Provided by: libbio-perl-perl_1.7.2-2_all bug


       Bio::Tools::Promoterwise - parser for Promoterwise tab format output


         use Bio::Tools::Promoterwise;

         my $pw = Bio::Tools::Promoterwise->new(-file=>"out",
         while (my $fp = $pw->next_result){
           print "Hit Length: ".$fp->feature1->length."\n";
           print "Hit Start: ".$fp->feature1->start."\n";
           print "Hit End: ".$fp->feature1->end."\n";
           print "Hsps: \n";
           my @first_hsp = $fp->feature1->sub_SeqFeature;
           my @second_hsp = $fp->feature2->sub_SeqFeature;
           foreach my $i (0..$#first_hsp){
             print $first_hsp[$i]->start. " ".$first_hsp[$i]->end." ".
                   $second_hsp[$i]->start. " ".$second_hsp[$i]->end."\n";


       Promoteriwise is an alignment algorithm that relaxes the constraint that local alignments
       have to be co-linear. Otherwise it provides a similar model to DBA, which is designed for
       promoter sequence alignments.  Promoterwise is written by Ewan Birney.  It is part of the
       wise2 package available at <>

       This module is the parser for the Promoterwise output in tab format.


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AUTHOR - Shawn Hoon



       The rest of the documentation details each of the object methods.  Internal methods are
       usually preceded with a _

        Title   : new
        Usage   : my $obj = Bio::Tools::Promoterwise->new();
        Function: Builds a new Bio::Tools::Promoterwise object
        Returns : L<Bio::Tools::Promoterwise>
        Args    : -fh/-file => $val, # for initing input, see Bio::Root::IO

        Title   : next_result
        Usage   : my $r = $rpt_masker->next_result
        Function: Get the next result set from parser data
        Returns : an  L<Bio::SeqFeature::FeaturePair>
        Args    : none