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().