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.\" ========================================================================
.\"
.IX Title "Bio::Search::Hit::BlastPullHit 3pm"
.TH Bio::Search::Hit::BlastPullHit 3pm "2020-10-28" "perl v5.30.3" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
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.SH "NAME"
Bio::Search::Hit::BlastPullHit \- A parser and hit object for BLASTN hits
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 4
\&    # generally we use Bio::SearchIO to build these objects
\&    use Bio::SearchIO;
\&    my $in = Bio::SearchIO\->new(\-format => \*(Aqblast_pull\*(Aq,
\&                                                           \-file   => \*(Aqresult.blast\*(Aq);
\&
\&    while (my $result = $in\->next_result) {
\&                while (my $hit = $result\->next_hit) {
\&                        print $hit\->name, "\en";
\&                        print $hit\->score, "\en";
\&                        print $hit\->significance, "\en";
\&
\&                        while (my $hsp = $hit\->next_hsp) {
\&                                # process HSPI objects
\&                        }
\&                }
\&    }
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
This object implements a parser for \s-1BLASTN\s0 hit output.
.SH "FEEDBACK"
.IX Header "FEEDBACK"
.SS "Mailing Lists"
.IX Subsection "Mailing Lists"
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list.  Your participation is much appreciated.
.PP
.Vb 2
\&  bioperl\-l@bioperl.org                  \- General discussion
\&  http://bioperl.org/wiki/Mailing_lists  \- About the mailing lists
.Ve
.SS "Support"
.IX Subsection "Support"
Please direct usage questions or support issues to the mailing list:
.PP
\&\fIbioperl\-l@bioperl.org\fR
.PP
rather than to the module maintainer directly. Many experienced and 
reponsive experts will be able look at the problem and quickly 
address it. Please include a thorough description of the problem 
with code and data examples if at all possible.
.SS "Reporting Bugs"
.IX Subsection "Reporting Bugs"
Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via the
web:
.PP
.Vb 1
\&  https://github.com/bioperl/bioperl\-live/issues
.Ve
.SH "AUTHOR \- Sendu Bala"
.IX Header "AUTHOR - Sendu Bala"
Email bix@sendu.me.uk
.SH "CONTRIBUTORS"
.IX Header "CONTRIBUTORS"
Additional contributors names and emails here
.SH "APPENDIX"
.IX Header "APPENDIX"
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
.SS "new"
.IX Subsection "new"
.Vb 7
\& Title   : new
\& Usage   : my $obj = Bio::Search::Hit::BlastNHit\->new();
\& Function: Builds a new Bio::Search::Hit::BlastNHit object.
\& Returns : Bio::Search::Hit::BlastNHit
\& Args    : \-chunk    => [Bio::Root::IO, $start, $end] (required if no \-parent)
\&           \-parent   => Bio::PullParserI object (required if no \-chunk)
\&           \-hit_data => array ref with [name description score significance]
\&
\&           where the array ref provided to \-chunk contains an IO object
\&           for a filehandle to something representing the raw data of the
\&           hit, and $start and $end define the tell() position within the
\&           filehandle that the hit data starts and ends (optional; defaults
\&           to start and end of the entire thing described by the filehandle)
.Ve
.SS "next_hsp"
.IX Subsection "next_hsp"
.Vb 6
\& Title    : next_hsp
\& Usage    : while( $hsp = $obj\->next_hsp()) { ... }
\& Function : Returns the next available High Scoring Pair
\& Example  : 
\& Returns  : L<Bio::Search::HSP::HSPI> object or null if finished
\& Args     : none
.Ve
.SS "hsps"
.IX Subsection "hsps"
.Vb 5
\& Usage     : $hit_object\->hsps();
\& Purpose   : Get a list containing all HSP objects.
\& Example   : @hsps = $hit_object\->hsps();
\& Returns   : list of L<Bio::Search::HSP::BlastHSP> objects.
\& Argument  : none
.Ve
.SS "hsp"
.IX Subsection "hsp"
.Vb 11
\& Usage     : $hit_object\->hsp( [string] );
\& Purpose   : Get a single HSPI object for the present HitI object.
\& Example   : $hspObj  = $hit_object\->hsp;  # same as \*(Aqbest\*(Aq
\&           : $hspObj  = $hit_object\->hsp(\*(Aqbest\*(Aq);
\&           : $hspObj  = $hit_object\->hsp(\*(Aqworst\*(Aq);
\& Returns   : Object reference for a L<Bio::Search::HSP::HSPI> object.
\& Argument  : String (or no argument).
\&           :   No argument (default) = highest scoring HSP (same as \*(Aqbest\*(Aq).
\&           :   \*(Aqbest\*(Aq  = highest scoring HSP.
\&           :   \*(Aqworst\*(Aq = lowest scoring HSP.
\& Throws    : Exception if an unrecognized argument is used.
.Ve
.PP
See Also   : \fBhsps()\fR, num_hsps()
.SS "rewind"
.IX Subsection "rewind"
.Vb 6
\& Title   : rewind
\& Usage   : $result\->rewind;
\& Function: Allow one to reset the HSP iterator to the beginning, so that
\&           next_hsp() will subsequently return the first hsp and so on.
\& Returns : n/a
\& Args    : none
.Ve