Bio::Tools::EUtilities::Link::UrlLink - class for EUtils UrlLinks
Index
Code Index:
NAME
Bio::Tools::EUtilities::Link::UrlLink - class for EUtils UrlLinks
SYNOPSIS
DESCRIPTION
FEEDBACK
Mailing Lists
User feedback is an integral part of the
evolution of this and other Bioperl modules. Send
your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation
is much appreciated.
bioperl-l@lists.open-bio.org - General discussion
http://www.bioperl.org/wiki/Mailing_lists - About the mailing lists
Support
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
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 the web.
https://redmine.open-bio.org/projects/bioperl/
AUTHOR
Email cjfields at bioperl dot org
APPENDIX
The rest of the documentation details each of the
object methods. Internal methods are usually
preceded with a _
get_dbfrom
Title : get_dbfrom
Usage :
Function :
Returns :
Args :
get_attribute
Title : get_attribute
Usage :
Function :
Returns :
Args :
get_icon_url
Title : get_icon_url
Usage :
Function :
Returns :
Args :
get_subject_type
Title :
Usage :
Function :
Returns :
Args :
get_url
Title : get_url
Usage :
Function :
Returns :
Args :
get_link_name
Title : get_link_name
Usage :
Function :
Returns :
Args :
get_provider_name
Title : get_provider_name
Usage :
Function :
Returns :
Args :
get_provider_abbr
Title : get_provider_abbr
Usage :
Function :
Returns :
Args :
get_provider_id
Title : get_provider_id
Usage :
Function :
Returns :
Args :
get_provider_icon_url
Title : get_provider_icon_url
Usage :
Function :
Returns :
Args :
get_provider_url
Title : get_provider_url
Usage :
Function :
Returns :
Args :
to_string
Title : to_string
Usage : $foo->to_string()
Function : converts current object to string
Returns : none
Args : (optional) simple data for text formatting
Note : Used generally for debugging and for various print methods
#
# BioPerl module for Bio::Tools::EUtilities::Link::UrlLink
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Chris Fields
#
# Copyright Chris Fields
#
# You may distribute this module under the same terms as perl itself
#
# POD documentation - main docs before the code
#
# Part of the EUtilities BioPerl package
# Let the code begin...
package Bio::Tools::EUtilities::Link::UrlLink;
use base qw(Bio::Root::Root Bio::Tools::EUtilities::EUtilDataI);
use Data::Dumper;
sub get_dbfrom { return shift->{'_dbfrom'}; }
sub get_attribute { return shift->{'_attribute'}; }
sub get_icon_url { return shift->{'_iconurl'}; }
sub get_subject_type { return shift->{'_subjecttype'}; }
sub get_url {
my $self = shift;
# fix Entrz LinkOut URLS without the full URL
if ($self->{'_url'} && $self->{'_url'} =~ m{^/}) {
$self->{'_url'} = 'http://www.ncbi.nih.gov'.$self->{'_url'};
}
return $self->{'_url'};
}
sub get_link_name { return shift->{'_linkname'}; }
sub get_provider_name { return shift->{'_provider_name'}; }
sub get_provider_abbr { return shift->{'_provider_nameabbr'}; }
sub get_provider_id { return shift->{'_provider_id'}[0]; }
sub get_provider_icon_url { return shift->{'_provider_iconurl'}; }
sub get_provider_url { return shift->{'_provider_url'}; }
# private method
sub _add_data {
my ($self, $data) = @_;
if (exists $data->{Provider}) {
map {$self->{'_provider_'.lc $_} = $data->{Provider}->{$_};
} keys %{$data->{Provider}};
delete $data->{Provider};
}
map {$self->{'_'.lc $_} = $data->{$_} if $data->{$_}} keys %$data;
}
sub to_string {
my $self = shift;
my $level = shift || 0;
my $pad = 20 - $level;
# order method name
my %tags = (1 => ['get_link_name' => 'Link Name'],
2 => ['get_subject_type' => 'Subject Type'],
3 => ['get_dbfrom' => 'DB From'],
4 => ['get_attribute' => 'Attribute'],
6 => ['get_icon_url' => 'IconURL'],
7 => ['get_url' => 'URL'],
8 => ['get_provider_name' => 'Provider'],
9 => ['get_provider_abbr' => 'ProvAbbr'],
10 => ['get_provider_id' => 'ProvID'],
11 => ['get_provider_url' => 'ProvURL'],
12 => ['get_provider_icon_url' => 'ProvIcon'],
);
my $string = '';
for my $tag (sort {$a <=> $b} keys %tags) {
my ($m, $nm) = ($tags{$tag}->[0], $tags{$tag}->[1]);
my $content = $self->$m();
next unless $content;
$string .= $self->_text_wrap(
sprintf("%-*s%-*s:",$level, '',$pad, $nm,),
' ' x ($pad).':',
$content)."\n";
}
return $string;
}
1;