diff variant_effect_predictor/Bio/Factory/SequenceFactoryI.pm @ 0:1f6dce3d34e0

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/Factory/SequenceFactoryI.pm	Thu Apr 11 02:01:53 2013 -0400
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+# $Id: SequenceFactoryI.pm,v 1.6 2002/10/22 07:45:14 lapp Exp $
+#
+# BioPerl module for Bio::Factory::SequenceFactoryI
+#
+# 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::Factory::SequenceFactoryI - This interface allows for generic building of sequences in factories which create sequences (like SeqIO) 
+
+=head1 SYNOPSIS
+
+# do not use this object directly it is an interface
+# get a Bio::Factory::SequenceFactoryI object like
+
+    use Bio::Seq::SeqFactory;
+    my $seqbuilder = new Bio::Seq::SeqFactory('type' => 'Bio::PrimarySeq');
+
+    my $seq = $seqbuilder->create(-seq => 'ACTGAT',
+				  -display_id => 'exampleseq');
+
+    print "seq is a ", ref($seq), "\n";
+
+=head1 DESCRIPTION
+
+Describe the interface here
+
+=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::Factory::SequenceFactoryI;
+
+use vars qw(@ISA);
+use strict;
+use Bio::Factory::ObjectFactoryI;
+
+@ISA = qw(Bio::Factory::ObjectFactoryI);
+
+=head2 create
+
+ Title   : create
+ Usage   : my $seq = $seqbuilder->create(-seq => 'CAGT', 
+					 -id => 'name');
+ Function: Instantiates new Bio::PrimarySeqI (or one of its child classes)
+           This object allows us to genericize the instantiation of sequence
+           objects.
+ Returns : Bio::PrimarySeqI
+ Args    : initialization parameters specific to the type of sequence
+           object we want.  Typically 
+           -seq        => $str,
+           -display_id => $name
+
+=cut
+
+1;