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# $Id: Info.pm 15160 2008-12-15 18:09:38Z cjfields $
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# BioPerl module for Bio::Tools::EUtilities::Info
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# Cared for by Chris Fields
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# Copyright Chris Fields
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# You may distribute this module under the same terms as perl itself
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# POD documentation - main docs before the code
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# Part of the EUtilities BioPerl package
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Bio::Tools::EUtilities::Info - interface class for storing einfo data
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#### should not create instance directly; Bio::Tools::EUtilities does this ####
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my $info = Bio::Tools::EUtilities->new(-eutil => 'einfo',
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-file => 'einfo.xml');
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# can also use '-response' (for HTTP::Response objects) or '-fh' (for filehandles)
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# print available databases (if data is present)
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print join(', ',$info->get_available_databases),"\n";
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my $db = $info->get_database; # in case you forgot...
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my $desc = $info->get_description;
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my $nm = $info->get_menu_name;
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my $ct = $info->get_record_count;
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my $dt = $info->get_last_update;
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# EUtilDataI interface methods
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my $eutil = $info->eutil;
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my $type = $info->datatype;
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# iterate through Field and Link objects
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while (my $field = $info->next_Field) {
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print "Field code: ",$field->get_field_code,"\n";
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print "Field name: ",$field->get_field_name,"\n";
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print "Field desc: ",$field->get_field_description,"\n";
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print "DB : ",$field->get_database,"\n";
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print "Term ct : ",$field->get_term_count,"\n";
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for my $att (qw(is_date is_singletoken is_hierarchy is_hidden is_numerical)) {
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print "\tField $att\n" if $field->$att;
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my @fields = $info->get_Fields; # grab them all (useful for grep)
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while (my $link = $info->next_LinkInfo) {
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print "Link name: ",$link->get_link_name,"\n";
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print "Link desc: ",$link->get_link_description,"\n";
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print "DBFrom: ",$link->get_dbfrom,"\n"; # same as get_database()
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print "DBTo: ",$link->get_dbto,"\n"; # database linked to
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my @links = $info->get_LinkInfo; # grab them all (useful for grep)
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$info->rewind(); # rewinds all iterators
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$info->rewind('links'); # rewinds Link iterator
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$info->rewind('fields'); # rewinds Field iterator
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This class handles data output (XML) from einfo.
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einfo is capable of returning two types of information: 1) a list of all
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available databases (when called w/o parameters) and 2) information about a
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specific database. The latter information includes the database description,
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record count, and date/time stamp for the last update, among other things. It
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also includes a list of fields (indices by which record data is stored which can
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be used in queries) and links (crossrefs between related records in other
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databases at NCBI). Data from the latter two are stored in two small subclasses
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(Field and Link) which can be iterated through or retrieved all at once, as
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demonstrated above. NOTE: Methods described for the Link and Field subclasses
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are unique to those classes (as they retrieve data unique to those data types).
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Further documentation for Link and Field subclass methods is included below.
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For more information on einfo see:
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http://eutils.ncbi.nlm.nih.gov/entrez/query/static/einfo_help.html
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User feedback is an integral part of the evolution of this and other Bioperl
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modules. Send your comments and suggestions preferably to one of the Bioperl
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mailing lists. Your participation is much appreciated.
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bioperl-l@lists.open-bio.org - General discussion
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http://www.bioperl.org/wiki/Mailing_lists - About the mailing lists
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=head2 Reporting Bugs
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Report bugs to the Bioperl bug tracking system to help us keep track the bugs
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and their resolution. Bug reports can be submitted via the web.
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http://bugzilla.open-bio.org/
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Email cjfields at uiuc dot edu
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The rest of the documentation details each of the object methods. Internal
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methods are usually preceded with a _
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# Let the code begin...
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package Bio::Tools::EUtilities::Info;
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use base qw(Bio::Tools::EUtilities Bio::Tools::EUtilities::EUtilDataI);
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use Bio::Tools::EUtilities::Info::LinkInfo;
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use Bio::Tools::EUtilities::Info::FieldInfo;
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Usage : $info->rewind() # rewinds all (default)
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$info->rewind('links') # rewinds only links
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Function : 'rewinds' (resets) specified interators (all if no arg)
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Args : [OPTIONAL] String:
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'all' - all iterators (default)
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'linkinfo' - LinkInfo objects only
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'fieldinfo' - FieldInfo objects only
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# private EUtilDataI method
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my ($self, $simple) = @_;
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if (exists $simple->{DbList} &&
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exists $simple->{DbList}->{DbName}) {
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$self->{'_available_databases'} = $simple->{DbList}->{DbName};
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# start setting internal variables
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if (exists $simple->{DbInfo}) {
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for my $key (sort keys %{ $simple->{DbInfo} }) {
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($key eq 'FieldList') ? $simple->{DbInfo}->{$key}->{Field} :
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($key eq 'LinkList' ) ? $simple->{DbInfo}->{$key}->{Link} :
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$simple->{DbInfo}->{$key};
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if ($key eq 'FieldList' || $key eq 'LinkList') {
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for my $chunk (@{$data}) {
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if (exists $simple->{DbInfo}->{DbName}) {
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$chunk->{DbFrom} = $simple->{DbInfo}->{DbName};
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my $type = ($key eq 'FieldList') ? 'FieldInfo' : 'LinkInfo';
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my $obj = "Bio::Tools::EUtilities::Info::$type"->new(
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-verbose => $self->verbose);
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$obj->_add_data($chunk);
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push @{ $self->{'_'.lc $type} }, $obj;
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$self->{'_'.lc $key} = $data;
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map { $self->{'_'.lc $_} = $simple->{$_} unless ref $simple->{$_}} keys %$simple;
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Usage : $foo->to_string()
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Function : converts current object to string
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Args : (optional) simple data for text formatting
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Note : Used generally for debugging and for various print methods
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my $string = $self->SUPER::to_string;
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if (my @dbs = $self->get_databases) {
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$string .= sprintf("%-20s:%s\n\n", 'DB',
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$self->_text_wrap('', ' 'x20 .':', join(', ',@dbs)));
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while (my $fi = $self->next_FieldInfo) {
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$string .= $fi->to_string."\n";
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while (my $li = $self->next_LinkInfo) {
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$string .= $li->to_string."\n";
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Bio/Tools/EUtilities/Info.pm
