diff variant_effect_predictor/Bio/Seq/SeqFastaSpeedFactory.pm @ 0:1f6dce3d34e0

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/Seq/SeqFastaSpeedFactory.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,142 @@
+# $Id: SeqFastaSpeedFactory.pm,v 1.3 2002/11/07 23:54:23 lapp Exp $
+#
+# BioPerl module for Bio::Seq::SeqFactory
+#
+# Cared for by Jason Stajich <[e-mail]>
+#
+# Copyright Jason Stajich
+#
+# You may distribute this module under the same terms as perl itself
+
+# POD documentation - main docs before the code
+
+=head1 NAME
+
+Bio::Seq::SeqFactory - Instantiates a new Bio::PrimarySeqI (or derived class) through a factory
+
+=head1 SYNOPSIS
+
+    use Bio::Seq::SeqFactory;
+    my $factory = new Bio::Seq::SeqFactory;
+    my $seq = $factory->create(-seq => 'WYRAVLC',
+			       -id  => 'name');
+
+    # If you want the factory to create Bio::Seq objects instead
+    # of the default Bio::PrimarySeq objects, use the -type parameter:
+
+    my $factory = new Bio::Seq::SeqFactory(-type => 'Bio::Seq');
+
+
+=head1 DESCRIPTION
+
+This object will build 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.
+
+  [e-mail]              - General discussion
+  http://bioperl.org/MailList.shtml  - About the mailing lists
+
+=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
+email or the web:
+
+  [e-mail]
+  http://bugzilla.bioperl.org/
+
+=head1 AUTHOR - Jason Stajich
+
+Email [e-mail]
+
+Describe contact details here
+
+=head1 CONTRIBUTORS
+
+Additional contributors names and emails here
+
+=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::Seq::SeqFastaSpeedFactory;
+use vars qw(@ISA);
+use strict;
+
+use Bio::Root::Root;
+use Bio::Factory::SequenceFactoryI;
+use Bio::Seq;
+use Bio::PrimarySeq;
+
+@ISA = qw(Bio::Root::Root Bio::Factory::SequenceFactoryI);
+
+=head2 new
+
+ Title   : new
+ Usage   : my $obj = new Bio::Seq::SeqFactory();
+ Function: Builds a new Bio::Seq::SeqFactory object 
+ Returns : Bio::Seq::SeqFactory
+ Args    : -type => string, name of a PrimarySeqI derived class
+                    This is optional. Default=Bio::PrimarySeq.
+
+=cut
+
+sub new {
+  my($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 Bio::Seq object, correctly built but very
+           fast, knowing stuff about Bio::PrimarySeq and Bio::Seq
+ Returns : Bio::Seq
+
+ Args    : initialization parameters specific to the type of sequence
+           object we want.  Typically 
+           -seq        => $str,
+           -id         => $name
+
+=cut
+
+sub create {
+    my ($self,%param) = @_;
+
+    my $sequence = $param{'-seq'}  || $param{'-SEQ'};
+    my $fulldesc = $param{'-desc'} || $param{'-DESC'};
+    my $id       = $param{'-id'}   || $param{'-ID'} ||
+	           $param{'-primary_id'}   || $param{'-PRIMARY_ID'};
+
+    my $seq = bless {}, "Bio::Seq";
+    my $t_pseq = $seq->{'primary_seq'} = bless {}, "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 Bio::Seq does not delegate this
+    if( $sequence ) {
+	$t_pseq->_guess_alphabet();
+    }
+
+    return $seq;
+}
+
+1;
+