Bio-KBase

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

		    'type' => 1,
	
    },
    'Triggers' => {
	to_link => 1, from_link => 1,
		    'optional' => 1,
		    'type' => 1,
	
    },
    'IsUsedAs' => {
	to_link => 1, from_link => 1,
	
    },
    'IsUseOf' => {
	to_link => 1, from_link => 1,
	
    },
    'Manages' => {
	to_link => 1, from_link => 1,
	
    },
    'IsManagedBy' => {
	to_link => 1, from_link => 1,
	
    },
    'OperatesIn' => {
	to_link => 1, from_link => 1,
	
    },
    'IsUtilizedIn' => {
	to_link => 1, from_link => 1,
	
    },
    'Overlaps' => {
	to_link => 1, from_link => 1,
	
    },
    'IncludesPartOf' => {
	to_link => 1, from_link => 1,
	
    },
    'ParticipatesAs' => {
	to_link => 1, from_link => 1,
	
    },
    'IsParticipationOf' => {
	to_link => 1, from_link => 1,
	
    },
    'ProducedResultsFor' => {
	to_link => 1, from_link => 1,
	
    },
    'HadResultsProducedBy' => {
	to_link => 1, from_link => 1,
	
    },
    'ProjectsOnto' => {
	to_link => 1, from_link => 1,
		    'gene_context' => 1,
		    'percent_identity' => 1,
		    'score' => 1,
	
    },
    'IsProjectedOnto' => {
	to_link => 1, from_link => 1,
		    'gene_context' => 1,
		    'percent_identity' => 1,
		    'score' => 1,
	
    },
    'Provided' => {
	to_link => 1, from_link => 1,
	
    },
    'WasProvidedBy' => {
	to_link => 1, from_link => 1,
	
    },
    'Shows' => {
	to_link => 1, from_link => 1,
		    'location' => 1,
	
    },
    'IsShownOn' => {
	to_link => 1, from_link => 1,
		    'location' => 1,
	
    },
    'Submitted' => {
	to_link => 1, from_link => 1,
	
    },
    'WasSubmittedBy' => {
	to_link => 1, from_link => 1,
	
    },
    'Uses' => {
	to_link => 1, from_link => 1,
	
    },
    'IsUsedBy' => {
	to_link => 1, from_link => 1,
	
    },

};

our $relationship_field_rels = {
    'AffectsLevelOf' => {
    },
    'IsAffectedIn' => {
    },
    'Aligns' => {
    },
    'IsAlignedBy' => {
    },
    'AssertsFunctionFor' => {
    },
    'HasAssertedFunctionFrom' => {
    },
    'Concerns' => {
    },
    'IsATopicOf' => {
    },
    'Contains' => {
    },
    'IsContainedIn' => {

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

{
    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 $msg = "Invalid arguments passed to get_relationship_HadResultsProducedBy:\n" . join("", map { "\t$_\n" } @_bad_arguments);
	Bio::KBase::Exceptions::ArgumentValidationError->throw(error => $msg,
							       method_name => 'get_relationship_HadResultsProducedBy');
    }

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

    $return = $self->_get_relationship($ctx, 'HadResultsProducedBy', 'ProducedResultsFor', 1, $ids, $from_fields, $rel_fields, $to_fields);
	
    #END get_relationship_HadResultsProducedBy
    my @_bad_returns;
    (ref($return) eq 'ARRAY') or push(@_bad_returns, "Invalid type for return variable \"return\" (value was \"$return\")");
    if (@_bad_returns) {
	my $msg = "Invalid returns passed to get_relationship_HadResultsProducedBy:\n" . join("", map { "\t$_\n" } @_bad_returns);
	Bio::KBase::Exceptions::ArgumentValidationError->throw(error => $msg,
							       method_name => 'get_relationship_HadResultsProducedBy');
    }
    return($return);
}




=head2 get_relationship_ProjectsOnto

  $return = $obj->get_relationship_ProjectsOnto($ids, $from_fields, $rel_fields, $to_fields)

=over 4

=item Parameter and return types

=begin html

<pre>
$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_ProteinSequence
	1: a fields_ProjectsOnto
	2: a fields_ProteinSequence
fields_ProteinSequence is a reference to a hash where the following keys are defined:
	id has a value which is a string
	sequence has a value which is a string
fields_ProjectsOnto is a reference to a hash where the following keys are defined:
	id has a value which is a string
	gene_context has a value which is an int
	percent_identity has a value which is a float
	score has a value which is a float

</pre>

=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_ProteinSequence
	1: a fields_ProjectsOnto
	2: a fields_ProteinSequence
fields_ProteinSequence is a reference to a hash where the following keys are defined:
	id has a value which is a string
	sequence has a value which is a string
fields_ProjectsOnto is a reference to a hash where the following keys are defined:
	id has a value which is a string
	gene_context has a value which is an int
	percent_identity has a value which is a float
	score has a value which is a float


=end text



=item Description

This relationship connects two protein sequences for which a clear
bidirectional best hit exists in known genomes. The attributes of the
relationship describe how good the relationship is between the proteins.
The relationship is bidirectional and symmetric, but is only stored in
one direction (lower ID to higher ID).
It has the following fields:

