Bio::Tools::EUtilities Info
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Summary
Bio::Tools::EUtilities::Info - interface class for storing einfo data
Package variables
No package variables defined.
Included modules
Bio::Tools::EUtilities::Info::FieldInfo
Bio::Tools::EUtilities::Info::LinkInfo
Inherit
Bio::Tools::EUtilities Bio::Tools::EUtilities::EUtilDataI
Synopsis
  #### should not create instance directly; Bio::Tools::EUtilities does this ####
my $info = Bio::Tools::EUtilities->new(-eutil => 'einfo', -file => 'einfo.xml'); # can also use '-response' (for HTTP::Response objects) or '-fh' (for filehandles) # print available databases (if data is present) print join(', ',$info->get_available_databases),"\n"; # get database info my $db = $info->get_database; # in case you forgot... my $desc = $info->get_description; my $nm = $info->get_menu_name; my $ct = $info->get_record_count; my $dt = $info->get_last_update; # EUtilDataI interface methods my $eutil = $info->eutil; my $type = $info->datatype; # iterate through Field and Link objects while (my $field = $info->next_Field) { print "Field code: ",$field->get_field_code,"\n"; print "Field name: ",$field->get_field_name,"\n"; print "Field desc: ",$field->get_field_description,"\n"; print "DB : ",$field->get_database,"\n"; print "Term ct : ",$field->get_term_count,"\n"; for my $att (qw(is_date is_singletoken is_hierarchy is_hidden is_numerical)) { print "\tField $att\n" if $field->$att; } } my @fields = $info->get_Fields; # grab them all (useful for grep) while (my $link = $info->next_LinkInfo) { print "Link name: ",$link->get_link_name,"\n"; print "Link desc: ",$link->get_link_description,"\n"; print "DBFrom: ",$link->get_dbfrom,"\n"; # same as get_database() print "DBTo: ",$link->get_dbto,"\n"; # database linked to } my @links = $info->get_LinkInfo; # grab them all (useful for grep) $info->rewind(); # rewinds all iterators $info->rewind('links'); # rewinds Link iterator $info->rewind('fields'); # rewinds Field iterator
Description
This class handles data output (XML) from einfo.
Einfo is capable of returning two types of information:
   * A list of all available databases (when called w/o parameters)
   * Information about a specific database.
The latter information includes the database description, record count, and
date/time stamp for the last update, among other things. It also includes a list
of fields (indices by which record data is stored which can be used in queries)
and links (crossrefs between related records in other databases at NCBI). Data
from the latter two are stored in two small subclasses (FieldInfo and LinkInfo)
which can be iterated through or retrieved all at once, as demonstrated above.
NOTE: Methods described for the LinkInfo and FieldInfo subclasses are unique to
those classes (as they retrieve data unique to those data types).
Further documentation for Link and Field subclass methods is included below.
For more information on einfo see:
   http://eutils.ncbi.nlm.nih.gov/entrez/query/static/einfo_help.html
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, $simple) = @_;
    if (exists $simple->{DbList} &&
        exists $simple->{DbList}->{DbName}) {
        $self->{'_available_databases'} = $simple->{DbList}->{DbName};
    }
    # start setting internal variables
if (exists $simple->{DbInfo}) { for my $key (sort keys %{ $simple->{DbInfo} }) { my $data = ($key eq 'FieldList') ? $simple->{DbInfo}->{$key}->{Field} : ($key eq 'LinkList' ) ? $simple->{DbInfo}->{$key}->{Link} : $simple->{DbInfo}->{$key}; if ($key eq 'FieldList' || $key eq 'LinkList') { for my $chunk (@{$data}) { if (exists $simple->{DbInfo}->{DbName}) { $chunk->{DbFrom} = $simple->{DbInfo}->{DbName}; } my $type = ($key eq 'FieldList') ? 'FieldInfo' : 'LinkInfo'; my $obj = "Bio::Tools::EUtilities::Info::$type"->new( -eutil => 'einfo', -type => lc $type, -verbose => $self->verbose); $obj->_add_data($chunk); push @{ $self->{'_'.lc $type} }, $obj; } } else { $self->{'_'.lc $key} = $data; } } } else { map { $self->{'_'.lc $_} = $simple->{$_} unless ref $simple->{$_}} keys %$simple; }
}
to_stringdescriptionprevnextTop
sub to_string {
    my $self = shift;
    my $string = $self->SUPER::to_string;
    if (my @dbs = $self->get_databases) {
        $string .= sprintf("%-20s:%s\n\n", 'DB',
            $self->_text_wrap('', ' 'x20 .':', join(', ',@dbs)));
    }
    while (my $fi = $self->next_FieldInfo) {
        $string .= $fi->to_string."\n";
    }
    while (my $li = $self->next_LinkInfo) {
        $string .= $li->to_string."\n";
    }
    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 _
rewindTop
 Title    : rewind
Usage : $info->rewind() # rewinds all (default)
$info->rewind('links') # rewinds only links
Function : 'rewinds' (resets) specified interators (all if no arg)
Returns : none
Args : [OPTIONAL] String:
'all' - all iterators (default)
'linkinfo' - LinkInfo objects only
'fieldinfo' - FieldInfo objects only