#-----------------------------------------------------------------
#
# BioPerl module Bio::Search::Result::ResultI
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Steve Chervitz <sac@bioperl.org>
#
# Originally created by Aaron Mackey <amackey@virginia.edu>
#
# You may distribute this module under the same terms as perl itself
#-----------------------------------------------------------------
# POD documentation - main docs before the code
=head1 NAME
Bio::Search::Result::ResultI - Abstract interface to Search Result objects
=head1 SYNOPSIS
# Bio::Search::Result::ResultI objects cannot be instantiated since this
# module defines a pure interface.
# Given an object that implements the Bio::Search::Result::ResultI interface,
# you can do the following things with it:
use Bio::SearchIO;
my $io = Bio::SearchIO->new(-format => 'blast',
-file => 't/data/HUMBETGLOA.tblastx');
my $result = $io->next_result;
while( $hit = $result->next_hit()) { # enter code here for hit processing
}
my $id = $result->query_name();
my $desc = $result->query_description();
my $dbname = $result->database_name();
my $size = $result->database_letters();
my $num_entries = $result->database_entries();
my $gap_ext = $result->get_parameter('gapext');
my @params = $result->available_parameters;
my $kappa = $result->get_statistic('kappa');
my @statnames = $result->available_statistics;
=head1 DESCRIPTION
Bio::Search::Result::ResultI objects are data structures containing
the results from the execution of a search algorithm. As such, it may
contain various algorithm specific information as well as details of
the execution, but will contain a few fundamental elements, including
the ability to return Bio::Search::Hit::HitI objects.
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this
and other Bioperl modules. Send your comments and suggestions preferably
to one of the Bioperl mailing lists.
Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<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.
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via the
web:
https://redmine.open-bio.org/projects/bioperl/
=head1 AUTHOR
Aaron Mackey E<lt>amackey@virginia.eduE<gt> (original author)
Steve Chervitz E<lt>sac@bioperl.orgE<gt>
See L<the FEEDBACK section | FEEDBACK> for where to send bug reports and comments.
=head1 COPYRIGHT
Copyright (c) 1999-2001 Aaron Mackey, Steve Chervitz. All Rights Reserved.
=head1 DISCLAIMER
This software is provided "as is" without warranty of any kind.
=head1 APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
=cut
#'
# Let the code begin...
package Bio::Search::Result::ResultI;
use strict;
use base qw(Bio::AnalysisResultI);
=head2 next_hit
Title : next_hit
Usage : while( $hit = $result->next_hit()) { ... }
Function: Returns the next available Hit object, representing potential
matches between the query and various entities from the database.
Returns : a Bio::Search::Hit::HitI object or undef if there are no more.
Args : none
=cut
sub next_hit {
my ($self,@args) = @_;
$self->throw_not_implemented;
}
=head2 sort_hits
Title : sort_hits
Usage : $result->sort_hits(\&sort_function)
Function : Sorts the available hit objects by a user-supplied function. Defaults to sort
by descending score.
Returns : n/a
Args : A coderef for the sort function. See the documentation on the Perl sort()
function for guidelines on writing sort functions.
Note : To access the special variables $a and $b used by the Perl sort() function
the user function must access Bio::Search::Result::ResultI namespace.
For example, use :
$result->sort_hits( sub{$Bio::Search::Result::ResultI::a->length <=>
$Bio::Search::Result::ResultI::b->length});
NOT $result->sort_hits($a->length <=>$b->length);
=cut
sub sort_hits {
my ($self, $coderef) = @_;
my @sorted_hits;
if ($coderef) {
$self->throw('sort_hits requires a sort function passed as a subroutine reference')
unless (ref($coderef) eq 'CODE');
}
else {
$coderef = \&_default_sort_hits;
# throw a warning?
}
my @hits = $self->hits();
eval {@sorted_hits = sort $coderef @hits };
if ($@) {
$self->throw("Unable to sort hits: $@");
}
else {
$self->{'_hits'} = \@sorted_hits;
$self->{'_no_iterations'} = 1; # to bypass iteration checking in hits() method
1;
}
}
=head2 _default sort_hits
Title : _default_sort_hits
Usage : Do not call directly.
Function: Sort hits in descending order by score
Args : None
Returns: 1 on success
Note : Used by $result->sort_hits()
=cut
sub _default_sort_hits {
$Bio::Search::Result::ResultI::b->score <=>
$Bio::Search::Result::ResultI::a->score;
}
=head2 query_name
Title : query_name
Usage : $id = $result->query_name();
Function: Get the string identifier of the query used by the
algorithm that performed the search.
Returns : a string.
Args : none
=cut
sub query_name {
my ($self,@args) = @_;
$self->throw_not_implemented;
}
=head2 query_accession
Title : query_accession
Usage : $id = $result->query_accession();
Function: Get the accession (if available) for the query sequence
Returns : a string
Args : none
=cut
sub query_accession {
my ($self,@args) = @_;
$self->throw_not_implemented;
}
=head2 query_length
Title : query_length
Usage : $id = $result->query_length();
Function: Get the length of the query sequence
used in the search.
Returns : a number
Args : none
=cut
sub query_length {
my ($self,@args) = @_;
$self->throw_not_implemented;
}
=head2 query_description
Title : query_description
Usage : $id = $result->query_description();
Function: Get the description of the query sequence
used in the search.
