Commit 5cc85aa2 authored by Kieron Taylor's avatar Kieron Taylor 😠
Browse files

Tidying up.

parent 95fdaec0
......@@ -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
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment