Bio::Search::Hit GenericHit
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Summary
Bio::Search::Hit::GenericHit - A generic implementation of the Bio::Search::Hit::HitI interface
Package variables
No package variables defined.
Included modules
Bio::Search::SearchUtils
Inherit
Bio::Root::Root Bio::Search::Hit::HitI
Synopsis
    use Bio::Search::Hit::GenericHit;
my $hit = Bio::Search::Hit::GenericHit->new(-algorithm => 'blastp');
# typically one gets HitI objects from a SearchIO stream via a ResultI use Bio::SearchIO; my $parser = Bio::SearchIO->new(-format => 'blast', -file => 'result.bls'); my $result = $parser->next_result; my $hit = $result->next_hit;
# TODO: Describe how to configure a SearchIO stream so that it generates
# GenericHit objects.
Description
This object handles the hit data from a Database Sequence Search such
as FASTA or BLAST.
Unless you're writing a parser, you won't ever need to create a
GenericHit 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.
For documentation on what you can do with GenericHit (and other HitI
objects), please see the API documentation in
Bio::Search::Hit::HitI.
Methods
newDescriptionCode
add_hspDescriptionCode
hsp_factoryDescriptionCode
nameDescriptionCode
accessionDescriptionCode
descriptionDescriptionCode
lengthDescriptionCode
algorithmDescriptionCode
raw_scoreDescriptionCode
scoreDescriptionCode
significanceDescriptionCode
bitsDescriptionCode
next_hspDescriptionCode
hspsDescriptionCode
num_hspsDescriptionCode
rewindDescriptionCode
ambiguous_alnDescriptionCode
overlapDescriptionCode
nDescriptionCode
pDescriptionCode
hspDescriptionCode
logical_lengthDescriptionCode
length_alnDescriptionCode
gapsDescriptionCode
matchesDescriptionCode
startDescriptionCode
endDescriptionCode
rangeDescriptionCode
frac_identicalDescriptionCode
frac_conservedDescriptionCode
frac_aligned_queryDescriptionCode
frac_aligned_hitDescriptionCode
num_unaligned_hitDescriptionCode
num_unaligned_queryDescriptionCode
seq_indsDescriptionCode
strandDescriptionCode
frameDescriptionCode
rankDescriptionCode
locusDescriptionCode
each_accession_numberDescriptionCode
tiled_hspsDescriptionCode
query_lengthDescriptionCode
ncbi_giDescriptionCode
sort_hsps
No description
Code
iterationDescriptionCode
found_againDescriptionCode
Methods description
newcode    nextTop
 Title   : new
Usage : my $obj = Bio::Search::Hit::GenericHit->new();
Function: Builds a new Bio::Search::Hit::GenericHit object
Returns : Bio::Search::Hit::GenericHit
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_hspcodeprevnextTop
 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_factorycodeprevnextTop
 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
namecodeprevnextTop
 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
accessioncodeprevnextTop
 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
descriptioncodeprevnextTop
 Title   : description
Usage : $desc = $hit->description();
Function: Retrieve the description for the hit
Returns : a scalar string
Args : [optional] scalar string to set the descrition
lengthcodeprevnextTop
 Title   : length
Usage : my $len = $hit->length
Function: Returns the length of the hit
Returns : integer
Args : [optional] integer to set the length
algorithmcodeprevnextTop
 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_scorecodeprevnextTop
 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
scorecodeprevnextTop
Equivalent to raw_score()
significancecodeprevnextTop
 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
bitscodeprevnextTop
 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_hspcodeprevnextTop
 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
hspscodeprevnextTop
 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_hspscodeprevnextTop
 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()
rewindcodeprevnextTop
 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_alncodeprevnextTop
 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"
overlapcodeprevnextTop
See documentation in Bio::Search::Hit::HitI::overlap()
ncodeprevnextTop
 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 (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 : num_hsps()
pcodeprevnextTop
 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 : expect(), significance(), Bio::Search::SearchUtils::get_exponent()
hspcodeprevnextTop
 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()
logical_lengthcodeprevnextTop
 Usage     : $hit_object->logical_length( [seq_type] );
: (mostly intended for internal use).
