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contrib/SynView/cgi-lib/DAS/GUS/Segment/Feature.pm  view on Meta::CPAN

=cut

sub gff_string { 

	my $self = shift; 
	my ($recurse,$parent) = @_; 
	my ($start,$stop) = ($self->start,$self->stop); 

	# the defined() tests prevent uninitialized variable warnings, 
	# when dealing with clone objects whose endpoints may be undefined 
	($start,$stop) = ($stop,$start) 
		if defined($start) && defined($stop) && $start > $stop;

	my $strand = ('-','.','+')[$self->strand+1]; 
	my $ref = $self->refseq; 
	my $n   = ref($ref) ? $ref->name : $ref; 
	my $phase = $self->phase; 
	$phase = '.' unless defined $phase;

	my ($class,$name) = ('',''); 

htdocs/tutorial/tutorial.html  view on Meta::CPAN

glyph        = span
height       = 5
description  = 1
key          = Example motifs
</pre></blockquote>

<p>

This defines a new track whose internal name is "Motifs."  The
corresponding feature type is "motif" and it uses the "span" glyph, a
graphic that displays a horizontal line capped by vertical endpoints.
The height is set to five pixels, and the human-readable key is set to
"Example motifs."  A new option, "description" is a flag that tells
GBrowse to display the Note attribute, if any.  Any non-zero value
means true.

<p>

After updating the configuration file, you will need to reload the
browser page and turn on the "Example motifs" checkbox below the main
image. The result is shown in Figure 4.

htdocs/tutorial/tutorial.html  view on Meta::CPAN

	Primer pairs available for the region produced by the
	<i>C. elegans</i> ORFeome project.
    </td>
  </TR>

  <TR>
    <td>
	<a href="data_files/elegans_deletion.gff3">elegans_deletion.gff3</a>
    </td>
    <td>
	Deletion endpoints from a targeted gene knockout project.
    </td>
  </TR>
    
  <TR>
    <td>
	<a href="data_files/elegans_repeats.gff3">elegans_repeats.gff3</a>
    </td>
    <td>
	Complex repetitive elements found using the RepeatMasker program.
    </td>

lib/Bio/Graphics/Browser2/Render/Slave/AWS_Balancer.pm  view on Meta::CPAN

	($min,$max) = @{$lt->{$l}} if $load >= $l;
    }
    return ($min,$max);
}

sub slave_instance_type { shift->option('SLAVE','instance_type') || 'm1.large' }
sub slave_spot_bid      { shift->option('SLAVE','spot_bid')      || 0.08       }
sub slave_ports         { my $p = shift->option('SLAVE','ports');
			  my @p = split /\s+/,$p;
			  return @p ? @p : (8101); }
sub slave_endpoint {
    my $self = shift;
    if ($self->running_as_instance) {
	my $zone =  $self->{instance_metadata}->endpoint;
	return $zone;
    } else {
	my $region = $self->option('SLAVE','region') || 'us-east-1';
	return "http://ec2.$region.amazonaws.com";
    }
}

sub slave_zone {
    my $self = shift;
    if ($self->running_as_instance) {

lib/Bio/Graphics/Browser2/Render/Slave/AWS_Balancer.pm  view on Meta::CPAN

	if $self->slave_ssh_key;
    
    $sg->update or croak $ec2->error_str;
    return $self->{slave_security_group} = $sg;
}

sub ec2 {
    my $self = shift;
    # create a new ec2 each time because security credentials may expire
    my @credentials = $self->ec2_credentials;
    return $self->{ec2} = VM::EC2->new(-endpoint    => $self->slave_endpoint,
				       -raise_error => 1,
				       @credentials);
}

sub internal_ip {
    my $self = shift;
    return unless $self->running_as_instance;
    return $self->{instance_metadata}->privateIpAddress;
}