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

BioPerl documentation Contained in the BioPerl distribution.

Index

Code Index:

NAME

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

SYNOPSIS

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  #### 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

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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.

FEEDBACK

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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

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Email cjfields at bioperl dot org

APPENDIX

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

get_term

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

get_database

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

get_count

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

get_status

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

get_menu_name

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

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 the print_GlobalQuery method
BioPerl documentation Contained in the BioPerl distribution. 
#
# BioPerl module for Bio::Tools::EUtilities::Query::GlobalQuery
#
# 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::Query::GlobalQuery;
use strict;
use warnings;

use base qw(Bio::Root::Root Bio::Tools::EUtilities::EUtilDataI);

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;