#
# BioPerl module for Bio::Tools::EUtilities::Link::LinkSet
#
# 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
=head1 NAME
Bio::Tools::EUtilities::Link::LinkSet - class for EUtils LinkSets
=head1 SYNOPSIS
# ...
=head1 DESCRIPTION
# ...
=head1 FEEDBACK
=head2 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
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<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.
=head2 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/
=head1 AUTHOR
Email cjfields at bioperl dot org
=head1 APPENDIX
The rest of the documentation details each of the
object methods. Internal methods are usually
preceded with a _
=cut
# Let the code begin...
package Bio::Tools::EUtilities::Link::LinkSet;
use strict;
use warnings;
use base qw(Bio::Root::Root Bio::Tools::EUtilities::HistoryI);
use Bio::Tools::EUtilities::Link::UrlLink;
use Bio::Tools::EUtilities::Info::LinkInfo;
sub new {
my ($class,@args) = @_;
my $self = $class->SUPER::new(@args);
my ($type) = $self->_rearrange([qw(DATATYPE)],@args);
$type ||= 'linkset';
$self->eutil('elink');
$self->datatype($type);
return $self;
}
=head2 get_ids
Title : get_ids
Usage : my @ids = $linkset->get_ids
Function : returns list of retrieved IDs
Returns : array of IDs
Args : none
Notes : Cmd Description
acheck same as get_submitted_ids
lcheck same as get_submitted_ids
ncheck same as get_submitted_ids
prlinks same as get_submitted_ids
llinks same as get_submitted_ids
llinkslib same as get_submitted_ids
neighbor linked IDs for database in get_database
neighbor_history linked IDs for database in get_database
=cut
sub get_ids {
my $self = shift;
unless ($self->{'_sorted_id'}) {
@{$self->{'_sorted_id'}} =
sort {
$self->{'_id'}->{$a}->[0] <=>
$self->{'_id'}->{$b}->[0]
} keys %{$self->{'_id'}};
}
return @{$self->{'_sorted_id'}};
}
=head2 get_database
Title : get_database
Usage : my $db = $info->get_database;
Function : returns single database name (eutil-compatible). This is the
queried database. For elinks (which have 'db' and 'dbfrom')
this is equivalent to db/dbto (use get_dbfrom() to for the latter).
Note that this only returns the first db; in some cases this may
not be what you want (when multiple dbs are queried, for instance)
Returns : string
Args : none
Notes : with all elink cmd arguments
=cut
sub get_database {
return ($_[0]->get_databases)[0];
}
=head2 get_db (alias for get_database)
=cut
sub get_db {
return shift->get_database;
}
=head2 get_dbto (alias for get_database)
=cut
sub get_dbto {
return shift->get_database;
}
=head2 get_databases
Title : get_databases
Usage : my $string = $linkset->get_databases;
Function : retrieve databases referred to for this linkset
these may be present as a single database or embedded in
Returns : array of strings
Args : none
=cut
sub get_databases {
my $self = shift;
my %tmp;
my @dbs = sort map {$_->get_database}
grep {!$tmp{$_->get_database}++} ($self->get_LinkInfo);
unshift @dbs, $self->{'_dbto'} if $self->{'_dbto'} && !$tmp{$self->{'_dbto'}}++;
return @dbs;
}
=head2 get_dbs (alias for get_databases)
=cut
sub get_dbs {
return shift->get_databases;
}
=head2 get_dbfrom
Title : get_dbfrom
Usage : my $string = $linkset->get_dbfrom;
Function : retrieve originating database for this linkset
Returns : string
Args : none
=cut
sub get_dbfrom { return shift->{'_dbfrom'} }
=head2 get_link_names
Title : get_link_names
Usage : my $string = $linkset->get_link_names;
Function : retrieve eutil-compatible link names
Returns : array of strings
Args : none
Notes : Each LinkSet can hold multiple LinkInfo objects (each containing
a link name). Also, some LinkSets define a single link name. This
returns an array with all unique linknames globbed both sources, if
present and defined
=cut
sub get_link_names {
my ($self) = shift;
my %tmps;
my @lns;
if ($self->{'_linkname'}) {
push @lns, $self->{'_linkname'};
$tmps{$self->{'_linkname'}}++;
}
push @lns, map {$_->get_link_name} $self->get_LinkInfo;
return @lns;
}
=head2 get_link_name
Title : get_link_name
Usage : my $string = $linkset->get_link_name;
Function : retrieve eutil-compatible link name
Returns : single link name
Args : none
=cut
sub get_link_name {
return ($_[0]->get_link_names)[0];
}
=head2 get_submitted_ids
Title : get_submitted_ids
Usage : my $string = $linkset->get_submitted_ids;
Function : retrieve original ID list
Returns : string
Args : none
=cut
sub get_submitted_ids {
my $self = shift;
my $datatype = $self->datatype;
if ($datatype eq 'idcheck' || $datatype eq 'urllink') {
return $self->get_ids;
} elsif ($self->{'_submitted_ids'}) {
return @{$self->{'_submitted_ids'}};
} else {
return ();
}
}
=head2 has_scores
Title : has_scores
Usage : if (my $linkset->has_scores) {...}
Function : returns TRUE if score data is present
Returns : Boolean
Args : none
=cut
sub has_scores {
my $self = shift;
return exists $self->{'_has_scores'} ? 1 : 0;
}
=head2 get_scores
Title : get_scores
Usage : %scores = $linkset->get_scores;
Function : returns flattened list or hash ref containing ID => score pairs
Returns : hash or hash ref (based on list or scalar context)
Args : none
=cut
sub get_scores {
my $self = shift;