=over 4


=item gene_context

number of homologous genes in the immediate context of the
two proteins, up to a maximum of 10


=item percent_identity

percent match between the two protein sequences


=item score

score describing the strength of the projection, from 0 to 1,
where 1 is the best



=back

=back

=cut

sub get_relationship_ProjectsOnto
{
    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 $msg = "Invalid arguments passed to get_relationship_ProjectsOnto:\n" . join("", map { "\t$_\n" } @_bad_arguments);
	Bio::KBase::Exceptions::ArgumentValidationError->throw(error => $msg,
							       method_name => 'get_relationship_ProjectsOnto');
    }

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

    $return = $self->_get_relationship($ctx, 'ProjectsOnto', 'ProjectsOnto', 0, $ids, $from_fields, $rel_fields, $to_fields);
	
    #END get_relationship_ProjectsOnto
    my @_bad_returns;
    (ref($return) eq 'ARRAY') or push(@_bad_returns, "Invalid type for return variable \"return\" (value was \"$return\")");
    if (@_bad_returns) {
	my $msg = "Invalid returns passed to get_relationship_ProjectsOnto:\n" . join("", map { "\t$_\n" } @_bad_returns);
	Bio::KBase::Exceptions::ArgumentValidationError->throw(error => $msg,
							       method_name => 'get_relationship_ProjectsOnto');
    }
    return($return);
}




=head2 get_relationship_IsProjectedOnto

  $return = $obj->get_relationship_IsProjectedOnto($ids, $from_fields, $rel_fields, $to_fields)

=over 4

=item Parameter and return types

=begin html

<pre>
$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_ProteinSequence
	1: a fields_ProjectsOnto
	2: a fields_ProteinSequence
fields_ProteinSequence is a reference to a hash where the following keys are defined:
	id has a value which is a string
	sequence has a value which is a string
fields_ProjectsOnto is a reference to a hash where the following keys are defined:
	id has a value which is a string
	gene_context has a value which is an int
	percent_identity has a value which is a float
	score has a value which is a float

</pre>

=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_ProteinSequence
	1: a fields_ProjectsOnto
	2: a fields_ProteinSequence
fields_ProteinSequence is a reference to a hash where the following keys are defined:
	id has a value which is a string
	sequence has a value which is a string
fields_ProjectsOnto is a reference to a hash where the following keys are defined:
	id has a value which is a string
	gene_context has a value which is an int
	percent_identity has a value which is a float
	score has a value which is a float


=end text



=item Description



=back

=cut

sub get_relationship_IsProjectedOnto
{
    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 $msg = "Invalid arguments passed to get_relationship_IsProjectedOnto:\n" . join("", map { "\t$_\n" } @_bad_arguments);
	Bio::KBase::Exceptions::ArgumentValidationError->throw(error => $msg,
							       method_name => 'get_relationship_IsProjectedOnto');
    }

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

    $return = $self->_get_relationship($ctx, 'IsProjectedOnto', 'ProjectsOnto', 1, $ids, $from_fields, $rel_fields, $to_fields);
	
    #END get_relationship_IsProjectedOnto
    my @_bad_returns;
    (ref($return) eq 'ARRAY') or push(@_bad_returns, "Invalid type for return variable \"return\" (value was \"$return\")");
    if (@_bad_returns) {
	my $msg = "Invalid returns passed to get_relationship_IsProjectedOnto:\n" . join("", map { "\t$_\n" } @_bad_returns);
	Bio::KBase::Exceptions::ArgumentValidationError->throw(error => $msg,
							       method_name => 'get_relationship_IsProjectedOnto');
    }
    return($return);
}




=head2 get_relationship_Provided

  $return = $obj->get_relationship_Provided($ids, $from_fields, $rel_fields, $to_fields)

=over 4

=item Parameter and return types

=begin html

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

</pre>

=end html

=begin text

a reference to a hash where the following keys are defined:
id has a value which is a string


=end text

=back



=head2 fields_ProducedResultsFor

=over 4



=item Definition

=begin html

<pre>
a reference to a hash where the following keys are defined:
id has a value which is a string

</pre>

=end html

=begin text

a reference to a hash where the following keys are defined:
id has a value which is a string


=end text

=back



=head2 fields_ProjectsOnto

=over 4



=item Definition

=begin html

<pre>
a reference to a hash where the following keys are defined:
id has a value which is a string
gene_context has a value which is an int
percent_identity has a value which is a float
score has a value which is a float

</pre>

=end html

=begin text

a reference to a hash where the following keys are defined:
id has a value which is a string
gene_context has a value which is an int
percent_identity has a value which is a float
score has a value which is a float


=end text

=back



=head2 fields_Provided

=over 4



=item Definition

=begin html

<pre>
a reference to a hash where the following keys are defined:
id has a value which is a string

</pre>

=end html

=begin text

a reference to a hash where the following keys are defined:
id has a value which is a string


=end text

=back



=head2 fields_Shows

=over 4



=item Definition

=begin html

<pre>
a reference to a hash where the following keys are defined:
id has a value which is a string
location has a value which is a rectangle

</pre>

=end html

=begin text