Purpose : Get the logical length of the hit sequence.
: This is necessary since the number of identical/conserved residues
: can be in terms of peptide sequence space, yet the query and/or hit
: sequence are in nucleotide space.
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 :
: In the case of BLAST flavors:
: For TBLASTN reports, the length of the aligned portion of the
: nucleotide hit sequence is divided by 3; for BLASTX reports,
: the length of the aligned portion of the nucleotide query
: sequence is divided by 3. For TBLASTX reports, the length of
: both hit and query sequence are converted.
:
: 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 : length(), frac_aligned_query(), frac_aligned_hit()
length_alncodeprevnextTop
 Usage     : $hit_object->length_aln( [seq_type] );
Purpose : Get the total length of the aligned region for query or sbjct seq.
: This number will include all HSPs
Example : $len = $hit_object->length_aln(); # default = query
: $lenAln = $hit_object->length_aln('query');
Returns : Integer
Argument : seq_Type = 'query' or 'hit' or 'sbjct' (Default = 'query')
('sbjct' is synonymous with 'hit')
Throws : Exception if the argument is not recognized.
Comments : This method will report the logical length of the alignment,
: meaning that for TBLAST[NX] reports, the length is reported
: using amino acid coordinate space (i.e., nucleotides / 3).
:
: 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 length() on each (use hsps() to get all HSPs).
See Also : length(), frac_aligned_query(), frac_aligned_hit(), gaps(), Bio::Search::SearchUtils::tile_hsps(), Bio::Search::HSP::BlastHSP::length()
gapscodeprevnextTop
 Usage     : $hit_object->gaps( [seq_type] );
Purpose : Get the number of gaps in the aligned query, hit, or both sequences.
: Data is summed across all HSPs.
Example : $qgaps = $hit_object->gaps('query');
: $hgaps = $hit_object->gaps('hit');
: $tgaps = $hit_object->gaps(); # default = total (query + hit)
Returns : scalar context: integer
: array context without args: two-element list of integers
: (queryGaps, hitGaps)
: Array context can be forced by providing an argument of 'list' or 'array'.
:
: CAUTION: Calling this method within printf or sprintf is arrray context.
: So this function may not give you what you expect. For example:
: printf "Total gaps: %d", $hit->gaps();
: Actually returns a two-element array, so what gets printed
: is the number of gaps in the query, not the total
:
Argument : seq_type: 'query' | 'hit' or 'sbjct' | 'total' | 'list' (default = 'total')
('sbjct' is synonymous with 'hit')
Throws : n/a
Comments : If you need data for each HSP, use hsps() and then interate
: through each HSP object.
: This method requires that all HSPs be tiled. If they have not
: already been tiled, they will be tiled first automatically..
: Not relying on wantarray since that will fail in situations
: such as printf "%d", $hit->gaps() in which you might expect to
: be printing the total gaps, but evaluates to array context.
See Also : length_aln()
matchescodeprevnextTop
See documentation in Bio::Search::Hit::HitI::matches()
startcodeprevnextTop
 Usage     : $sbjct->start( [seq_type] );
Purpose : Gets the start coordinate for the query, sbjct, or both sequences
: in the BlastHit object. If there is more than one HSP, the lowest start
: value of all HSPs is returned.
Example : $qbeg = $sbjct->start('query');
: $sbeg = $sbjct->start('hit');
: ($qbeg, $sbeg) = $sbjct->start();
Returns : scalar context: integer
: array context without args: list of two integers (queryStart, sbjctStart)
: 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
See Also : end(), range(), strand(),
Bio::Search::HSP::BlastHSP::start
endcodeprevnextTop
 Usage     : $sbjct->end( [seq_type] );
Purpose : Gets the end coordinate for the query, sbjct, or both sequences
: in the BlastHit object. If there is more than one HSP,
the largest end
: value of all HSPs is returned.
Example : $qend = $sbjct->end('query');
: $send = $sbjct->end('hit');
: ($qend, $send) = $sbjct->end();
Returns : scalar context: integer
: array context without args: list of two integers
: (queryEnd, sbjctEnd)
: Array context can be "induced" by providing an argument
: of 'list' or 'array'.
Argument : In scalar context: seq_type = 'query' or 'sbjct'
: (case insensitive). If not supplied, 'query' is used.
Throws : n/a
See Also : start(), range(), strand()
rangecodeprevnextTop
 Usage     : $sbjct->range( [seq_type] );
