Raw content of Bio::Tools::Grail
<$/;
my $prednr = $1;
if($seqobj->display_id() !~ /_predicted_\w+_$prednr\|/) {
# this is not our sequence, so push back for the next prediction
push(@{$self->{'_seqstack'}}, $seqobj);
} else {
$gene->predicted_protein($seqobj);
# CDS prediction, too?
if($self->_has_cds()) {
($id, $seq) = $self->_read_fasta_seq();
$seqobj = Bio::PrimarySeq->new('-seq' => $seq,
'-display_id' => $id,
'-alphabet' => "dna");
$gene->predicted_cds($seqobj);
}
}
}
return $gene;
}
=head2 _parse_predictions
Title : _parse_predictions()
Usage : $obj->_parse_predictions()
Function: Parses the prediction section. Automatically called by
next_prediction() if not yet done.
Example :
Returns :
=cut
sub _parse_predictions {
my ($self) = @_;
# code needs to go here
$self->_predictions_parsed(1);
}
=head2 _prediction
Title : _prediction()
Usage : $gene = $obj->_prediction()
Function: internal
Example :
Returns :
=cut
sub _prediction {
my ($self) = @_;
return undef unless(exists($self->{'_preds'}) && @{$self->{'_preds'}});
return shift(@{$self->{'_preds'}});
}
=head2 _add_prediction
Title : _add_prediction()
Usage : $obj->_add_prediction($gene)
Function: internal
Example :
Returns :
=cut
sub _add_prediction {
my ($self, $gene) = @_;
if(! exists($self->{'_preds'})) {
$self->{'_preds'} = [];
}
push(@{$self->{'_preds'}}, $gene);
}
=head2 _predictions_parsed
Title : _predictions_parsed
Usage : $obj->_predictions_parsed
Function: internal
Example :
Returns : TRUE or FALSE
=cut
sub _predictions_parsed {
my ($self, $val) = @_;
$self->{'_preds_parsed'} = $val if $val;
if(! exists($self->{'_preds_parsed'})) {
$self->{'_preds_parsed'} = 0;
}
return $self->{'_preds_parsed'};
}
=head2 _has_cds
Title : _has_cds()
Usage : $obj->_has_cds()
Function: Whether or not the result contains the predicted CDSs, too.
Example :
Returns : TRUE or FALSE
=cut
sub _has_cds {
my ($self, $val) = @_;
$self->{'_has_cds'} = $val if $val;
if(! exists($self->{'_has_cds'})) {
$self->{'_has_cds'} = 0;
}
return $self->{'_has_cds'};
}
1;
]]>