Raw content of Bio::EnsEMBL::Pipeline::Rule
<![CDATA[# Perl module for Bio::EnsEMBL::Pipeline::Rule
#
# Creator: Arne Stabenau <stabenau@ebi.ac.uk>
# Date of creation: 10.09.2000
# Last modified : 10.09.2000 by Arne Stabenau
#
# Copyright EMBL-EBI 2000
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::EnsEMBL::Pipeline::Rule
=head1 SYNOPSIS
=head1 DESCRIPTION
=head1 CONTACT
Contact Arne Stabenau on implemetation/design detail: stabenau@ebi.ac.uk
Contact Ewan Birney on EnsEMBL in general: birney@sanger.ac.uk
=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::EnsEMBL::Pipeline::Rule;
use vars qw(@ISA);
use strict;
use Bio::EnsEMBL::Utils::Exception qw(verbose throw warning info);
use Bio::EnsEMBL::Utils::Argument qw( rearrange );
@ISA = qw();
=head2 Constructor
Title : new
Usage : ...Rule->new($analysis);
Function: Constructor for Rule object
Returns : Bio::EnsEMBL::Pipeline::Rule
Args : A Bio::EnsEMBL::Analysis object. Conditions are added later,
adaptor and dbid only used from the adaptor.
=cut
sub new {
my ($class,@args) = @_;
my $self = bless {},$class;
my ( $goal, $adaptor, $dbID ) =
rearrange( [ qw ( GOALANALYSIS
ADAPTOR
DBID
) ], @args );
if ( $goal ) {
throw( "Wrong parameter" ) unless
$goal->isa( "Bio::EnsEMBL::Analysis" );
}
$self->dbID( $dbID );
$self->goalAnalysis( $goal );
$self->adaptor( $adaptor );
$self->{'_condition_type_cache'} = {};
return $self;
}
=head2 add_condition
Title : add_condition
Usage : $self->add_conditon($logic_name);
Function: Add method for conditions for the rule.
Returns : nothing
Args : a string describing a testable condition on an object
For now a logic_name of an analysis.
=cut
sub add_condition {
my $self = shift;
my $condition = shift;
push( @{$self->{'_conditions'}}, $condition );
}
=head2 list_conditions
Title : list_conditions
Usage : $self->list_conditions();
Function: Give a list of all conditions you have to fulfill to make this
Rule evaluate to true.
Returns : a list of strings which are probably logic_names
Args : -
=cut
sub list_conditions {
my $self = shift;
my @conditions;
if ($self->{'_conditions'}) {
@conditions = @{$self->{'_conditions'}};
}
if (! scalar (@conditions) ) {
throw("No conditions found for this Rule");
}
return \@conditions;
}
sub has_condition_of_input_id_type {
my $self = shift;
my $id_type = shift;
my $ana_adaptor = $self->goalAnalysis->adaptor;
if (!scalar (@{$self->{'_conditions'}})) {
throw("No conditions found for this Rule");
}
return 1 if (exists($self->{'_condition_type_cache'}{$id_type}));
foreach my $cond (@{$self->{'_conditions'}}) {
my $cond_anal = $ana_adaptor->fetch_by_logic_name($cond);
if ($cond_anal->input_id_type eq $id_type) {
#print " Condition of " . $cond_anal->logic_name . " is of type $id_type\n";
$self->{'_condition_type_cache'}{$id_type} = 1;
return 1;
}
}
return 0;
}
=head2 goalAnalysis
Title : goalAnalysis
Usage : $self->goalAnalysis($anal);
Function: Get/set method for the goal analysis object of this rule.
Returns : Bio::EnsEMBL::Analysis
Args : Bio::EnsEMBL::Analysis
=cut
sub goalAnalysis {
my ($self,$arg) = @_;
( defined $arg ) &&
( $self->{'_goal'} = $arg );
$self->{'_goal'};
}
=head2 check_for_analysis
-args: [analysis list], 'input id type', {completed accumulators}, verbose
-returns: Either bits for status if nothing can be done;
1 - Failed Input_Id_Type Check.
2 - Failed Already Complete Check [so is complete].
4 - Failed Condition Check.
Or;
$goalAnalysis if it should be done
=cut
sub check_for_analysis {
my $self = shift;
my ($analist, $input_id_type, $completed_accumulator_href, $verbose) = @_;
my %anaHash;
my $return = 0;
# reimplement with proper identity check!
my $goal_anal = $self->goalAnalysis;
my $goal = $goal_anal->dbID;
my $goal_id_type = $goal_anal->input_id_type;
print "\nHave goal type ".$goal_id_type." and input id type ".$input_id_type."\n" if($verbose);
#This id isn't of the right type so doesn't satify goal
if ($goal_id_type ne 'ACCUMULATOR' &&
$goal_id_type ne $input_id_type) {
print "In check_for_analysis failed input_id_type check as goal input_id type ".
"isn't the same as the input_id type\n" if ($verbose);
$return += 1;
}
print " My goal is " . $goal_anal->logic_name . "\n" if($verbose);
print " Completed anals on this id:\n" if ($verbose);
for my $analysis ( @$analist ) {
print " Analysis " . $analysis->logic_name . " " . $analysis->dbID . "\n" if($verbose);
$anaHash{$analysis->logic_name} = $analysis;
if ($goal == $analysis->dbID) {
# already done
print $goal_anal->logic_name." already done\n" if ($verbose);
$return += 2;
}
}
#the completed_accumulator_href contains input_id_type ACCUMULATOR anals that have completed
print " Checking conditions:\n" if ($verbose);
for my $cond ( @{$self->{'_conditions'}} ) {
# remove any trailing whitespace because the matches won't happen if there is whitespace in, eg. your rule_conditions table.
$cond =~ s/\s+//g;
if ( ! exists $anaHash{$cond} && ! exists $completed_accumulator_href->{$cond}) {
print " failed condition check for $cond\n" if ($verbose);
$return += 4;
}
}
if ($return < 4) {
print " All conditions satisfied\n" if ($verbose);
}
return $return if $return;
return $goal_anal;
}
sub dbID {
my ( $self, $dbID ) = @_;
( defined $dbID ) &&
( $self->{'_dbID'} = $dbID );
$self->{'_dbID'};
}
sub adaptor {
my ( $self, $adaptor ) = @_;
( defined $adaptor ) &&
( $self->{'_adaptor'} = $adaptor );
$self->{'_adaptor'};
}
1;
]]>