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.\" ========================================================================
.\"
.IX Title "Bio::SearchIO::sim4 3pm"
.TH Bio::SearchIO::sim4 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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.SH "NAME"
Bio::SearchIO::sim4 \- parser for Sim4 alignments
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 4
\&  # do not use this module directly, it is a driver for SearchIO
\&  use Bio::SearchIO;
\&  my $searchio = Bio::SearchIO\->new(\-file => \*(Aqresults.sim4\*(Aq,
\&                                   \-format => \*(Aqsim4\*(Aq);
\&
\&  while ( my $result = $searchio\->next_result ) {
\&      while ( my $hit = $result\->next_hit ) {
\&          while ( my $hsp = $hit\->next_hsp ) {
\&              # ...
\&          }
\&      }
\&  }
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
This is a driver for the SearchIO system for parsing Sim4.
http://globin.cse.psu.edu/html/docs/sim4.html
.PP
Cannot parse \s-1LAV\s0 or 'exon file' formats (A=2 or A=5)
.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 "CONTRIBUTORS"
.IX Header "CONTRIBUTORS"
Luc Gauthier (lgauthie@hotmail.com)
.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::sim4\->new();
\& Function: Builds a new Bio::SearchIO::sim4 object
\& Returns : an instance of Bio::SearchIO::sim4
\& Args    :
.Ve
.SS "next_result"
.IX Subsection "next_result"
.Vb 5
\& Title   : next_result
\& Usage   : my $result = $searchio\->next_result;
\& Function: Returns the next Result from a search
\& Returns : Bio::Search::Result::ResultI object
\& 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   : start_element
\& Usage   : $eventgenerator\->end_element
\& Function: Handles an end element event
\& Returns : none
\& 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 "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: Handle 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 "_will_handle"
.IX Subsection "_will_handle"
.Vb 8
\& Title   : _will_handle
\& Usage   : Private method. For internal use only.
\&              if( $self\->_will_handle($type) ) { ... }
\& Function: Provides an optimized way to check whether or not an element of a 
\&           given type is to be handled.
\& Returns : Reference to EventHandler object if the element type is to be handled.
\&           undef if the element type is not to be handled.
\& Args    : string containing type of element.
.Ve
.PP
Optimizations:
.PP
.Vb 3
\&  1. Using the cached pointer to the EventHandler to minimize repeated lookups.
\&  2. Caching the will_handle status for each type that is encountered
\&     so that it only need be checked by calling handler\->will_handle($type) once.
.Ve
.PP
This does not lead to a major savings by itself (only 5\-10%).
In combination with other optimizations, or for large parse jobs, the
savings good be significant.
.PP
To test against the unoptimized version, remove the parentheses from
around the third term in the ternary \*(L" ? : \*(R" operator and add two
calls to \f(CW$self\fR\->\fB_eventHandler()\fR.