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::HitImethods
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
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