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lib/Bio/KBase/CDMI/Client.pm  view on Meta::CPAN

    }
}



=head2 $result = get_relationship_IsInstanceOf(ids, from_fields, rel_fields, to_fields)



=cut

sub get_relationship_IsInstanceOf
{
    my($self, @args) = @_;

    if ((my $n = @args) != 4)
    {
	Bio::KBase::Exceptions::ArgumentValidationError->throw(error =>
							       "Invalid argument count for function get_relationship_IsInstanceOf (received $n, expecting 4)");
    }
    {
	my($ids, $from_fields, $rel_fields, $to_fields) = @args;

	my @_bad_arguments;
        (ref($ids) eq 'ARRAY') or push(@_bad_arguments, "Invalid type for argument 1 \"ids\" (value was \"$ids\")");
        (ref($from_fields) eq 'ARRAY') or push(@_bad_arguments, "Invalid type for argument 2 \"from_fields\" (value was \"$from_fields\")");
        (ref($rel_fields) eq 'ARRAY') or push(@_bad_arguments, "Invalid type for argument 3 \"rel_fields\" (value was \"$rel_fields\")");
        (ref($to_fields) eq 'ARRAY') or push(@_bad_arguments, "Invalid type for argument 4 \"to_fields\" (value was \"$to_fields\")");
        if (@_bad_arguments) {
	    my $msg = "Invalid arguments passed to get_relationship_IsInstanceOf:\n" . join("", map { "\t$_\n" } @_bad_arguments);
	    Bio::KBase::Exceptions::ArgumentValidationError->throw(error => $msg,
								   method_name => 'get_relationship_IsInstanceOf');
	}
    }

    my $result = $self->{client}->call($self->{url}, {
	method => "CDMI_EntityAPI.get_relationship_IsInstanceOf",
	params => \@args,
    });
    if ($result) {
	if ($result->is_error) {
	    Bio::KBase::Exceptions::JSONRPC->throw(error => $result->error_message,
					       code => $result->content->{code},
					       method_name => 'get_relationship_IsInstanceOf',
					      );
	} else {
	    return wantarray ? @{$result->result} : $result->result->[0];
	}
    } else {
        Bio::KBase::Exceptions::HTTP->throw(error => "Error invoking method get_relationship_IsInstanceOf",
					    status_line => $self->{client}->status_line,
					    method_name => 'get_relationship_IsInstanceOf',
				       );
    }
}



=head2 $result = get_relationship_IsLocatedIn(ids, from_fields, rel_fields, to_fields)

A feature is a set of DNA sequence fragments. Most features
are a single contiquous fragment, so they are located in only one
DNA sequence; however, fragments have a maximum length, so even a
single contiguous feature may participate in this relationship
multiple times. A few features belong to multiple DNA sequences. In
that case, however, all the DNA sequences belong to the same genome.
A DNA sequence itself will frequently have thousands of features
connected to it.
It has the following fields:

=over 4


=item ordinal

Sequence number of this segment, starting from 1
and proceeding sequentially forward from there.


=item begin

Index (1-based) of the first residue in the contig
that belongs to the segment.


=item len

Length of this segment.


=item dir

Direction (strand) of the segment: "+" if it is
forward and "-" if it is backward.



=back

=cut

sub get_relationship_IsLocatedIn
{
    my($self, @args) = @_;

    if ((my $n = @args) != 4)
    {
	Bio::KBase::Exceptions::ArgumentValidationError->throw(error =>
							       "Invalid argument count for function get_relationship_IsLocatedIn (received $n, expecting 4)");
    }
    {
	my($ids, $from_fields, $rel_fields, $to_fields) = @args;

	my @_bad_arguments;
        (ref($ids) eq 'ARRAY') or push(@_bad_arguments, "Invalid type for argument 1 \"ids\" (value was \"$ids\")");
        (ref($from_fields) eq 'ARRAY') or push(@_bad_arguments, "Invalid type for argument 2 \"from_fields\" (value was \"$from_fields\")");
        (ref($rel_fields) eq 'ARRAY') or push(@_bad_arguments, "Invalid type for argument 3 \"rel_fields\" (value was \"$rel_fields\")");
        (ref($to_fields) eq 'ARRAY') or push(@_bad_arguments, "Invalid type for argument 4 \"to_fields\" (value was \"$to_fields\")");
        if (@_bad_arguments) {
	    my $msg = "Invalid arguments passed to get_relationship_IsLocatedIn:\n" . join("", map { "\t$_\n" } @_bad_arguments);
	    Bio::KBase::Exceptions::ArgumentValidationError->throw(error => $msg,
								   method_name => 'get_relationship_IsLocatedIn');
	}