Purpose : Gets the (start, end) coordinates for the query or sbjct sequence
: in the HSP alignment.
Example : ($qbeg, $qend) = $sbjct->range('query');
: ($sbeg, $send) = $sbjct->range('hit');
Returns : Two-element array of integers
Argument : seq_type = string, 'query' or 'hit' or 'sbjct' (default = 'query')
('sbjct' is synonymous with 'hit')
Throws : n/a
See Also : start(), end()
frac_identicalcodeprevnextTop
 Usage     : $hit_object->frac_identical( [seq_type] );
Purpose : Get the overall fraction of identical positions across all HSPs.
: The number refers to only the aligned regions and does not
: account for unaligned regions in between the HSPs, if any.
Example : $frac_iden = $hit_object->frac_identical('query');
Returns : Float (2-decimal precision, e.g., 0.75).
Argument : seq_type: 'query' | 'hit' or 'sbjct' | 'total'
: default = 'query' (but see comments below).
: ('sbjct' is synonymous with 'hit')
Throws : n/a
Comments :
: To compute the fraction identical, the logical length of the
: aligned portion of the sequence is used, meaning that
: in the case of BLAST flavors, for TBLASTN reports, the length of
: the aligned portion of the
: nucleotide hit sequence is divided by 3; for BLASTX reports,
: the length of the aligned portion of the nucleotide query
: sequence is divided by 3. For TBLASTX reports, the length of
: both hit and query sequence are converted.
: This is necessary since the number of identical residues is
: in terms of peptide sequence space.
:
: Different versions of Blast report different values for the total
: length of the alignment. This is the number reported in the
: denominators in the stats section:
: "Identical = 34/120 Positives = 67/120".
: NCBI BLAST uses the total length of the alignment (with gaps)
: WU-BLAST uses the length of the query sequence (without gaps).
:
: Therefore, when called with an argument of 'total',
: this method will report different values depending on the
: version of BLAST used. Total does NOT take into account HSP
: tiling, so it should not be used.
:
: To get the fraction identical among only the aligned residues,
: ignoring the gaps, call this method without an argument or
: with an argument of 'query' or 'hit'.
:
: If you need data for each HSP, use hsps() and then iterate
: through the HSP objects.
: This method requires that all HSPs be tiled. If they have not
: already been tiled, they will be tiled first automatically.
See Also : frac_conserved(), frac_aligned_query(), matches(), Bio::Search::SearchUtils::tile_hsps()
frac_conservedcodeprevnextTop
 Usage     : $hit_object->frac_conserved( [seq_type] );
Purpose : Get the overall fraction of conserved positions across all HSPs.
: The number refers to only the aligned regions and does not
: account for unaligned regions in between the HSPs, if any.
Example : $frac_cons = $hit_object->frac_conserved('hit');
Returns : Float (2-decimal precision, e.g., 0.75).
Argument : seq_type: 'query' | 'hit' or 'sbjct' | 'total'
: default = 'query' (but see comments below).
: ('sbjct' is synonymous with 'hit')
Throws : n/a
Comments :
: To compute the fraction conserved, the logical length of the
: aligned portion of the sequence is used, meaning that
: in the case of BLAST flavors, for TBLASTN reports, the length of
: the aligned portion of the
: nucleotide hit sequence is divided by 3; for BLASTX reports,
: the length of the aligned portion of the nucleotide query
: sequence is divided by 3. For TBLASTX reports, the length of
: both hit and query sequence are converted.
: This is necessary since the number of conserved residues is
: in terms of peptide sequence space.
:
: Different versions of Blast report different values for the total
: length of the alignment. This is the number reported in the
: denominators in the stats section:
: "Positives = 34/120 Positives = 67/120".
: NCBI BLAST uses the total length of the alignment (with gaps)
: WU-BLAST uses the length of the query sequence (without gaps).
:
: Therefore, when called with an argument of 'total',
: this method will report different values depending on the
: version of BLAST used. Total does NOT take into account HSP
: tiling, so it should not be used.
:
: To get the fraction conserved among only the aligned residues,
: ignoring the gaps, call this method without an argument or
: with an argument of 'query' or 'hit'.
:
: If you need data for each HSP, use hsps() and then interate
: through the HSP objects.
: This method requires that all HSPs be tiled. If they have not
