diff variant_effect_predictor/Bio/DB/UpdateableSeqI.pm @ 0:1f6dce3d34e0

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/DB/UpdateableSeqI.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,232 @@
+#
+# $Id: UpdateableSeqI.pm,v 1.6 2002/12/01 00:05:19 jason Exp $
+#
+# BioPerl module for Bio::DB::UpdateableSeqI
+#
+# Cared for by Jason Stajich <[e-mail]>
+#
+# Copyright Jason Stajich
+#
+# You may distribute this module under the same terms as perl itself
+#
+# _history
+# June 18, 2000 - module begun
+#
+# POD Doc - main docs before code
+
+=head1 NAME
+
+Bio::DB::UpdateableSeqI - An interface for writing to a database of sequences.
+
+=head1 SYNOPSIS 
+
+    # get a Bio::DB::UpdateableSeqI somehow
+    eval {
+	my ( @updatedseqs, @newseqs, @deadseqs);
+	my $seq = $db->get_Seq_by_id('ROA1_HUMAN');
+	$seq->desc('a new description');
+
+	push @updatedseqs, $seq;
+
+	$db->write_seq(\@updatedseqs, \@newseqs, \@deadseqs);
+    };
+    if( $@ ) {
+	print STDERR "an error when trying to write seq : $@\n";
+    }
+
+=head1 DESCRIPTION
+
+This module seeks to provide a simple method for pushing sequence changes 
+back to a Sequence Database - which can be an SQL compliant database, a file 
+based database, AceDB, etc.
+
+=head1 AUTHOR
+
+Jason Stajich E<lt>[e-mail]<gt>
+
+=head2 Reporting Bugs
+
+Report bugs to the Bioperl bug tracking system to help us keep track
+the bugs and their resolution. Bug reports can be submitted via email
+or the web:
+
+    [e-mail]                   
+    http://bugzilla.bioperl.org/           
+
+=head1 APPENDIX
+
+The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
+
+=cut
+
+#Lets start some code
+
+package Bio::DB::UpdateableSeqI;
+
+use strict;
+
+use vars qw( @ISA );
+
+use Bio::DB::SeqI;
+
+@ISA = qw(Bio::DB::SeqI);
+
+=head2 write_seq
+
+  Title   : write_seq
+  Usage   : write_seq(\@updatedseqs, \@addedseqs, \@deadseqs)
+  Function: updates sequences in first array,
+            adds sequences in the second array,
+            and removes sequences in the third array.
+  Example :
+  Returns :
+  Args    : arrays of sequence objects that must be obtained from
+            Bio::DB::UpdateableSeqI.
+
+=cut
+
+sub write_seq {
+    my ($self) = @_;
+    
+    $self->throw("Abstract database call of write_seq. Your database has not implemented this method!");
+
+}
+
+=head2 _add_seq
+
+ Title   : _add_seq
+ Usage   : _add_seq($seq)
+ Function: Adds a new sequence
+ Example : 
+ Returns : will throw an exception if
+           sequences accession number already exists
+ Args    : a new seq object - should have an accession number
+
+=cut
+
+sub _add_seq {
+    my ($self ) = @_;
+    
+    $self->throw("Abstract database call of _add_seq. Your database has not implemented this method!");
+
+}
+
+=head2 _remove_seq
+
+ Title   : _remove_seq
+ Usage   : _remove_seq($seq)
+ Function: Removes an existing sequence
+ Example : 
+ Returns : will throw an exception if
+           sequence does not exists for the primary_id
+ Args    : a seq object that was retrieved from Bio::DB::UpdateableSeqI
+
+=cut
+
+sub _remove_seq {
+    my ($self) = @_;
+    
+    $self->throw("Abstract database call of _remove_seq. Your database has not implemented this method!");
+
+}
+
+=head2 _update_seq
+
+ Title   : _update_seq
+ Usage   : _update_seq($seq)
+ Function: Updates a sequence
+ Example : 
+ Returns : will throw an exception if
+           sequence is out of sync from expected val.
+ Args    : a seq object that was retrieved from Bio::DB::UpdateableSeqI
+
+=cut
+
+sub _update_seq {
+    my ($self) = @_;
+    
+    $self->throw("Abstract database call of _update_seq. Your database has not implemented this method!");
+
+}
+
+
+=head1 Methods inherieted from Bio::DB::RandomAccessI
+
+=head2 get_Seq_by_id
+
+ Title   : get_Seq_by_id
+ Usage   : $seq = $db->get_Seq_by_id('ROA1_HUMAN')
+ Function: Gets a Bio::Seq object by its name
+ Returns : a Bio::Seq object
+ Args    : the id (as a string) of a sequence
+ Throws  : "id does not exist" exception
+
+
+=cut
+
+=head2 get_Seq_by_acc
+
+ Title   : get_Seq_by_acc
+ Usage   : $seq = $db->get_Seq_by_acc('X77802');
+ Function: Gets a Bio::Seq object by accession number
+ Returns : A Bio::Seq object
+ Args    : accession number (as a string)
+ Throws  : "acc does not exist" exception
+
+
+=cut
+
+=head1 Methods inheirited from Bio::DB::SeqI
+
+=head2 get_PrimarySeq_stream
+
+ Title   : get_PrimarySeq_stream
+ Usage   : $stream = get_PrimarySeq_stream
+ Function: Makes a Bio::DB::SeqStreamI compliant object
+           which provides a single method, next_primary_seq
+ Returns : Bio::DB::SeqStreamI
+ Args    : none
+
+
+=cut
+
+=head2 get_all_primary_ids
+
+ Title   : get_all_ids
+ Usage   : @ids = $seqdb->get_all_primary_ids()
+ Function: gives an array of all the primary_ids of the 
+           sequence objects in the database. These
+           maybe ids (display style) or accession numbers
+           or something else completely different - they
+           *are not* meaningful outside of this database
+           implementation.
+ Example :
+ Returns : an array of strings
+ Args    : none
+
+
+=cut
+
+=head2 get_Seq_by_primary_id
+
+ Title   : get_Seq_by_primary_id
+ Usage   : $seq = $db->get_Seq_by_primary_id($primary_id_string);
+ Function: Gets a Bio::Seq object by the primary id. The primary
+           id in these cases has to come from $db->get_all_primary_ids.
+           There is no other way to get (or guess) the primary_ids
+           in a database.
+
+           The other possibility is to get Bio::PrimarySeqI objects
+           via the get_PrimarySeq_stream and the primary_id field
+           on these objects are specified as the ids to use here.
+ Returns : A Bio::Seq object
+ Args    : accession number (as a string)
+ Throws  : "acc does not exist" exception
+
+
+=cut
+
+1;
+
+
+