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Summary

Bio::Tools::EUtilities::Link - general API for accessing data retrieved from elink queries

Package variables

Included modules

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

Methods description

 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

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;
            }
        }
    }
}

}

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

User feedback is an integral part of the
evolution of this and other Bioperl modules. Send
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is much appreciated.

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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.

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/

Email cjfields at bioperl dot org

The rest of the documentation details each of the
object methods. Internal methods are usually
preceded with a _