: already been tiled, they will be tiled first automatically.
See Also : frac_identical(), matches(), Bio::Search::SearchUtils::tile_hsps()
frac_aligned_querycodeprevnextTop
 Usage     : $hit_object->frac_aligned_query();
Purpose : Get the fraction of the query sequence which has been aligned
: across all HSPs (not including intervals between non-overlapping
: HSPs).
Example : $frac_alnq = $hit_object->frac_aligned_query();
Returns : Float (2-decimal precision, e.g., 0.75).
Argument : n/a
Throws : n/a
Comments : If you need data for each HSP, use hsps() and then interate
: through the HSP objects.
: This method requires that all HSPs be tiled. If they have not
: already been tiled, they will be tiled first automatically.
See Also : frac_aligned_hit(), logical_length(), length_aln(), Bio::Search::SearchUtils::tile_hsps()
frac_aligned_hitcodeprevnextTop
 Usage     : $hit_object->frac_aligned_hit();
Purpose : Get the fraction of the hit (sbjct) sequence which has been aligned
: across all HSPs (not including intervals between non-overlapping
: HSPs).
Example : $frac_alnq = $hit_object->frac_aligned_hit();
Returns : Float (2-decimal precision, e.g., 0.75).
Argument : n/a
Throws : n/a
Comments : If you need data for each HSP, use hsps() and then interate
: through the HSP objects.
: This method requires that all HSPs be tiled. If they have not
: already been tiled, they will be tiled first automatically.
See Also : frac_aligned_query(), matches(), , logical_length(), length_aln(), Bio::Search::SearchUtils::tile_hsps()
num_unaligned_hitcodeprevnextTop
 Usage     : $hit_object->num_unaligned_hit();
Purpose : Get the number of the unaligned residues in the hit sequence.
: Sums across all all HSPs.
Example : $num_unaln = $hit_object->num_unaligned_hit();
Returns : Integer
Argument : n/a
Throws : n/a
Comments : See notes regarding logical lengths in the comments for frac_aligned_hit().
: They apply here as well.
: If you need data for each HSP, use hsps() and then interate
: through the HSP objects.
: This method requires that all HSPs be tiled. If they have not
: already been tiled, they will be tiled first automatically..
See Also : num_unaligned_query(), Bio::Search::SearchUtils::tile_hsps(), frac_aligned_hit()
num_unaligned_querycodeprevnextTop
 Usage     : $hit_object->num_unaligned_query();
Purpose : Get the number of the unaligned residues in the query sequence.
: Sums across all all HSPs.
Example : $num_unaln = $hit_object->num_unaligned_query();
Returns : Integer
Argument : n/a
Throws : n/a
Comments : See notes regarding logical lengths in the comments for frac_aligned_query().
: They apply here as well.
: If you need data for each HSP, use hsps() and then interate
: through the HSP objects.
: This method requires that all HSPs be tiled. If they have not
: already been tiled, they will be tiled first automatically..
See Also : num_unaligned_hit(), frac_aligned_query(), Bio::Search::SearchUtils::tile_hsps()
seq_indscodeprevnextTop
 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 : Bio::Search::HSP::BlastHSP::seq_inds()
strandcodeprevnextTop
See documentation in Bio::Search::Hit::HitI::strand()
framecodeprevnextTop
See documentation in Bio::Search::Hit::HitI::frame()
rankcodeprevnextTop
 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)
locuscodeprevnextTop
 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_numbercodeprevnextTop
 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_hspscodeprevnextTop
See documentation in Bio::Search::SearchUtils::tile_hsps()
query_lengthcodeprevnextTop
 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_gicodeprevnextTop
 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
iterationcodeprevnextTop
 Usage     : $hit->iteration( $iteration_num );
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 may report iteration as 1, but this number
is only meaningful for PSI-BLAST reports.
Argument : iteration_num (optional, used when setting only)
Throws : none
See Also : found_again()
found_againcodeprevnextTop
 Title     : found_again
Usage : $hit->found_again;
$hit->found_again(1);
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( $hit->found_again()) { ... }; Returns : Boolean, true (1) if the hit has been found in a previous PSI-BLAST iteration. Returns false (0 or undef) for hits that have not occurred in a previous PSI-BLAST iteration. Argument : Boolean (1 or 0). Only used for setting. Throws : none
See Also : iteration()
Methods code
newdescriptionprevnextTop
sub new {
  my($class,@args) = @_;

