Raw content of Bio::Search::Hit::HitI
<![CDATA[#-----------------------------------------------------------------
# $Id: HitI.pm,v 1.17 2002/11/13 11:16:37 sac Exp $
#
# BioPerl module Bio::Search::Hit::HitI
#
# 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::Hit::HitI - Interface for a hit in a similarity search result
=head1 SYNOPSIS
Bio::Search::Hit::HitI objects should not be instantiated since this
module defines a pure interface.
Given an object that implements the Bio::Search::Hit::HitI interface,
you can do the following things with it:
$hit_name = $hit->name();
$desc = $hit->description();
$len = $hit->length
$alg = $hit->algorithm();
$score = $hit->raw_score();
$significance = $hit->significance();
$rank = $hit->rank(); # the Nth hit for a specific query
while( $hsp = $obj->next_hsp()) { ... } # process in iterator fashion
for my $hsp ( $obj->hsps()()) { ... } # process in list fashion
=head1 DESCRIPTION
Bio::Search::Hit::* objects are data structures that contain information
about specific hits obtained during a library search. Some information will
be algorithm-specific, but others will be generally defined.
=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://bio.perl.org/MailList.html - About the mailing lists
=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 email
or the web:
bioperl-bugs@bio.perl.org
http://bugzilla.bioperl.org/
=head1 AUTHOR - Aaron Mackey, Steve Chervitz
Email amackey@virginia.edu (original author)
Email sac@bioperl.org
=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::Hit::HitI;
use Bio::Root::RootI;
use vars qw(@ISA);
use strict;
@ISA = qw( Bio::Root::RootI );
=head2 name
Title : name
Usage : $hit_name = $hit->name();
Function: returns the name of the Hit sequence
Returns : a scalar string
Args : none
=cut
sub name {
my ($self,@args) = @_;
$self->throw_not_implemented;
}
=head2 description
Title : description
Usage : $desc = $hit->description();
Function: Retrieve the description for the hit
Returns : a scalar string
Args : none
=cut
sub description {
my ($self,@args) = @_;
$self->throw_not_implemented;
}
=head2 accession
Title : accession
Usage : $acc = $hit->accession();
Function: Retrieve the accession (if available) for the hit
Returns : a scalar string (empty string if not set)
Args : none
=cut
sub accession {
my ($self,@args) = @_;
$self->throw_not_implemented;
}
=head2 locus
Title : locus
Usage : $acc = $hit->locus();
Function: Retrieve the locus(if available) for the hit
Returns : a scalar string (empty string if not set)
Args : none
=cut
sub locus {
my ($self,@args) = @_;
$self->throw_not_implemented;
}
=head2 length
Title : length
Usage : my $len = $hit->length
Function: Returns the length of the hit
Returns : integer
Args : none
=cut
sub length {
my ($self,@args) = @_;
$self->throw_not_implemented;
}
=head2 algorithm
Title : algorithm
Usage : $alg = $hit->algorithm();
Function: Gets the algorithm specification that was used to obtain the hit
For BLAST, the algorithm denotes what type of sequence was aligned
against what (BLASTN: dna-dna, BLASTP prt-prt, BLASTX translated
dna-prt, TBLASTN prt-translated dna, TBLASTX translated
dna-translated dna).
Returns : a scalar string
Args : none
=cut
sub algorithm {
my ($self,@args) = @_;
$self->throw_not_implemented;
}
=head2 raw_score
Title : raw_score
Usage : $score = $hit->raw_score();
Function: Gets the "raw score" generated by the algorithm. What
this score is exactly will vary from algorithm to algorithm,
returning undef if unavailable.
Returns : a scalar value
Args : none
=cut
sub raw_score {
$_[0]->throw_not_implemented;
}
=head2 significance
Title : significance
Usage : $significance = $hit->significance();
Function: Used to obtain the E or P value of a hit, i.e. the probability that
this particular hit was obtained purely by random chance. If
information is not available (nor calculatable from other
information sources), return undef.
Returns : a scalar value or undef if unavailable
Args : none
=cut
sub significance {
$_[0]->throw_not_implemented;
}
=head2 bits
Usage : $hit_object->bits();
Purpose : Gets the bit score of the best HSP for the current hit.
Example : $bits = $hit_object->bits();
Returns : Integer or double for FASTA reports
Argument : n/a
Comments : For BLAST1, the non-bit score is listed in the summary line.
See Also : L<score()|score>
=cut
#---------
sub bits {
#---------
$_[0]->throw_not_implemented();
}
=head2 next_hsp
Title : next_hsp
Usage : while( $hsp = $obj->next_hsp()) { ... }
Function : Returns the next available High Scoring Pair
Example :
Returns : Bio::Search::HSP::HSPI object or null if finished
Args : none
=cut
sub next_hsp {
my ($self,@args) = @_;
$self->throw_not_implemented;
}
=head2 hsps
Usage : $hit_object->hsps();
Purpose : Get a list containing all HSP objects.
