[DAS] Re: DAS 0.7 Entry_points.pm modules missing in distribution?

[Lincoln Stein]

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Hi,

It has recently come to my attention that I failed to commit the=20
Entry_points.pm module to the new (0.7) version of Bio::Das beta.  The=20
OpenBio machines are down at the moment, so I can't commit, and I am abou=
t to=20
go on a one week vacation away from Internet access.  So I am e-mailing t=
his=20
file out to the das list.  It belongs in the subdirectory=20
Das/Request/Entry_points.pm

Lincoln

On Thursday 12 September 2002 05:09 am, Tony Cox wrote:
> Hi Lincoln,
>
> just grabbed the beta 0.7 release to give it a try but get:
>
> [Thu Sep 12 10:02:06 2002] [error] Can't locate
> Bio/Das/Request/Entry_points.pm in @INC (@INC
> ....
> BEGIN failed--compilation aborted at
> /ensweb/wwwdev/server/modules/Bio/Das.pm line 12.
> Compilation failed in require at
> /ensweb/wwwdev/server/ensembl-external/modules/Bio/EnsEMBL/ExternalData=
/DAS
>/DASAdaptor.pm line 54.
>
> but:
>
> l-s -l Bio/Das/Request/
> total 24
> -rw-rw-r--   1 w3adm    system      1736 Apr 30 14:25 Dnas.pm
> -rw-rw-r--   1 w3adm    system      1604 Apr 30 14:25 Dsn.pm
> -rw-rw-r--   1 w3adm    system      5636 Apr 30 14:25 Features.pm
> -rw-rw-r--   1 w3adm    system      2247 Apr 30 14:25 Types.pm
>
> Could you check in the module please?
>
> thanks
>
> Tony

--=20
Lincoln Stein
lstein@cshl.org

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package Bio::Das::Request::Entry_points;
# $Id: Entry_points.pm,v 1.1 2002/08/31 23:32:53 lstein Exp $
# this module issues and parses the entry_points command, with the ref argument

use strict;
use Bio::Das::DSN;
use Bio::Das::Request;
use Bio::Das::Util 'rearrange';

use vars '@ISA';
@ISA = 'Bio::Das::Request';

sub new {
  my $pack = shift;
  my ($dsn,$ref,$callback) = rearrange(['dsn',
					'ref',
					'callback',
				       ],@_);

  return $pack->SUPER::new(-dsn=>$dsn,
			   -callback=>$callback,
			   -args   => {ref => $ref}
			  );
}

sub command { 'entry_points' }

# top-level tag
sub t_DASEP {
  my $self  = shift;
  my $attrs = shift;
  if ($attrs) {  # section is starting
    $self->clear_results;
  }
  $self->{current_ep} = undef;
}

sub t_ENTRY_POINTS {
# nothing to do there
}

# segment is beginning
sub t_SEGMENT {
  my $self  = shift;
  my $attrs = shift;
  if ($attrs) {    # segment section is starting
    $self->{current_ep} = Bio::Das::Segment->new($attrs->{id},
						 $attrs->{start}||1,
						 $attrs->{stop}||$attrs->{size},
						 $attrs->{version}||'1.0');
    $self->{current_ep}->size($attrs->{size});
    $self->{current_ep}->class($attrs->{class});
    $self->{current_ep}->orientation($attrs->{orientation});
    $self->{current_ep}->subparts(1) if defined $attrs->{subparts} 
      && $attrs->{subparts} eq 'yes';
  }
  else {  # reached the end of the segment, so push result
    $self->add_object($self->{current_ep});
  }
}

1;


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