———#
# BioPerl module for FAST::Bio::Seq::SeqFastaSpeedFactory
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Jason Stajich <jason@bioperl.org>
#
# Copyright Jason Stajich
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
FAST::Bio::Seq::SeqFastaSpeedFactory - Instantiates a new FAST::Bio::PrimarySeqI (or derived class) through a factory
=head1 SYNOPSIS
use FAST::Bio::Seq::SeqFastaSpeedFactory;
my $factory = FAST::Bio::Seq::SeqFastaSpeedFactory->new();
my $seq = $factory->create(-seq => 'WYRAVLC',
-id => 'name');
# If you want the factory to create FAST::Bio::Seq objects instead
# of the default FAST::Bio::PrimarySeq objects, use the -type parameter:
my $factory = FAST::Bio::Seq::SeqFastaSpeedFactory->new(-type => 'FAST::Bio::Seq');
=head1 DESCRIPTION
This object will build FAST::Bio::Seq objects generically.
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<bioperl-l@bioperl.org>
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via the
web:
=head1 AUTHOR - Jason Stajich
Email jason@bioperl.org
=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
FAST::Bio::Seq::SeqFastaSpeedFactory;
use
strict;
use
FAST::Bio::Seq;
=head2 new
Title : new
Usage : my $obj = FAST::Bio::Seq::SeqFastaSpeedFactory->new();
Function: Builds a new FAST::Bio::Seq::SeqFastaSpeedFactory object
Returns : FAST::Bio::Seq::SeqFastaSpeedFactory
Args : -type => string, name of a PrimarySeqI derived class
This is optional. Default=FAST::Bio::PrimarySeq.
=cut
sub
new {
my
(
$class
,
@args
) =
@_
;
my
$self
=
$class
->SUPER::new(
@args
);
return
$self
;
}
=head2 create
Title : create
Usage : my $seq = $seqbuilder->create(-seq => 'CAGT', -id => 'name');
Function: Instantiates a new FAST::Bio::Seq object, correctly built but very
fast, knowing stuff about FAST::Bio::PrimarySeq and FAST::Bio::Seq
Returns : FAST::Bio::Seq
Args : initialization parameters specific to the type of sequence
object we want. Typically
-seq => $str,
-id => $name
=cut
sub
create {
my
(
$self
,
@args
) =
@_
;
my
%param
=
@args
;
@param
{
map
{
lc
$_
}
keys
%param
} =
values
%param
;
# lowercase keys
my
$sequence
=
$param
{
'-seq'
};
my
$fulldesc
=
$param
{
'-desc'
};
my
$id
=
defined
$param
{
'-id'
} ?
$param
{
'-id'
} :
$param
{
'-primary_id'
};
my
$alphabet
=
$param
{
'-alphabet'
};
my
$seq
=
bless
{},
"FAST::Bio::Seq"
;
my
$t_pseq
=
$seq
->{
'primary_seq'
} =
bless
{},
"FAST::Bio::PrimarySeq"
;
$t_pseq
->{
'seq'
} =
$sequence
;
$t_pseq
->{
'desc'
} =
$fulldesc
;
$t_pseq
->{
'display_id'
} =
$id
;
$t_pseq
->{
'primary_id'
} =
$id
;
$seq
->{
'primary_id'
} =
$id
;
# currently FAST::Bio::Seq does not delegate this
if
(
$sequence
and !
$alphabet
) {
$t_pseq
->_guess_alphabet();
}
elsif
(
$sequence
and
$alphabet
) {
$t_pseq
->{
'alphabet'
} =
$alphabet
;
}
return
$seq
;
}
1;