: Get the numbers of HSPs for the current hit.
Example : @hsps = $hit_object->hsps();
: $num = $hit_object->hsps(); # alternatively, use num_hsps()
Returns : Array context : list of Bio::Search::HSP::BlastHSP.pm objects.
: Scalar context: integer (number of HSPs).
: (Equivalent to num_hsps()).
Argument : n/a. Relies on wantarray
Throws : Exception if the HSPs have not been collected.
See Also : L<hsp()|hsp>, L<num_hsps()|num_hsps>
=cut
#---------
sub hsps {
#---------
my $self = shift;
$self->throw_not_implemented();
}
=head2 num_hsps
Usage : $hit_object->num_hsps();
Purpose : Get the number of HSPs for the present Blast hit.
Example : $nhsps = $hit_object->num_hsps();
Returns : Integer
Argument : n/a
Throws : Exception if the HSPs have not been collected.
See Also : L<hsps()|hsps>
=cut
#-------------
sub num_hsps {
#-------------
shift->throw_not_implemented();
}
=head2 seq_inds
Usage : $hit->seq_inds( seq_type, class, collapse );
Purpose : Get a list of residue positions (indices) across all HSPs
: for identical or conserved residues in the query or sbjct sequence.
Example : @s_ind = $hit->seq_inds('query', 'identical');
: @h_ind = $hit->seq_inds('hit', 'conserved');
: @h_ind = $hit->seq_inds('hit', 'conserved', 1);
Returns : Array of integers
: May include ranges if collapse is non-zero.
Argument : [0] seq_type = 'query' or 'hit' or 'sbjct' (default = 'query')
: ('sbjct' is synonymous with 'hit')
: [1] class = 'identical' or 'conserved' (default = 'identical')
: (can be shortened to 'id' or 'cons')
: (actually, anything not 'id' will evaluate to 'conserved').
: [2] collapse = boolean, if non-zero, consecutive positions are merged
: using a range notation, e.g., "1 2 3 4 5 7 9 10 11"
: collapses to "1-5 7 9-11". This is useful for
: consolidating long lists. Default = no collapse.
Throws : n/a.
See Also : L<Bio::Search::HSP::BlastHSP::seq_inds()|Bio::Search::HSP::BlastHSP>
=cut
#-------------
sub seq_inds {
#-------------
my ($self, $seqType, $class, $collapse) = @_;
$seqType ||= 'query';
$class ||= 'identical';
$collapse ||= 0;
$seqType = 'sbjct' if $seqType eq 'hit';
my (@inds, $hsp);
foreach $hsp ($self->hsps) {
# This will merge data for all HSPs together.
push @inds, $hsp->seq_inds($seqType, $class);
}
# Need to remove duplicates and sort the merged positions.
if(@inds) {
my %tmp = map { $_, 1 } @inds;
@inds = sort {$a <=> $b} keys %tmp;
}
$collapse ? &Bio::Search::BlastUtils::collapse_nums(@inds) : @inds;
}
=head2 rewind
Title : rewind
Usage : $hit->rewind;
Function: Allow one to reset the HSP iteration to the beginning
if possible
Returns : none
Args : none
=cut
sub rewind{
my ($self) = @_;
$self->throw_not_implemented();
}
=head2 iteration
Usage : $hit->iteration( );
Purpose : Gets the iteration number in which the Hit was found.
Example : $iteration_num = $sbjct->iteration();
Returns : Integer greater than or equal to 1
Non-PSI-BLAST reports will report iteration as 1, but this number
is only meaningful for PSI-BLAST reports.
Argument : none
Throws : none
See Also : L<found_again()|found_again>
=cut
#----------------
sub iteration { shift->throw_not_implemented }
#----------------
=head2 found_again
Usage : $hit->found_again;
Purpose : Gets a boolean indicator whether or not the hit has
been found in a previous iteration.
This is only applicable to PSI-BLAST reports.
This method indicates if the hit was reported in the
"Sequences used in model and found again" section of the
PSI-BLAST report or if it was reported in the
"Sequences not found previously or not previously below threshold"
section of the PSI-BLAST report. Only for hits in iteration > 1.
Example : if( $sbjct->found_again()) { ... };
Returns : Boolean (1 or 0) for PSI-BLAST report iterations greater than 1.
Returns undef for PSI-BLAST report iteration 1 and non PSI_BLAST
reports.
Argument : none
Throws : none
See Also : L<found_again()|found_again>
=cut
#----------------
sub found_again { shift->throw_not_implemented }
#----------------
=head2 overlap
Usage : $hit_object->overlap( [integer] );
Purpose : Gets/Sets the allowable amount overlap between different HSP sequences.
