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.\" ========================================================================
.\"
.IX Title "Bio::SearchIO::psl 3pm"
.TH Bio::SearchIO::psl 3pm "2021-08-15" "perl v5.32.1" "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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.nh
.SH "NAME"
Bio::SearchIO::psl \- A parser for PSL output (UCSC)
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 5
\&  use Bio::SearchIO;
\&  my $parser = Bio::SearchIO\->new(\-file   => \*(Aqfile.psl\*(Aq,
\&                                 \-format => \*(Aqpsl\*(Aq);
\&  while( my $result = $parser\->next_result ) {
\&  }
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
This is a SearchIO driver for \s-1PSL\s0 format.
\&\s-1PSL\s0 format is documented here:
http://genome.ucsc.edu/goldenPath/help/customTrack.html#PSL
.PP
By default it assumes \s-1PSL\s0 output came from \s-1BLAT\s0 you can override that
by specifying \-program_name => '\s-1BLASTZ\s0' when initializing the
SearchIO object.
.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 \- Jason Stajich"
.IX Header "AUTHOR - Jason Stajich"
Email jason-at-bioperl-dot-org
.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 5
\& Title   : new
\& Usage   : my $obj = Bio::SearchIO::psl\->new();
\& Function: Builds a new Bio::SearchIO::psl object 
\& Returns : an instance of Bio::SearchIO::psl
\& Args    :
.Ve
.SS "next_result"
.IX Subsection "next_result"
.Vb 5
\& Title   : next_result
\& Usage   : my $result = $parser\->next_result
\& Function: Parse the next result from the data stream
\& Returns : L<Bio::Search::Result::ResultI> or undef if no more results
\& Args    : none
.Ve
.SS "start_element"
.IX Subsection "start_element"
.Vb 5
\& Title   : start_element
\& Usage   : $eventgenerator\->start_element
\& Function: Handles a start element event
\& Returns : none
\& Args    : hashref with at least 2 keys \*(AqData\*(Aq and \*(AqName\*(Aq
.Ve
.SS "end_element"
.IX Subsection "end_element"
.Vb 5
\& Title   : end_element
\& Usage   : $eventgenerator\->end_element
\& Function: Handles an end element event
\& Returns : return value from the associated end_$type event handler
\& Args    : hashref with at least 2 keys \*(AqData\*(Aq and \*(AqName\*(Aq
.Ve
.SS "element"
.IX Subsection "element"
.Vb 5
\& Title   : element
\& Usage   : $eventhandler\->element({\*(AqName\*(Aq => $name, \*(AqData\*(Aq => $str});
\& Function: Convience method that calls start_element, characters, end_element
\& Returns : none
\& Args    : Hash ref with the keys \*(AqName\*(Aq and \*(AqData\*(Aq
.Ve
.SS "characters"
.IX Subsection "characters"
.Vb 5
\& Title   : characters
\& Usage   : $eventgenerator\->characters($str)
\& Function: Send a character events
\& Returns : none
\& Args    : string
.Ve
.SS "_mode"
.IX Subsection "_mode"
.Vb 6
\& Title   : _mode
\& Usage   : $obj\->_mode($newval)
\& Function: 
\& Example : 
\& Returns : value of _mode
\& Args    : newvalue (optional)
.Ve
.SS "within_element"
.IX Subsection "within_element"
.Vb 7
\& Title   : within_element
\& Usage   : if( $eventgenerator\->within_element($element) ) {}
\& Function: Test if we are within a particular element
\&           This is different than \*(Aqin\*(Aq because within can be tested
\&           for a whole block.
\& Returns : boolean
\& Args    : string element name
.Ve
.SS "in_element"
.IX Subsection "in_element"
.Vb 7
\& Title   : in_element
\& Usage   : if( $eventgenerator\->in_element($element) ) {}
\& Function: Test if we are in a particular element
\&           This is different than \*(Aqin\*(Aq because within can be tested
\&           for a whole block.
\& Returns : boolean
\& Args    : string element name
.Ve
.SS "start_document"
.IX Subsection "start_document"
.Vb 5
\& Title   : start_document
\& Usage   : $eventgenerator\->start_document
\& Function: Handles a start document event
\& Returns : none
\& Args    : none
.Ve
.SS "end_document"
.IX Subsection "end_document"
.Vb 5
\& Title   : end_document
\& Usage   : $eventgenerator\->end_document
\& Function: Handles an end document event
\& Returns : Bio::Search::Result::ResultI object
\& Args    : none
.Ve
.SS "result_count"
.IX Subsection "result_count"
.Vb 5
\& Title   : result_count
\& Usage   : my $count = $searchio\->result_count
\& Function: Returns the number of results we have processed
\& Returns : integer
\& Args    : none
.Ve
.SS "program_name"
.IX Subsection "program_name"
.Vb 5
\& Title   : program_name
\& Usage   : $obj\->program_name($newval)
\& Function: Get/Set the program name
\& Returns : value of program_name (a scalar)
\& Args    : on set, new value (a scalar or undef, optional)
.Ve