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Bio/SearchIO/SearchResultEventBuilder.pm  view on Meta::CPAN

 Title   : start_result
 Usage   : $handler->start_result($resulttype)
 Function: Begins a result event cycle
 Returns : none
 Args    : Type of Report

=cut

sub start_result {
   my ($self,$type) = @_;
   $self->{'_resulttype'} = $type;
   $self->{'_hits'} = [];
   $self->{'_hsps'} = [];
   $self->{'_hitcount'} = 0;
   return;
}

=head2 end_result

 Title   : end_result
 Usage   : my @results = $parser->end_result
 Function: Finishes a result handler cycle
 Returns : A Bio::Search::Result::ResultI
 Args    : none

=cut

# this is overridden by IteratedSearchResultEventBuilder
# so keep that in mind when debugging

sub end_result {
    my ($self,$type,$data) = @_;

    if( defined $data->{'runid'} &&
        $data->{'runid'} !~ /^\s+$/ ) {

        if( $data->{'runid'} !~ /^lcl\|/) {
            $data->{"RESULT-query_name"} = $data->{'runid'};
        } else {
            ($data->{"RESULT-query_name"},
             $data->{"RESULT-query_description"}) =
                split(/\s+/,$data->{"RESULT-query_description"},2);
        }

        if( my @a = split(/\|/,$data->{'RESULT-query_name'}) ) {
            my $acc = pop @a ; # this is for accession |1234|gb|AAABB1.1|AAABB1
            # this is for |123|gb|ABC1.1|
            $acc = pop @a if( ! defined $acc || $acc =~ /^\s+$/);
            $data->{"RESULT-query_accession"}= $acc;
        }
        delete $data->{'runid'};
    }
    my %args = map { my $v = $data->{$_}; s/RESULT//; ($_ => $v); }
               grep { /^RESULT/ } keys %{$data};

    $args{'-algorithm'} =  uc(   $args{'-algorithm_name'}
                              || $data->{'RESULT-algorithm_name'}
                              || $type);
    ($self->isa('Bio::SearchIO::IteratedSearchResultEventBuilder')) ?
          ( $args{'-iterations'} = $self->{'_iterations'} )
        : ( $args{'-hits'}       = $self->{'_hits'} );

    my $result = $self->factory('result')->create_object(%args);
    $result->hit_factory($self->factory('hit'));

    ($self->isa('Bio::SearchIO::IteratedSearchResultEventBuilder')) ?
          ( $self->{'_iterations'} = [] )
        : ( $self->{'_hits'}       = [] );

    return $result;
}

=head2 start_hsp

 Title   : start_hsp
 Usage   : $handler->start_hsp($name,$data)
 Function: Begins processing a HSP event
 Returns : none
 Args    : type of element
           associated data (hashref)

=cut

sub start_hsp {
    my ($self,@args) = @_;
    return;
}

=head2 end_hsp

 Title   : end_hsp
 Usage   : $handler->end_hsp()
 Function: Finish processing a HSP event
 Returns : none
 Args    : type of event and associated hashref


=cut

sub end_hsp {
    my ($self,$type,$data) = @_;

    if( defined $data->{'runid'} &&
        $data->{'runid'} !~ /^\s+$/ ) {

        if( $data->{'runid'} !~ /^lcl\|/) {
            $data->{"RESULT-query_name"}= $data->{'runid'};
        } else {
            ($data->{"RESULT-query_name"},
             $data->{"RESULT-query_description"}) =
                 split(/\s+/,$data->{"RESULT-query_description"},2);
        }

        if( my @a = split(/\|/,$data->{'RESULT-query_name'}) ) {
            my $acc = pop @a ; # this is for accession |1234|gb|AAABB1.1|AAABB1
            # this is for |123|gb|ABC1.1|
            $acc = pop @a if( ! defined $acc || $acc =~ /^\s+$/);
            $data->{"RESULT-query_accession"}= $acc;
        }
        delete $data->{'runid'};
    }

    # this code is to deal with the fact that Blast XML data
    # always has start < end and one has to infer strandedness
    # from the frame which is a problem for the Search::HSP object
    # which expect to be able to infer strand from the order of
    # of the begin/end of the query and hit coordinates