  my $self = $class->SUPER::new(@args);
  my ($hsps, $name,$query_len,$desc, $acc, $locus, $length,
      $score,$algo,$signif,$bits, $p,
      $rank, $hsp_factory, $gi, $iter, $found) = $self->_rearrange([qw(HSPS
                                     NAME 
                                     QUERY_LEN
                                     DESCRIPTION
                                     ACCESSION
                                     LOCUS
                                     LENGTH SCORE ALGORITHM 
                                     SIGNIFICANCE BITS P
                                     RANK
                                     HSP_FACTORY
                                     NCBI_GI
                                     ITERATION
                                     FOUND_AGAIN)], @args);
  
  defined $query_len && $self->query_length($query_len);

  if( ! defined $name ) { 
      $self->throw("Must have defined a valid name for Hit");
  } else { 
      $self->name($name);
  }  

  defined $acc         && $self->accession($acc);
  defined $locus       && $self->locus($locus);
  defined $desc        && $self->description($desc);
  defined $length      && $self->length($length);
  defined $algo        && $self->algorithm($algo);
  defined $signif      && $self->significance($signif);
  defined $score       && $self->raw_score($score);
  defined $bits        && $self->bits($bits);
  defined $rank        && $self->rank($rank);
  defined $hsp_factory && $self->hsp_factory($hsp_factory);
  defined $gi          && $self->ncbi_gi($gi);
  defined $iter        && $self->iteration($iter);
  defined $found       && $self->found_again($found);  
  # p() has a weird interface, so this is a hack workaround
if (defined $p) { $self->{_p} = $p; } $self->{'_iterator'} = 0; if( defined $hsps ) { if( ref($hsps) !~ /array/i ) { $self->warn("Did not specify a valid array ref for the param HSPS ($hsps)"); } else { my $hspcount=0; while( @{$hsps} ) { $hspcount++; $self->add_hsp(shift @{$hsps} ); } $self->{'_hsps'} = undef if $hspcount == 0; } } else { $self->{'_hsps'} = undef; } return $self;
}
add_hspdescriptionprevnextTop
sub add_hsp {
   my ($self,$hsp) = @_;
   if (!defined $hsp || (ref($hsp) ne 'HASH' && !$hsp->isa('Bio::Search::HSP::HSPI'))) { 
       $self->throw("Must provide a valid Bio::Search::HSP::HSPI object or hash ref to object: $self method: add_hsp value: $hsp");
       return;
   }
   
