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Summary

Bio::Tools::EUtilities::Query::GlobalQuery - container class for egquery data

Package variables

Inherit

Bio::Root::Root Bio::Tools::EUtilities::EUtilDataI

Synopsis

  #### should not create instance directly; Bio::Tools::EUtilities does this ####

  my $parser = Bio::Tools::EUtilities->new(-eutil => 'egquery',
                                           -term  => 'BRCA1');

  # $gquery is a Bio::Tools::EUtilities::Query::GlobalQuery
  while (my $gquery = $parser->next_GlobalQuery) {
     print $gquery->to_string."\n"; # stringify
     print "DB:".$gquery->get_db."\t".$gquery->get_count;
  }

Description

This is a simple container class for egquery data. Currently this just contains
various accessors for the data, such as get_database(), get_count(), etc. for
each item in a global query.

Methods

Methods description

 Title   : get_term
 Usage   : $st = $qd->get_term;
 Function: retrieve the term for the global search
 Returns : string
 Args    : none

 Title   : get_database
 Usage   : $ct = $qd->get_database;
 Function: retrieve the database
 Returns : string
 Args    : none

 Title   : get_count
 Usage   : $ct = $qd->get_count;
 Function: retrieve the count for the database
 Returns : string
 Args    : none

 Title   : get_status
 Usage   : $st = $qd->get_status;
 Function: retrieve the query status for database in db()
 Returns : string
 Args    : none

 Title   : get_menu_name
 Usage   : $ct = $qd->get_menu_name;
 Function: retrieve the full name for the database in db()
 Returns : string
 Args    : None

 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 the print_GlobalQuery method

Methods code

sub new {

    my ($class, @args) = @_;
    my $self = $class->SUPER::new(@args);
    $self->eutil('egquery');
    $self->datatype('globalquery');
    return $self;

}

sub get_term {

    my ($self) = @_;
    return $self->{'_term'};

}

sub get_database {

    my ($self) = @_;
    return $self->{'_dbname'};

}

sub get_count {

    my ($self) = @_;
    return $self->{'_count'};

}

sub get_status {

    my ($self) = @_;
    return $self->{'_status'};

}

sub get_menu_name {

    my $self = shift;
    return $self->{'_menuname'};
}

# private method

}

sub _add_data {

    my ($self, $data) = @_;
    map {$self->{'_'.lc $_} = $data->{$_}} keys %$data;

}

sub to_string {

    my $self = shift;
    my $string .= sprintf("%-20s Total:%-10d Status:%s\n",
        $self->get_database,
        $self->get_count,
        $self->get_status);
    return $string;
}

1;

}

General documentation

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

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 _