Example : $hit_object->overlap(5);
: $overlap = $hit_object->overlap;
Returns : Integer.
Argument : integer.
Throws : n/a
Status : Experimental
Comments : Any two HSPs whose sequences overlap by less than or equal
: to the overlap() number of resides will be considered separate HSPs
: and will not get tiled by Bio::Search::BlastUtils::_adjust_contigs().
See Also : L<Bio::Search::BlastUtils::_adjust_contigs()|Bio::Search::BlastUtils>, L<BUGS | BUGS>
=cut
#-------------
sub overlap { shift->throw_not_implemented }
=head2 n
Usage : $hit_object->n();
Purpose : Gets the N number for the current Blast hit.
: This is the number of HSPs in the set which was ascribed
: the lowest P-value (listed on the description line).
: This number is not the same as the total number of HSPs.
: To get the total number of HSPs, use num_hsps().
Example : $n = $hit_object->n();
Returns : Integer
Argument : n/a
Throws : Exception if HSPs have not been set (BLAST2 reports).
Comments : Note that the N parameter is not reported in gapped BLAST2.
: Calling n() on such reports will result in a call to num_hsps().
: The num_hsps() method will count the actual number of
: HSPs in the alignment listing, which may exceed N in
: some cases.
See Also : L<num_hsps()|num_hsps>
=cut
#-----
sub n { shift->throw_not_implemented }
=head2 p
Usage : $hit_object->p( [format] );
Purpose : Get the P-value for the best HSP of the given BLAST hit.
: (Note that P-values are not provided with NCBI Blast2 reports).
Example : $p = $sbjct->p;
: $p = $sbjct->p('exp'); # get exponent only.
: ($num, $exp) = $sbjct->p('parts'); # split sci notation into parts
Returns : Float or scientific notation number (the raw P-value, DEFAULT).
: Integer if format == 'exp' (the magnitude of the base 10 exponent).
: 2-element list (float, int) if format == 'parts' and P-value
: is in scientific notation (See Comments).
Argument : format: string of 'raw' | 'exp' | 'parts'
: 'raw' returns value given in report. Default. (1.2e-34)
: 'exp' returns exponent value only (34)
: 'parts' returns the decimal and exponent as a
: 2-element list (1.2, -34) (See Comments).
Throws : Warns if no P-value is defined. Uses expect instead.
Comments : Using the 'parts' argument is not recommended since it will not
: work as expected if the P-value is not in scientific notation.
: That is, floats are not converted into sci notation before
: splitting into parts.
See Also : L<expect()|expect>, L<signif()|signif>, L<Bio::Search::BlastUtils::get_exponent()|Bio::Search::BlastUtils>
=cut
#--------
sub p { shift->throw_not_implemented() }
=head2 hsp
Usage : $hit_object->hsp( [string] );
Purpose : Get a single HSPI object for the present HitI object.
Example : $hspObj = $hit_object->hsp; # same as 'best'
: $hspObj = $hit_object->hsp('best');
: $hspObj = $hit_object->hsp('worst');
Returns : Object reference for a Bio::Search::HSP::BlastHSP.pm object.
Argument : String (or no argument).
: No argument (default) = highest scoring HSP (same as 'best').
: 'best' or 'first' = highest scoring HSP.
: 'worst' or 'last' = lowest scoring HSP.
Throws : Exception if the HSPs have not been collected.
: Exception if an unrecognized argument is used.
See Also : L<hsps()|hsps>, L<num_hsps>()
=cut
#----------
sub hsp { shift->throw_not_implemented }
=head2 logical_length
Usage : $hit_object->logical_length( [seq_type] );
: (mostly intended for internal use).
Purpose : Get the logical length of the hit sequence.
: If the Blast is a TBLASTN or TBLASTX, the returned length
: is the length of the would-be amino acid sequence (length/3).
: For all other BLAST flavors, this function is the same as length().
Example : $len = $hit_object->logical_length();
Returns : Integer
Argument : seq_type = 'query' or 'hit' or 'sbjct' (default = 'query')
('sbjct' is synonymous with 'hit')
Throws : n/a
Comments : This is important for functions like frac_aligned_query()
: which need to operate in amino acid coordinate space when dealing
: with [T]BLAST[NX] type reports.
See Also : L<length()|length>, L<frac_aligned_query()|frac_aligned_query>, L<frac_aligned_hit()|frac_aligned_hit>
=cut
#--------------------
sub logical_length { shift->throw_not_implemented() }
=head2 rank
Title : rank
Usage : $obj->rank($newval)
Function: Get/Set the rank of this Hit in the Query search list
i.e. this is the Nth hit for a specific query
Returns : value of rank
Args : newvalue (optional)
=cut
sub rank{
my ($self,$value) = @_;
$self->throw_not_implemented();
}
=head2 each_accession_number
Title : each_accession_number
Usage : $obj->each_accession_number
Function: Get each accession number listed in the description of the hit.