   push @{$self->{'_hsps'}}, $hsp;
   if (ref($hsp) eq 'HASH') {
       $self->{_hashes}->{$#{$self->{'_hsps'}}} = 1;
   }
   return scalar @{$self->{'_hsps'}};
}
hsp_factorydescriptionprevnextTop
sub hsp_factory {
    my $self = shift;
    if (@_) { $self->{_hsp_factory} = shift }
    return $self->{_hsp_factory} || return;
}
namedescriptionprevnextTop
sub name {
    my ($self,$value) = @_;
    my $previous = $self->{'_name'};
    if( defined $value || ! defined $previous ) {
        $value = $previous = '' unless defined $value;
        $self->{'_name'} = $value;
    } 
    return $previous;
}
accessiondescriptionprevnextTop
sub accession {
    my ($self,$value) = @_;
    my $previous = $self->{'_accession'};
    if( defined $value || ! defined $previous ) { 
        $value = $previous = '' unless defined $value;
        $self->{'_accession'} = $value;
    } 
        return $previous;
}
descriptiondescriptionprevnextTop
sub description {
    my ($self,$value) = @_;
    my $previous = $self->{'_description'};
    if( defined $value || ! defined $previous ) { 
        $value = $previous = '' unless defined $value;
        $self->{'_description'} = $value;
    } 
    return $previous;
}
lengthdescriptionprevnextTop
sub length {
    my ($self,$value) = @_;
    my $previous = $self->{'_length'};
    if( defined $value || ! defined $previous ) { 
        $value = $previous = 0 unless defined $value;
        $self->{'_length'} = $value;
    } 
    return $previous;
}
algorithmdescriptionprevnextTop
sub algorithm {
    my ($self,$value) = @_;
    my $previous = $self->{'_algorithm'};
    if( defined $value || ! defined $previous ) { 
        $value = $previous = '' unless defined $value;
        $self->{'_algorithm'} = $value;
    } 
    return $previous;
}
raw_scoredescriptionprevnextTop
sub raw_score {
    my ($self,$value) = @_; 
    my $previous = $self->{'_score'};
    if( defined $value ) { 
        $self->{'_score'} = $value;
    } elsif ( ! defined $previous ) {
        # Set the bits of the Hit to that of the top HSP.
unless( defined $self->{'_hsps'}->[0] ) { $self->warn("No HSPs for this minimal Hit (".$self->name.")\n". "If using NCBI BLAST, check bits() instead"); return; } # use 'score' if available
if ( defined( ($self->hsps)[0]->score ) ) { $previous = $self->{'_score'} = ($self->hsps)[0]->score; } # otherwise use 'bits'
elsif ( defined( ($self->hsps)[0]->bits ) ) { $previous = $self->{'_score'} = ($self->hsps)[0]->bits; } } return $previous;
}
scoredescriptionprevnextTop
sub score {
 shift->raw_score(@_);
}
significancedescriptionprevnextTop
sub significance {
    my ($self,$value) = @_;
    my $previous = $self->{'_significance'};
    if( defined $value ) { 
        $self->{'_significance'} = $value;
    } elsif ( ! defined $previous ) {
	unless( defined $self->{'_hsps'}->[0] ) {
	    $self->warn("No HSPs for this Hit (".$self->name.")");
	    return;
	}
        # Set the significance of the Hit to that of the top HSP.
$previous = $self->{'_significance'} = ($self->hsps)[0]->significance; } return $previous;
}
bitsdescriptionprevnextTop
sub bits {
    my ($self,$value) = @_; 
    my $previous = $self->{'_bits'};
    if( defined $value ) { 
        $self->{'_bits'} = $value;
    } elsif ( ! defined $previous ) {
        # Set the bits of the Hit to that of the top HSP.
unless( defined $self->{'_hsps'}->[0] ) { $self->warn("No HSPs for this minimal Hit (".$self->name.")\n". "If using WU-BLAST, check raw_score() instead"); return; } $previous = $self->{'_bits'} = ($self->hsps)[0]->bits; } return $previous;
}
next_hspdescriptionprevnextTop
sub next_hsp {
    my $self = shift;
    $self->{'_iterator'} = 0 unless defined $self->{'_iterator'};
    return unless
        defined($self->{'_hsps'}) 
        && $self->{'_iterator'} <= scalar @{$self->{'_hsps'}};
    
