NAME¶
Bio::Search::Iteration::GenericIteration - A generic implementation of the
Bio::Search::Iteration::IterationI interface.
SYNOPSIS¶
use Bio::Search::Iteration::GenericIteration;
my $it = Bio::Search::GenericIteration->new(
-number => 1,
-converged => 0,
-newhits_unclassified => [@newhits_unclass],
-newhits_below => [@newhits_below_threshold],
-newhits_not_below => [@newhits_not_below_threshold],
-oldhits_below => [@oldhits_below_threshold],
-oldhits_newly_below => [@oldhits_newly_below_threshold],
-oldhits_not_below => [@oldhits_not_below_threshold],
);
# TODO: Describe how to configure a SearchIO stream so that it generates #
GenericIteration objects.
DESCRIPTION¶
This module acts as a container for Bio::Search::Hit::HitI objects, allowing a
Search::Result::ResultI object to partition its hits based on which iteration
the hit occurred in (e.g., a PSI-BLAST round).
Unless you're writing a parser, you won't ever need to create a GenericIteration
or any other IterationI-implementing object. If you use the SearchIO system,
IterationI objects are created automatically from a SearchIO stream which
returns Bio::Search::Result::ResultI objects and you get the IterationI
objects via the ResultI API.
For documentation on what you can do with GenericIteration (and other IterationI
objects), please see the API documentation in
Bio::Search::Iteration::IterationI.
Bio::Search::Iteration::GenericIteration is similar in spirit to the deprecated
Bio::Tools::BPlite::Iteration modules in bioperl releases prior to 1.6, except
that Bio::Search::Iteration::GenericIteration is a pure container, without any
parsing functionality as is in Bio::Tools::BPlite::Iteration.
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 - Steve Chervitz¶
Email sac@bioperl.org
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::Search::Iteration->new(%args);
Function: Builds a new Bio::Search::Iteration object
Returns : Bio::Search::Iteration::GenericIteration object
Args : -number => integer for the number of this iteration (required)
-converged => boolean value whether or not the iteration converged
-newhits_unclassified => array reference to hits that were not found
in a previous iteration for the iteration and have not been
classified with regard to the inclusion threshold
# The following are only used for PSI-BLAST reports:
-newhits_below => array reference to hits were not found in a
previous iteration and are below the inclusion threshold.
-newhits_not_below => array reference to hits that were not found in a
previous iteration below threshold that and are not below
the inclusion threshold threshold.
-oldhits_below => array reference to hits that were found
in a previous iteration below inclusion threshold and are
still below threshold in the current iteration.
-oldhits_newly_below => array reference to hits that were found
in a previous iteration above threshold but are below
threshold in the current iteration.
-oldhits_not_below => array reference to hits that were found in a
previous iteration above threshold that and are still above
the inclusion threshold threshold.
-hit_factory => Bio::Factory::ObjectFactoryI capable of making
Bio::Search::Hit::HitI objects
number¶
See documentation in Bio::Search::Iteration::IterationI.
converged¶
See documentation in Bio::Search::Iteration::IterationI.
hit_factory¶
Title : hit_factory
Usage : $hit->hit_factory($hit_factory)
Function: Get/set the factory used to build HitI objects if necessary.
Returns : Bio::Factory::ObjectFactoryI
Args : Bio::Factory::ObjectFactoryI
next_hit¶
This iterates through all old hits as returned by oldhits followed by all new
hits as returned by newhits.
For more documentation see
Bio::Search::Iteration::IterationI::next_hit().
next_hit_new¶
See documentation in
Bio::Search::Iteration::IterationI::next_hit_new().
next_hit_old¶
See documentation in
Bio::Search::Iteration::IterationI::next_hit_old().
rewind¶
Title : rewind
Usage : $iteration->rewind;
Function: Allow one to reset the Hit iterators to the beginning
Since this is an in-memory implementation
Returns : none
Args : none
num_hits¶
See documentation in
Bio::Search::Iteration::IterationI::num_hits().
num_hits_new¶
See documentation in
Bio::Search::Iteration::IterationI::num_hits_new().
num_hits_old¶
See documentation in
Bio::Search::Iteration::IterationI::num_hits_old().
add_hit¶
See documentation in
Bio::Search::Iteration::IterationI::add_hit().
hits¶
See Documentation in InterfaceI.
newhits¶
Returns a list containing all newhits in this order:
newhits_below_threshold newhits_not_below_threshold newhits_unclassified
See more documentation in InterfaceI.
newhits_below_threshold¶
See documentation in
Bio::Search::Iteration::IterationI::newhits_below_threshold().
newhits_not_below_threshold¶
See documentation in
Bio::Search::Iteration::IterationI::newhits_not_below_threshold().
newhits_unclassified¶
Title : newhits_unclassified
Usage : foreach( $iteration->hits_unclassified ) {...}
Function: Gets all newhits that have not been partitioned into
sets relative to the inclusion threshold.
Returns : Array of Bio::Search::Hit::HitI objects.
Args : none
oldhits¶
Returns a list containing all oldhits in this order:
oldhits_below_threshold oldhits_newly_below_threshold
oldhits_not_below_threshold
See more documentation in InterfaceI.
oldhits_below_threshold¶
See documentation in
Bio::Search::Iteration::IterationI::oldhits_below_threshold().
oldhits_newly_below_threshold¶
See documentation in
Bio::Search::Iteration::IterationI::oldhits_newly_below_threshold().
oldhits_not_below_threshold¶
See documentation in
Bio::Search::Iteration::IterationI::oldhits_not_below_threshold().
hits_below_threshold¶
See documentation in
Bio::Search::Iteration::IterationI::hits_below_threshold().
get_hit¶
See documentation in
Bio::Search::Iteration::IterationI::get_hit().
To free up the memory used by the
get_hit() functionality, call
free_hit_lookup().
This functionality might be useful at the Result level, too.
BlastResult::get_hit() would return a list of HitI objects for hits
that occur in multiple iterations.
free_hit_lookup¶
Purpose : Frees up the memory used by the get_hit() functionality.
For the memory-conscious.