Provided by: libbio-perl-perl_1.7.8-1_all 
NAME
Bio::Search::Hit::ModelHit - A model-based implementation of the Bio::Search::Hit::HitI
interface
SYNOPSIS
use Bio::Search::Hit::ModelHit;
my $hit = Bio::Search::Hit::ModelHit->new(-algorithm => 'rnamotif');
# typically one gets HitI objects from a SearchIO stream via a ResultI
use Bio::SearchIO;
my $parser = Bio::SearchIO->new(-format => 'infernal', -file => 'trap.inf');
my $result = $parser->next_result;
my $hit = $result->next_hit;
DESCRIPTION
This object handles the hit data from a database search using models or descriptors
instead of sequences, such as Infernal, HMMER, RNAMotif, etc.
Unless you're writing a parser, you won't ever need to create a ModelHit or any other
HitI-implementing object. If you use the SearchIO system, HitI objects are created
automatically from a SearchIO stream which returns Bio::Search::Hit::HitI objects.
Note that several HitI-based methods have been overridden from ModelHit due to their
unreliability when dealing with queries that aren't sequence-based. It may be possible to
reimplement these at a later point, but for the time being they will throw warnings and
return w/o results.
For documentation on what you can do with ModelHit (and other HitI objects), please see
the API documentation in Bio::Search::Hit::HitI.
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 - Chris Fields
Email cjfields at bioperl dot org
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are
usually preceded with a _
HitI methods implemented in parent class Bio::Search::Hit::ModelHit
new
Title : new
Usage : my $obj = Bio::Search::Hit::ModelHit->new();
Function: Builds a new Bio::Search::Hit::ModelHit object
Returns : Bio::Search::Hit::ModelHit
Args : -name => Name of Hit (required)
-description => Description (optional)
-accession => Accession number (optional)
-ncbi_gi => NCBI GI UID (optional)
-length => Length of the Hit (optional)
-score => Raw Score for the Hit (optional)
-bits => Bit Score for the Hit (optional)
-significance => Significance value for the Hit (optional)
-algorithm => Algorithm used (BLASTP, FASTX, etc...)
-hsps => Array ref of HSPs for this Hit.
-found_again => boolean, true if hit appears in a
"previously found" section of a PSI-Blast report.
-hsp_factory => Bio::Factory::ObjectFactoryI able to create HSPI
objects.
add_hsp
Title : add_hsp
Usage : $hit->add_hsp($hsp)
Function: Add a HSP to the collection of HSPs for a Hit
Returns : number of HSPs in the Hit
Args : Bio::Search::HSP::HSPI object, OR hash ref containing data suitable
for creating a HSPI object (&hsp_factory must be set to get it back)
hsp_factory
Title : hsp_factory
Usage : $hit->hsp_factory($hsp_factory)
Function: Get/set the factory used to build HSPI objects if necessary.
Returns : Bio::Factory::ObjectFactoryI
Args : Bio::Factory::ObjectFactoryI
Bio::Search::Hit::HitI methods
Implementation of Bio::Search::Hit::HitI methods
name
Title : name
Usage : $hit_name = $hit->name();
Function: returns the name of the Hit sequence
Returns : a scalar string
Args : [optional] scalar string to set the name
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
description
Title : description
Usage : $desc = $hit->description();
Function: Retrieve the description for the hit
Returns : a scalar string
Args : [optional] scalar string to set the description
length
Title : length
Usage : my $len = $hit->length
Function: Returns the length of the hit
Returns : integer
Args : [optional] integer to set the length
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 : [optional] scalar string to set the algorithm
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 : [optional] scalar value to set the raw score
score
Equivalent to raw_score()
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 : [optional] scalar value to set the significance
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 undef if bit score is not set
Argument : n/a
Comments : For BLAST1, the non-bit score is listed in the summary line.
See Also : score()
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
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 : hsp(), num_hsps()
num_hsps
Usage : $hit_object->num_hsps();
Purpose : Get the number of HSPs for the present hit.
Example : $nhsps = $hit_object->num_hsps();
Returns : Integer or '-' if HSPs have not been callected
Argument : n/a
See Also : hsps()
rewind
Title : rewind
Usage : $hit->rewind;
Function: Allow one to reset the HSP iterator to the beginning
Since this is an in-memory implementation
Returns : none
Args : none
ambiguous_aln
Usage : $ambig_code = $hit_object->ambiguous_aln();
Purpose : Sets/Gets ambiguity code data member.
Example : (see usage)
Returns : String = 'q', 's', 'qs', '-'
: 'q' = query sequence contains overlapping sub-sequences
: while sbjct does not.
: 's' = sbjct sequence contains overlapping sub-sequences
: while query does not.
: 'qs' = query and sbjct sequence contains overlapping sub-sequences
: relative to each other.
: '-' = query and sbjct sequence do not contains multiple domains
: relative to each other OR both contain the same distribution
: of similar domains.
Argument : n/a
Throws : n/a
Comment : Note: "sbjct" is synonymous with "hit"
overlap
See documentation in Bio::Search::Hit::HitI::overlap()
n
Usage : $hit_object->n();
Purpose : Gets the N number for the current 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.
Comments : 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 : num_hsps()
p
Usage : $hit_object->p( [format] );
Purpose : Get the P-value for the best HSP
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 : expect(), signif(), Bio::Search::SearchUtils::get_exponent()
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 : hsps(), num_hsps()
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)
locus
Title : locus
Usage : $locus = $hit->locus();
Function: Retrieve the locus (if available) for the hit
Returns : a scalar string (empty string if not set)
Args : none
each_accession_number
Title : each_accession_number
Usage : @each_accession_number = $hit->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
tiled_hsps
See documentation in Bio::Search::SearchUtils::tile_hsps()
query_length
Title : query_length
Usage : $obj->query_length($newval)
Function: Get/Set the query_length
Returns : value of query_length (a scalar)
Args : on set, new value (a scalar or undef, optional)
ncbi_gi
Title : ncbi_gi
Usage : $acc = $hit->ncbi_gi();
Function: Retrieve the NCBI Unique ID (aka the GI #),
if available, for the hit
Returns : a scalar string (empty string if not set)
Args : none
Note : As of Sept. 2016 NCBI records will no longer have a
GI; this attributue will remain in place for older
records
ModelHit methods overridden in ModelHit
The following methods have been overridden due to their current reliance on sequence-based
queries. They may be implemented in future versions of this class.
length_aln
gaps
matches
start
end
range
frac_identical
frac_conserved
frac_aligned_query
frac_aligned_hit
num_unaligned_hit
num_unaligned_query
seq_inds
strand
frame
logical_length