view release on metacpan or  search on metacpan

lib/LiteratureBasedDiscovery/Filters.pm  view on Meta::CPAN

	}
    }
    print "   number of keys before filtering = ".(scalar keys %termsHash)."\n";
=cut

    #eliminate values that are incorrect semantic groups
    #do each row at a time, remove column values that 
    #are the incorrect semantic type
    my %cuisChecked = ();
    #cuisChecked keeps track of cuis that have been checked 
    # for elimination. If the cui has been checked its key
    # will exist in the hash. Values of -1 indicate it should
    # be eliminated, values of 1 indicate it should stay.
    #eliminate cuis from columns
    foreach my $cui1 (keys %{$matrixRef}) {
	foreach my $cui2 (keys %{${$matrixRef}{$cui1}}) {
	    #update cui checked hash
	    if (!exists $cuisChecked{$cui2}) {
		$cuisChecked{$cui2} = -1;

		my $typesRef = $umls->getSt($cui2);
		foreach my $type(@{$typesRef}) {
		    my $abr = $umls->getStAbr($type);

		    #check the cui for removal
		    if (exists ${$acceptTypesRef}{$type}) {
			$cuisChecked{$cui2} = 1;
			last;
		    }
		}
	    }

	    #eliminate if needed
	    if ($cuisChecked{$cui2} < 0) {
		delete ${${$matrixRef}{$cui1}}{$cui2};
	    }
	}
    }

=comment
    #Count the number of keys after filtering (for debugging)
    %termsHash = ();
    foreach my $key1 (keys %{$matrixRef}) {
	foreach my $key2 (keys %{${$matrixRef}{$key1}}) {
	    $termsHash{$key2} = 1;
	}
    }
    print "   number of keys after filtering = ".(scalar keys %termsHash)."\n";
=cut

}

# gets the semantic types of the group
# input:  $group <- a string specifying a semantic group
#         $umls <- an instance of UMLS::Interface
# output: a ref to a hash of TUIs
sub getTypesOfGroup {
    my $group = shift;
    my $umls = shift;

    #add each type of the group to the set of accept types
    my %acceptTuis = ();
    my @groupTypes = @{ $umls->getStsFromSg($group) };
    foreach my $abr(@groupTypes) {
	#check that it is defined (types that are no longer in 
	#the UMLS may be returned as part of the group)
	if (defined $abr) {
	    my $tui = uc $umls->getStTui($abr);
	    $acceptTuis{$tui} = 1;
	}
    }

    return \%acceptTuis;
}

# gets all semantic types of the UMLS
# input:  $umls <- an instance of UMLS::Interface
# output: a ref to an array of TUIs
sub getAllTypes {
    my $umls = shift;

    my $abrRef = $umls->getAllSts();
    my @tuis = ();
    foreach my $abr(@{$abrRef}) {
	push @tuis, uc $umls->getStTui($abr);
    }

    return \@tuis;
}

# gets all semantic groups of the UMLS
# input:  $umls <- an instance of UMLS::Interface
# output: a ref to a hash of semantic groups
sub getAllGroups {
    my $umls = shift;
    my $groupsRef = $umls->getAllSemanticGroups();
    return $groupsRef;
}

1;