Bio::Tools::EUtilities Link
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Summary
Bio::Tools::EUtilities::Link - general API for accessing data retrieved from elink queries
Package variables
Privates (from "my" definitions)
%SUBCLASS = ( 'LinkSetDb' => 'dblink', 'LinkSetDbHistory' => 'history', 'IdUrlList' => 'urllink', 'IdCheckList' => 'idcheck', 'NoLinks' => 'nolinks', )
Included modules
Bio::Tools::EUtilities::Link::LinkSet
Data::Dumper
Inherit
Bio::Tools::EUtilities Bio::Tools::EUtilities::EUtilDataI
Synopsis
  ...TODO
Description
Bio::Tools::EUtilities::Link is a loadable plugin for Bio::Tools::EUtilities
that specifically handles NCBI elink-related data.
Methods
_add_data
No description
Code
to_stringDescriptionCode
Methods description
to_stringcode    nextTop
 Title    : to_string
Usage : $foo->to_string()
Function : converts current object to string
Returns : none
Args : (optional) simple data for text formatting
Note : Used generally for debugging and for various print methods
Methods code
_add_datadescriptionprevnextTop
sub _add_data {
    my ($self, $data) = @_;
    # divide up per linkset
if (!exists $data->{LinkSet}) { $self->warn("No linksets returned"); return; } for my $ls (@{ $data->{LinkSet} }) { my $subclass; # attempt to catch linkset errors
if (exists $ls->{ERROR}) { my ($error, $dbfrom) = ($ls->{ERROR},$ls->{DbFrom}); $self->warn("NCBI LinkSet error: $dbfrom: $error\n"); # try to save the rest of the data, if any
next; } # caching for efficiency; no need to recheck
if (!exists $self->{'_subclass_type'}) { ($subclass) = grep { exists $ls->{$_} } qw(LinkSetDb LinkSetDbHistory IdUrlList IdCheckList); $subclass ||= 'NoLinks'; $self->{'_subclass_type'} = $subclass; } else { $subclass = $self->{'_subclass_type'}; } # split these up by ID, since using correspondence() clobbers them...
if ($subclass eq 'IdUrlList' || $subclass eq 'IdCheckList') { my $list = $subclass eq 'IdUrlList' ? 'IdUrlSet' : $subclass eq 'IdCheckList' && exists $ls->{$subclass}->{IdLinkSet} ? 'IdLinkSet' : 'Id'; $ls->{$subclass} = $ls->{$subclass}->{$list}; } # divide up linkset per link
for my $ls_sub (@{ $ls->{$subclass} }) { for my $key (qw(WebEnv DbFrom IdList)) { $ls_sub->{$key} = $ls->{$key} if exists $ls->{$key}; } my $obj = Bio::Tools::EUtilities::Link::LinkSet->new(-eutil => 'elink', -datatype => $SUBCLASS{$subclass}, -verbose => $self->verbose); $obj->_add_data($ls_sub); push @{$self->{'_linksets'}}, $obj; # push only potential history-carrying objects into history queue
if ($subclass eq 'LinkSetDbHistory') { push @{$self->{'_histories'}}, $obj; } } } }
}
to_stringdescriptionprevnextTop
sub to_string {
    my $self = shift;
    my $string = $self->SUPER::to_string;
    while (my $ls = $self->next_LinkSet) {
        $string .= $ls->to_string;
    }
    return $string;
}

1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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 Top
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 BugsTop
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 Top
Email cjfields at bioperl dot org
APPENDIXTop
The rest of the documentation details each of the
object methods. Internal methods are usually
preceded with a _