From e4e2fa36c5b54a65f45e3e44ef3816e36cb13d1a Mon Sep 17 00:00:00 2001
From: Tony Cox <avc@sanger.ac.uk>
Date: Mon, 17 Apr 2000 07:51:15 +0000
Subject: [PATCH] Added $vc->extend_maximally(_left/right) to virtual contig
code Not the prettiest way to do it but it works.
---
modules/Bio/EnsEMBL/DB/VirtualContig.pm | 74 ++++++++++++++++++++++++-
1 file changed, 73 insertions(+), 1 deletion(-)
diff --git a/modules/Bio/EnsEMBL/DB/VirtualContig.pm b/modules/Bio/EnsEMBL/DB/VirtualContig.pm
index 6277105d59..1f52557867 100755
--- a/modules/Bio/EnsEMBL/DB/VirtualContig.pm
+++ b/modules/Bio/EnsEMBL/DB/VirtualContig.pm
@@ -150,7 +150,7 @@ These functions are to implement the ContigI interface
Title : extend
Usage : $new_vc = $vc->extend(100,100);
- Function: Make a new vc by entending an existing one
+ Function: Make a new vc by extending an existing one
Example :
Returns : Bio::EnsEMBL::DB::VirtualContig
Args :
@@ -182,6 +182,78 @@ sub extend {
}
+=head2 extend_maximally
+
+ Title : extend_maximally
+ Usage : $new_vc = $vc->extend_maximally();
+ Function: Extends an existing vc as far as possible in both directions
+ Example :
+ Returns : Bio::EnsEMBL::DB::VirtualContig
+ Args :
+
+
+=cut
+
+sub extend_maximally {
+ my ($self) = @_;
+
+ if( !ref $self || ! $self->isa('Bio::EnsEMBL::DB::VirtualContigI') ) {
+ $self->throw("Can only extend a VirtualContigI, Bailing out...");
+ }
+ # based on an original idea by Ewan Birney. ;)
+ my $nvc = $self->extend(100000000000,100000000000);
+ return $nvc;
+}
+
+
+=head2 extend_maximally_left
+
+ Title : extend_maximally_left
+ Usage : $new_vc = $vc->extend_maximally_left();
+ Function: Extends an existing vc as far as possible in both directions
+ Example :
+ Returns : Bio::EnsEMBL::DB::VirtualContig
+ Args :
+
+
+=cut
+
+sub extend_maximally_left {
+ my ($self) = @_;
+
+ if( !ref $self || ! $self->isa('Bio::EnsEMBL::DB::VirtualContigI') ) {
+ $self->throw("Can only extend a VirtualContigI, Bailing out...");
+ }
+ # based on an original idea by Ewan Birney. ;)
+ my $nvc = $self->extend(100000000000,0);
+ return $nvc;
+}
+
+
+=head2 extend_maximally_right
+
+ Title : extend_maximally_right
+ Usage : $new_vc = $vc->extend_maximally_right();
+ Function: Extends an existing vc as far as possible in both directions
+ Example :
+ Returns : Bio::EnsEMBL::DB::VirtualContig
+ Args :
+
+
+=cut
+
+sub extend_maximally_right {
+ my ($self) = @_;
+
+ if( !ref $self || ! $self->isa('Bio::EnsEMBL::DB::VirtualContigI') ) {
+ $self->throw("Can only extend a VirtualContigI, Bailing out...");
+ }
+ # based on an original idea by Ewan Birney. ;)
+ my $nvc = $self->extend(0,100000000000);
+ return $nvc;
+}
+
+
=head2 primary_seq
Title : primary_seq
--
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