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#
# BioPerl module for Bio::Tools::AlignFactory
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Ewan Birney <birney@sanger.ac.uk>
#
# Copyright Ewan Birney
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::Tools::AlignFactory - Base object for alignment factories
=head1 SYNOPSIS
You won't be using this as an object, but using a dervied class
like Bio::Tools::pSW
=head1 DESCRIPTION
Holds common Alignment Factory attributes in place
=head1 CONTACT
http://bio.perl.org/ or birney@sanger.ac.uk
=head1 APPENDIX
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::Tools::AlignFactory;
use strict;
use base qw(Bio::Root::Root);
BEGIN {
eval {
require Bio::Ext::Align;
};
if ( $@ ) {
print STDERR ("\nThe C-compiled engine for Smith Waterman alignments (Bio::Ext::Align) has not been installed.\n Please install the bioperl-ext package\n\n");
exit(1);
}
}
sub new {
my($class,@args) = @_;
my $self = $class->SUPER::new(@args);
$self->_initialize(@args);
# set up defaults
$self->{'kbyte'} = 20000;
$self->{'report'} = 0;
return $self;
}
=head2 kbyte
Title : kbyte()
Usage : set/gets the amount of memory able to be used
Function :
: $factory->kbyte(200);
:
Returns :
Argument : memory in kilobytes
=cut
sub kbyte {
my ($self,$value) = @_;
if( defined $value ) {
$self->{'kbyte'} = $value;
}
return $self->{'kbyte'};
}
=head2 report
Title : report()
Usage : set/gets the report boolean to issue reports or not
Function :
: $factory->report(1); # reporting goes on
:
Returns : n/a
Argument : 1 or 0
=cut
sub report {
my ($self,$value) = @_;
if( defined $value ) {
if( $value != 1 && $value != 0 ) {
$self->throw("Attempting to modify AlignFactory Report with no boolean value!");
}
$self->{'report'} = $value;
}
return $self->{'report'};
}
=head2 set_memory_and_report
Title : set_memory_and_report
Usage : Only used by subclasses.
Function:
Example :
Returns :
Args :
=cut
sub set_memory_and_report{
my ($self) = @_;
if( $self->{'kbyte'} < 5 ) {
$self->throw("You can suggest aligning things with less than 5kb");
}
&Bio::Ext::Align::change_max_BaseMatrix_kbytes($self->{'kbyte'});
if( $self->{'report'} == 0 ) {
&Bio::Ext::Align::error_off(16);
} else {
&Bio::Ext::Align::error_on(16);
}
}
1;
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