# do we want to cache this or generate only when needed? Likely won't be
# called more than once...
return unless $self->has_scores;
my %scores = map {$_ => $self->{'_id'}->{$_}->[1]} keys %{$self->{'_id'}};
return %scores;
}
=head2 get_score_by_id
Title : get_score_by_id
Usage : $score = $linkset->get_score_by_id($id);
Function : returns the score for a particular primary ID
Returns : integer
Args : [REQUIRED] Primary ID for the score lookup
=cut
sub get_score_by_id {
my ($self, $id) = @_;
($id && exists $self->{'_id'}->{$id}) ? return $self->{'_id'}->{$id}->[1] :
return;
}
=head2 has_linkout
Title : has_linkout
Usage : if ($linkset->has_linkout) {...}
Function : returns TRUE if the single ID present in this linkset has a linkout
Returns : boolean
Args : none
Notes : this checks cmd=lcheck (boolean for a linkout) and also backchecks
cmd=acheck for databases with name 'LinkOut'
=cut
sub has_linkout {
my $self = shift;
if (exists $self->{'_haslinkout'}) {
return $self->{'_haslinkout'} eq 'Y' ? 1 : 0;
} else {
return (grep {$_ eq 'LinkOut'} $self->get_databases) ? 1 : 0;
}
}
=head2 has_neighbor
Title : has_neighbor
Usage : if ($linkset->has_neighbor) {...}
Function : returns TRUE if the single ID present in this linkset has a neighbor
in the same database
Returns : boolean
Args : none
Notes : this checks cmd=ncheck (boolean for a neighbor in same database); no
other checks performed at this time
=cut
sub has_neighbor {
my $self = shift;
if (exists $self->{'_hasneighbor'}) {
return $self->{'_hasneighbor'} eq 'Y' ? 1 : 0;
} else {
return 0;
}
}
=head2 next_UrlLink
Title : next_UrlLink
Usage : while (my $url = $linkset->next_UrlLink) {...}
Function : iterate through UrlLink objects
Returns : Bio::Tools::EUtilities::Link::UrlLink
Args :
=cut
sub next_UrlLink {
my $self = shift;
unless ($self->{"_urllinks_it"}) {
my @ul = $self->get_UrlLinks;
$self->{"_urllinks_it"} = sub {return shift @ul}
}
$self->{'_urllinks_it'}->();
}
=head2 get_UrlLinks
Title : get_UrlLinks
Usage : my @urls = $linkset->get_UrlLinks
Function : returns all UrlLink objects
Returns : list of Bio::Tools::EUtilities::Link::UrlLink
Args :
=cut
sub get_UrlLinks {
my $self = shift;
return ref $self->{'_urllinks'} ? @{ $self->{'_urllinks'} } : return;
}
=head2 next_LinkInfo
Title : next_LinkInfo
Usage : while (my $info = $linkset->next_LinkInfo) {...}
Function : iterate through LinkInfo objects
Returns : Bio::Tools::EUtilities::Link::LinkInfo
Args :
=cut
sub next_LinkInfo {
my $self = shift;
unless ($self->{"_linkinfo_it"}) {
my @li = $self->get_LinkInfo;
$self->{"_linkinfo_it"} = sub {return shift @li}
}
$self->{'_linkinfo_it'}->();
}
=head2 get_LinkInfo
Title : get_LinkInfo
Usage : my @links = $linkset->get_LinkInfo
Function : returns all LinkInfo objects
Returns : list of Bio::Tools::EUtilities::Link::LinkInfo
Args :
=cut
sub get_LinkInfo {
my $self = shift;
return ref $self->{'_linkinfo'} ? @{ $self->{'_linkinfo'} } : return ();
}
=head2 rewind
Title : rewind
Usage : $info->rewind() # rewinds all (default)
$info->rewind('links') # rewinds only links
Function : 'rewinds' (resets) specified interators (all if no arg)
Returns : none
Args : [OPTIONAL] String:
'all' - all iterators (default)
'linkinfo' or 'linkinfos' - LinkInfo objects only
'urllinks' - UrlLink objects only
=cut
{
my %VALID_DATA = ('linkinfo' => 'linkinfo',
'linkinfos' => 'linkinfo',
'urllinks' => 'urllinks');
sub rewind {
my ($self, $arg) = @_;
