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

$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_Feature
	1: a fields_IsLocatedIn
	2: a fields_Contig
fields_Feature is a reference to a hash where the following keys are defined:
	id has a value which is a string
	feature_type has a value which is a string
	source_id has a value which is a string
	sequence_length has a value which is an int
	function has a value which is a string
	alias has a value which is a reference to a list where each element is a string
fields_IsLocatedIn is a reference to a hash where the following keys are defined:
	id has a value which is a string
	ordinal has a value which is an int
	begin has a value which is an int
	len has a value which is an int
	dir has a value which is a string
fields_Contig is a reference to a hash where the following keys are defined:
	id has a value which is a string
	source_id has a value which is a string

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=end html

=begin text

$ids is a reference to a list where each element is a string
$from_fields is a reference to a list where each element is a string
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_Feature
	1: a fields_IsLocatedIn
	2: a fields_Contig
fields_Feature is a reference to a hash where the following keys are defined:
	id has a value which is a string
	feature_type has a value which is a string
	source_id has a value which is a string
	sequence_length has a value which is an int
	function has a value which is a string
	alias has a value which is a reference to a list where each element is a string
fields_IsLocatedIn is a reference to a hash where the following keys are defined:
	id has a value which is a string
	ordinal has a value which is an int
	begin has a value which is an int
	len has a value which is an int
	dir has a value which is a string
fields_Contig is a reference to a hash where the following keys are defined:
	id has a value which is a string
	source_id has a value which is a string


=end text



=item Description

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

=back

=cut

sub get_relationship_IsLocatedIn
{
    my $self = shift;
    my($ids, $from_fields, $rel_fields, $to_fields) = @_;

    my @_bad_arguments;
    (ref($ids) eq 'ARRAY') or push(@_bad_arguments, "Invalid type for argument \"ids\" (value was \"$ids\")");
    (ref($from_fields) eq 'ARRAY') or push(@_bad_arguments, "Invalid type for argument \"from_fields\" (value was \"$from_fields\")");
    (ref($rel_fields) eq 'ARRAY') or push(@_bad_arguments, "Invalid type for argument \"rel_fields\" (value was \"$rel_fields\")");
    (ref($to_fields) eq 'ARRAY') or push(@_bad_arguments, "Invalid type for argument \"to_fields\" (value was \"$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');
    }

    my $ctx = $Bio::KBase::CDMI::Service::CallContext;
    my($return);
    #BEGIN get_relationship_IsLocatedIn