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Bio/Search/Hit/PsiBlastHit.pm  view on Meta::CPAN

sub seq_inds {
#-------------
    my ($self, $seqType, $class, $collapse) = @_;

    $seqType  ||= 'query';
    $class ||= 'identical';
    $collapse ||= 0;

    $seqType = 'sbjct' if $seqType eq 'hit';

    my (@inds, $hsp);
    foreach $hsp ($self->hsps) {
        # This will merge data for all HSPs together.
        push @inds, $hsp->seq_inds($seqType, $class);
    }

    # Need to remove duplicates and sort the merged positions.
    if(@inds) {
        my %tmp = map { $_, 1 } @inds;
        @inds = sort {$a <=> $b} keys %tmp;
    }

    $collapse ?  &Bio::Search::BlastUtils::collapse_nums(@inds) : @inds;
}


=head2 iteration

 Usage     : $sbjct->iteration( );
 Purpose   : Gets the iteration number in which the Hit was found.
 Example   : $iteration_num = $sbjct->iteration();
 Returns   : Integer greater than or equal to 1
             Non-PSI-BLAST reports will report iteration as 1, but this number
             is only meaningful for PSI-BLAST reports.
 Argument  : none
 Throws    : none

See Also   : L<found_again()|found_again>

=cut

#----------------
sub iteration { shift->{'_iteration'} }
#----------------


=head2 found_again

 Usage     : $sbjct->found_again;
 Purpose   : Gets a boolean indicator whether or not the hit has
             been found in a previous iteration.
             This is only applicable to PSI-BLAST reports.

              This method indicates if the hit was reported in the
              "Sequences used in model and found again" section of the
              PSI-BLAST report or if it was reported in the
              "Sequences not found previously or not previously below threshold"
              section of the PSI-BLAST report. Only for hits in iteration > 1.

 Example   : if( $sbjct->found_again()) { ... };
 Returns   : Boolean (1 or 0) for PSI-BLAST report iterations greater than 1.
             Returns undef for PSI-BLAST report iteration 1 and non PSI_BLAST
             reports.
 Argument  : none
 Throws    : none

See Also   : L<found_again()|found_again>

=cut

#----------------
sub found_again { shift->{'_found_again'} }
#----------------


=head2 strand

 Usage     : $sbjct->strand( [seq_type] );
 Purpose   : Gets the strand(s) for the query, sbjct, or both sequences
           : in the best HSP of the PsiBlastHit object after HSP tiling.
           : Only valid for BLASTN, TBLASTX, BLASTX-query, TBLASTN-hit.
 Example   : $qstrand = $sbjct->strand('query');
           : $sstrand = $sbjct->strand('hit');
           : ($qstrand, $sstrand) = $sbjct->strand();
 Returns   : scalar context: integer '1', '-1', or '0'
           : array context without args: list of two strings (queryStrand, sbjctStrand)
           : Array context can be "induced" by providing an argument of 'list' or 'array'.
 Argument  : In scalar context: seq_type = 'query' or 'hit' or 'sbjct' (default = 'query')
             ('sbjct' is synonymous with 'hit')
 Throws    : n/a
 Comments  : This method requires that all HSPs be tiled. If they have not
           : already been tiled, they will be tiled first automatically..
           : If you don't want the tiled data, iterate through each HSP
           : calling strand() on each (use hsps() to get all HSPs).
           :
           : Formerly (prior to 10/21/02), this method would return the
           : string "-1/1" for hits with HSPs on both strands.
           : However, now that strand and frame is properly being accounted
           : for during HSP tiling, it makes more sense for strand()
           : to return the strand data for the best HSP after tiling.
           :
           : If you really want to know about hits on opposite strands,
           : you should be iterating through the HSPs using methods on the
           : HSP objects.
           :
           : A possible use case where knowing whether a hit has HSPs
           : on both strands would be when filtering via SearchIO for hits with
           : this property. However, in this case it would be better to have a
           : dedicated method such as $hit->hsps_on_both_strands(). Similarly
           : for frame. This could be provided if there is interest.

See Also   : L<Bio::Search::HSP::BlastHSP::strand>()

=cut

#----------'
sub strand {
#----------
    my ($self, $seqType) = @_;

    Bio::Search::BlastUtils::tile_hsps($self) if not $self->{'_tile_hsps'};