If there are no alternatives, then only the primary accession will
be given
Returns : list of all accession numbers in the description
Args : none
=cut
sub each_accession_number{
my ($self,$value) = @_;
$self->throw_not_implemented();
}
=head2 tiled_hsps
Usage : $hit_object->tiled_hsps( [integer] );
Purpose : Gets/Sets an indicator for whether or not the HSPs in this Hit
: have been tiled.
: Methods that rely on HSPs being tiled should check this
: and then call SearchUtils::tile_hsps() if not.
Example : $hit_object->tiled_hsps(1);
: if( $hit_object->tiled_hsps ) { # do something }
Returns : Boolean (1 or 0)
Argument : integer (optional)
Throws : n/a
=cut
sub tiled_hsps { shift->throw_not_implemented }
=head2 strand
Usage : $sbjct->strand( [seq_type] );
Purpose : Gets the strand(s) for the query, sbjct, or both sequences
: in the best HSP of the BlastHit object after HSP tiling.
: Only valid for BLASTN, TBLASTX, BLASTX-query, TBLASTN-hit.
Example : $qstrand = $sbjct->strand('query');
: $sstrand = $sbjct->strand('hit');
: ($qstrand, $sstrand) = $sbjct->strand();
Returns : scalar context: integer '1', '-1', or '0'
: array context without args: list of two strings (queryStrand, sbjctStrand)
: Array context can be "induced" by providing an argument of 'list' or 'array'.
Argument : In scalar context: seq_type = 'query' or 'hit' or 'sbjct' (default = 'query')
('sbjct' is synonymous with 'hit')
Throws : n/a
Comments : This method requires that all HSPs be tiled. If they have not
: already been tiled, they will be tiled first automatically..
: If you don't want the tiled data, iterate through each HSP
: calling strand() on each (use hsps() to get all HSPs).
:
: Formerly (prior to 10/21/02), this method would return the
: string "-1/1" for hits with HSPs on both strands.
: However, now that strand and frame is properly being accounted
: for during HSP tiling, it makes more sense for strand()
: to return the strand data for the best HSP after tiling.
:
: If you really want to know about hits on opposite strands,
: you should be iterating through the HSPs using methods on the
: HSP objects.
:
: A possible use case where knowing whether a hit has HSPs
: on both strands would be when filtering via SearchIO for hits with
: this property. However, in this case it would be better to have a
: dedicated method such as $hit->hsps_on_both_strands(). Similarly
: for frame. This could be provided if there is interest.
See Also : B<Bio::Search::HSP::BlastHSP::strand>()
=cut
#---------'
sub strand { shift->throw_not_implemented }
=head2 frame
Usage : $hit_object->frame();
Purpose : Gets the reading frame for the best HSP after HSP tiling.
: This is only valid for BLASTX and TBLASTN/X type reports.
Example : $frame = $hit_object->frame();
Returns : Integer (-2 .. +2)
Argument : n/a
Throws : Exception if HSPs have not been set.
Comments : This method requires that all HSPs be tiled. If they have not
: already been tiled, they will be tiled first automatically..
: If you don't want the tiled data, iterate through each HSP
: calling frame() on each (use hsps() to get all HSPs).
See Also : L<hsps()|hsps>
=cut
#---------'
sub frame { shift->throw_not_implemented }
=head2 matches
Usage : $hit_object->matches( [class] );
Purpose : Get the total number of identical or conserved matches
: (or both) across all HSPs.
: (Note: 'conservative' matches are indicated as 'positives'
: in BLAST reports.)
Example : ($id,$cons) = $hit_object->matches(); # no argument
: $id = $hit_object->matches('id');
: $cons = $hit_object->matches('cons');
Returns : Integer or a 2-element array of integers
Argument : class = 'id' | 'cons' OR none.
: If no argument is provided, both identical and conservative
: numbers are returned in a two element list.
: (Other terms can be used to refer to the conservative
: matches, e.g., 'positive'. All that is checked is whether or
: not the supplied string starts with 'id'. If not, the
: conservative matches are returned.)
Throws : Exception if the requested data cannot be obtained.
Comments : This method requires that all HSPs be tiled. If there is more than one
: HSP and they have not already been tiled, they will be tiled first automatically..
:
: If you need data for each HSP, use hsps() and then interate
: through the HSP objects.
: Does not rely on wantarray to return a list. Only checks for
: the presence of an argument (no arg = return list).
See Also : L<Bio::Search::HSP::GenericHSP::matches()|Bio::Search::HSP::GenericHSP>, L<hsps()|hsps>
=cut
sub matches { shift->throw_not_implemented }
1;
]]>