Returns : a string
Args : none
=cut
sub query_description {
my ($self,@args) = @_;
$self->throw_not_implemented;
}
=head2 database_name
Title : database_name
Usage : $name = $result->database_name()
Function: Used to obtain the name of the database that the query was searched
against by the algorithm.
Returns : a scalar string
Args : none
=cut
sub database_name {
my ($self,@args) = @_;
$self->throw_not_implemented;
}
=head2 database_letters
Title : database_letters
Usage : $size = $result->database_letters()
Function: Used to obtain the size of database that was searched against.
Returns : a scalar integer (units specific to algorithm, but probably the
total number of residues in the database, if available) or undef if
the information was not available to the Processor object.
Args : none
=cut
sub database_letters {
my ($self,@args) = @_;
$self->throw_not_implemented();
}
=head2 database_entries
Title : database_entries
Usage : $num_entries = $result->database_entries()
Function: Used to obtain the number of entries contained in the database.
Returns : a scalar integer representing the number of entities in the database
or undef if the information was not available.
Args : none
=cut
sub database_entries {
my ($self,@args) = @_;
$self->throw_not_implemented();
}
=head2 get_parameter
Title : get_parameter
Usage : my $gap_ext = $result->get_parameter('gapext')
Function: Returns the value for a specific parameter used
when running this result
Returns : string
Args : name of parameter (string)
=cut
sub get_parameter{
my ($self,@args) = @_;
$self->throw_not_implemented();
}
=head2 available_parameters
Title : available_parameters
Usage : my @params = $result->available_parameters
Function: Returns the names of the available parameters
Returns : Return list of available parameters used for this result
Args : none
=cut
sub available_parameters{
my ($self) = @_;
$self->throw_not_implemented();
}
=head2 get_statistic
Title : get_statistic
Usage : my $gap_ext = $result->get_statistic('kappa')
Function: Returns the value for a specific statistic available
from this result
Returns : string
Args : name of statistic (string)
=cut
sub get_statistic{
my ($self,@args) = @_;
$self->throw_not_implemented();
}
=head2 available_statistics
Title : available_statistics
Usage : my @statnames = $result->available_statistics
Function: Returns the names of the available statistics
Returns : Return list of available statistics used for this result
Args : none
=cut
sub available_statistics{
my ($self) = @_;
$self->throw_not_implemented();
}
=head2 algorithm
Title : algorithm
Usage : my $r_type = $result->algorithm
Function: Obtain the name of the algorithm used to obtain the Result
Returns : string (e.g., BLASTP)
Args : [optional] scalar string to set value
=cut
sub algorithm{
my ($self) = @_;
$self->throw_not_implemented();
}
=head2 algorithm_version
Title : algorithm_version
Usage : my $r_version = $result->algorithm_version
Function: Obtain the version of the algorithm used to obtain the Result
Returns : string (e.g., 2.1.2)
Args : [optional] scalar string to set algorithm version value
=cut
sub algorithm_version{
my ($self) = @_;
$self->throw_not_implemented();
}
=head2 algorithm_reference
Title : algorithm_reference
Usage : $obj->algorithm_reference($newval)
Function:
Returns : value of the literature reference for the algorithm
Args : newvalue (optional)
Comments: The default implementation in ResultI returns an empty string
rather than throwing a NotImplemented exception, since
the ref may not always be available and is not critical.
=cut
sub algorithm_reference{
my ($self) = @_;
return '';
}
=head2 rid
Title : rid
Usage : $obj->rid($newval)
Function:
Returns : value of the BLAST Request ID (eg. RID: ZABJ4EA7014)
Args : newvalue (optional)
Comments: The default implementation in ResultI returns an empty string
rather than throwing a NotImplemented exception, since
the RID may not always be available and is not critical.
See: (1) http://www.ncbi.nlm.nih.gov/Class/MLACourse/Modules/BLAST/rid.html
(2) http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/new/node63.html
=cut
sub rid{
my ($self) = @_;
return '';
}
=head2 num_hits
Title : num_hits
Usage : my $hitcount= $result->num_hits
Function: returns the number of hits for this query result
Returns : integer
Args : none
=cut
sub num_hits{
my ($self,@args) = @_;
$self->throw_not_implemented();
}
=head2 hits
Title : hits
Usage : my @hits = $result->hits
Function: Returns the HitI objects contained within this Result
Returns : Array of Bio::Search::Hit::HitI objects
Args : none
See Also: L<Bio::Search::Hit::HitI>
=cut
sub hits{
my ($self,@args) = @_;
$self->throw_not_implemented();
}
=head2 no_hits_found
Usage : $nohits = $blast->no_hits_found();
Purpose : Get boolean indicator indicating whether or not any hits
were present in the report.
This is NOT the same as determining the number of hits via
the hits() method, which will return zero hits if there were no
hits in the report or if all hits were filtered out during the parse.
Thus, this method can be used to distinguish these possibilities
for hitless reports generated when filtering.
Returns : Boolean
Argument : none
=cut
#-----------
sub no_hits_found { shift->throw_not_implemented }
=head2 set_no_hits_found
Usage : $blast->set_no_hits_found();
Purpose : Set boolean indicator indicating whether or not any hits
were present in the report.
Returns : n/a
Argument : none
=cut
sub set_no_hits_found { shift->throw_not_implemented }
1;