$arg ||= 'all';
if (exists $VALID_DATA{$arg}) {
delete $self->{'_'.$arg.'_it'};
} elsif ($arg eq 'all') {
delete $self->{'_'.$_.'_it'} for values %VALID_DATA;
}
}
}
# private methods and handlers
{
my %DATA_HANDLER = (
'IdList' => \&_add_submitted_ids,
'Id' => \&_add_retrieved_ids,
'LinkInfo' => \&_add_linkinfo,
'Link' => \&_add_retrieved_ids,
'ObjUrl' => \&_add_objurls,
);
sub _add_data {
my ($self, $data) = @_;
for my $key (qw(IdList Link Id ObjUrl LinkInfo)) {
next if !exists $data->{$key};
my $handler = $DATA_HANDLER{$key};
$self->$handler($data);
delete $data->{$key};
}
# map the rest
if ($self->datatype eq 'idcheck' && exists $data->{content}) {
%{$self->{'_id'} } = ($data->{content} => [1]);
delete $data->{content}
}
map {$self->{'_'.lc $_} = $data->{$_}} keys %$data;
}
}
sub _add_submitted_ids {
my ($self, $data) = @_;
if (exists $data->{IdList}->{Id}) {
@{$self->{'_submitted_ids'}} = @{$data->{IdList}->{Id}} ;
}
}
sub _add_retrieved_ids {
my ($self, $data) = @_;
# map all IDs to deal with possible scores
# ID => {'count' = POSITION, 'score' => SCORE}
if (exists $data->{Link}) {
my $ct = 0;
for my $link (@{$data->{Link}}) {
if (exists $link->{Score}) {
$self->{'_has_scores'}++;
$self->{'_id'}->{$link->{Id}->[0]} = [ $ct++,$link->{Score}];
} else {
$self->{'_id'}->{$link->{Id}->[0]} = [ $ct++ ];
}
}
}
elsif (exists $data->{Id}) { # urls
%{$self->{'_id'} } = ($data->{Id}->[0] => [1]);
}
}
sub _add_objurls {
my ($self, $data) = @_;
for my $urldata (@{$data->{ObjUrl}}) {
$urldata->{dbfrom} = $data->{DbFrom} if exists $data->{DbFrom};
my $obj = Bio::Tools::EUtilities::Link::UrlLink->new(-eutil => 'elink',
-datatype => 'urldata',
-verbose => $self->verbose
);
$obj->_add_data($urldata);
push @{$self->{'_urllinks'}}, $obj;
}
}
sub _add_linkinfo {
my ($self, $data) = @_;
for my $linkinfo (@{$data->{LinkInfo}}) {
$linkinfo->{dbfrom} = $data->{DbFrom} if exists $data->{DbFrom};
my $obj = Bio::Tools::EUtilities::Info::LinkInfo->new(-eutil => 'elink',
-datatype => 'linkinfo',
-verbose => $self->verbose
);
$obj->_add_data($linkinfo);
push @{$self->{'_linkinfo'}}, $obj;
}
}
=head2 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 various print methods
=cut
sub to_string {
my $self = shift;
my $level = shift || 0;
my $pad = 20 - $level;
# order method name
my %tags = (1 => ['get_databases' => 'DB'],
2 => ['get_ids' => 'ID'],
3 => ['get_link_names' => 'Link Names'],
5 => ['get_submitted_ids' => 'Submitted IDs'],
6 => ['has_scores' => 'Scores?'],
7 => ['has_linkout' => 'LinkOut?'],
8 => ['has_neighbor' => 'DB Neighbors?'],
9 => ['get_webenv' => 'WebEnv'],
10 => ['get_query_key' => 'Key'],
);
my $string;
for my $tag (sort {$a <=> $b} keys %tags) {
my ($m, $nm) = (@{$tags{$tag}}[0..1]);
# using this awkward little construct to deal with both lists and scalars
my @content = grep {defined $_} $self->$m();
next unless @content;
$string .= $self->_text_wrap(
sprintf("%-*s%-*s:",$level, '',$pad, $nm,),
' ' x ($pad).':',
join(', ',@content))."\n";
}
while (my $li = $self->next_LinkInfo) {
$string .= $li->to_string(4);
}
while (my $ui = $self->next_UrlLink) {
$string .= $ui->to_string(4);
}
if ($self->has_scores) {
$string .= "Scores:\n";
my %scores = $self->get_scores;
$string .= sprintf("%-*s%-*s%s\n",
$level + 4, '',
$pad - 4, 'ID', 'Score'
);
for my $id ($self->get_ids) {
$string .= sprintf("%-*s%-*s%s\n",
$level + 4, '',
$pad - 4, $id, $scores{$id}
);
}
}
$string .= "\n";
return $string;
}
1;