NAME

Bio::SearchIO::sim4 - parser for Sim4 alignments

SYNOPSIS

  # do not use this module directly, it is a driver for SearchIO
  use Bio::SearchIO;
  my $searchio = Bio::SearchIO->new(-file => 'results.sim4',
                                   -format => 'sim4');

  while ( my $result = $searchio->next_result ) {
      while ( my $hit = $result->next_hit ) {
          while ( my $hsp = $hit->next_hsp ) {
              # ...
          }
      }
  }

DESCRIPTION

This is a driver for the SearchIO system for parsing Sim4. http://globin.cse.psu.edu/html/docs/sim4.html

Cannot parse LAV or 'exon file' formats (A=2 or A=5)

FEEDBACK

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.

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

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.

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:

  https://github.com/bioperl/bioperl-live/issues

AUTHOR - Jason Stajich

Email jason-at-bioperl-dot-org

CONTRIBUTORS

Luc Gauthier (lgauthie@hotmail.com)

APPENDIX

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

new

 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    :

next_result

 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

start_element

 Title   : start_element
 Usage   : $eventgenerator->start_element
 Function: Handles a start element event
 Returns : none
 Args    : hashref with at least 2 keys 'Data' and 'Name'

end_element

 Title   : start_element
 Usage   : $eventgenerator->end_element
 Function: Handles an end element event
 Returns : none
 Args    : hashref with at least 2 keys 'Data' and 'Name'

element

 Title   : element
 Usage   : $eventhandler->element({'Name' => $name, 'Data' => $str});
 Function: Convience method that calls start_element, characters, end_element
 Returns : none
 Args    : Hash ref with the keys 'Name' and 'Data'

characters

 Title   : characters
 Usage   : $eventgenerator->characters($str)
 Function: Send a character events
 Returns : none
 Args    : string

within_element

 Title   : within_element
 Usage   : if( $eventgenerator->within_element($element) ) {}
 Function: Test if we are within a particular element
           This is different than 'in' because within can be tested
           for a whole block.
 Returns : boolean
 Args    : string element name

in_element

 Title   : in_element
 Usage   : if( $eventgenerator->in_element($element) ) {}
 Function: Test if we are in a particular element
           This is different than 'in' because within can be tested
           for a whole block.
 Returns : boolean
 Args    : string element name

start_document

 Title   : start_document
 Usage   : $eventgenerator->start_document
 Function: Handle a start document event
 Returns : none
 Args    : none

end_document

 Title   : end_document
 Usage   : $eventgenerator->end_document
 Function: Handles an end document event
 Returns : Bio::Search::Result::ResultI object
 Args    : none

_will_handle

 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.

Optimizations:

  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.

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.

To test against the unoptimized version, remove the parentheses from around the third term in the ternary " ? : " operator and add two calls to $self->_eventHandler().