [1] : Bio::EnsEMBL::Slice or other Bio::PrimarySeqI compliant object
+ Arg [1] : Bio::EnsEMBL::Slice or other Bio::PrimarySeqI compliant object
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.
+ While other Bioperl PrimarySeqI implementations can be used,
+ a custom header function will be required to accommodate it.
Returntype : None
@@ -184,7 +183,7 @@ sub print_Seq {
=head2 line_width
- Arg [1] : Integer e.g. 60 or 80
+ Arg [1] : Integer e.g. 60 or 80
Description: Set and get FASTA format line width. Default is 60
Returntype : Integer
@@ -198,10 +197,12 @@ sub line_width {
}
=head2 chunk_factor
- Arg [1] : Integer e.g. 1000
+
+ Arg [1] : Integer e.g. 1000
Description: Set and get the multiplier used to dictate buffer size
- Chunk factor x line width = buffer size in bases.
+ Chunk factor x line width = buffer size in bases.
Returntype : Integer
+
=cut
sub chunk_factor {
@@ -213,10 +214,10 @@ sub chunk_factor {
=head2 set_custom_header
- Arg [1] : CODE reference
+ Arg [1] : CODE reference
Description: Set the custom header function. Normally this is done at
- construction time, but can be overridden here.
- Example : $serializer->set_custom_header( sub { return 'New header'});
+ construction time, but can be overridden here.
+ Example : $serializer->set_custom_header( sub { return 'New header'});
Returntype :
=cut
@@ -229,10 +230,10 @@ sub set_custom_header {
=head2 header_function
- Arg [1] : CODE reference (optional)
- Description: Getter/setter for the custom header code
- Example : $serializer->header_function( sub { return 'New header'});
- Returntype : CODE
+ Arg [1] : CODE reference (optional)
+ Description : Getter/setter for the custom header code
+ Example : $serializer->header_function( sub { return 'New header'});
+ Returntype : CODE
=cut
--
GitLab