    my $iterator = $self->{'_iterator'}++;
    my $hsp = $self->{'_hsps'}->[$iterator] || return;
    if (ref($hsp) eq 'HASH') {
        my $factory = $self->hsp_factory || $self->throw("Tried to get a HSP, but it was a hash ref and we have no hsp factory");
        $hsp = $factory->create_object(%{$hsp});
        $self->{'_hsps'}->[$iterator] = $hsp;
        delete $self->{_hashes}->{$iterator};
    }
    return $hsp;
}
hspsdescriptionprevnextTop
sub hsps {
    my $self = shift;
    foreach my $i (keys %{$self->{_hashes} || {}}) {
        my $factory = $self->hsp_factory || $self->throw("Tried to get a HSP, but it was a hash ref and we have no hsp factory");
        $self->{'_hsps'}->[$i] = $factory->create_object(%{$self->{'_hsps'}->[$i]});
        delete $self->{_hashes}->{$i};
    }
    
    return wantarray() ? @{$self->{'_hsps'} || []} : scalar(@{$self->{'_hsps'} || []});
}
num_hspsdescriptionprevnextTop
sub num_hsps {
    my $self = shift;
    
    unless ($self->{'_hsps'}) {
        return '-';
    }
    
    return scalar(@{$self->{'_hsps'}});
}
rewinddescriptionprevnextTop
sub rewind {
   my ($self) = @_;
   $self->{'_iterator'} = 0;
}
ambiguous_alndescriptionprevnextTop
sub ambiguous_aln {
    my $self = shift;
    if(@_) { $self->{'_ambiguous_aln'} = shift; }
    $self->{'_ambiguous_aln'} || '-';
}
overlapdescriptionprevnextTop
sub overlap {
    my $self = shift; 
    if(@_) { $self->{'_overlap'} = shift; }
    defined $self->{'_overlap'} ? $self->{'_overlap'} : 0;
}
ndescriptionprevnextTop
sub n {
    my $self = shift; 

    # The check for $self->{'_n'} is a remnant from the 'query' mode days
# in which the sbjct object would collect data from the description
# line only.
my ($n); if(not defined($self->{'_n'})) { if( $self->hsp ) { $n = $self->hsp->n; } } else { $n = $self->{'_n'}; } $n ||= $self->num_hsps; return $n;
}
pdescriptionprevnextTop
sub p {
# Some duplication of logic for p(), expect() and signif() for the sake of performance.
my ($self, $fmt) = @_; my $val = $self->{'_p'}; # $val can be zero.
if(!defined $val) { # P-value not defined, must be a NCBI Blast2 report.
# Use expect instead.
$self->warn( "P-value not defined. Using significance() instead."); $val = $self->significance(); } return $val if not $fmt or $fmt =~ /^raw/i; ## Special formats: exponent-only or as list.
return &Bio::Search::SearchUtils::get_exponent($val) if $fmt =~ /^exp/i; return (split (/eE/, $val)) if $fmt =~ /^parts/i; ## Default: return the raw P-value.
return $val;
}
hspdescriptionprevnextTop
sub hsp {
    my( $self, $option ) = @_;
    $option ||= 'best';
    
    if (not ref $self->{'_hsps'}) {
        $self->throw("Can't get HSPs: data not collected.");
    }

    my @hsps = $self->hsps;
    
    return $hsps[0]      if $option =~ /best|first|1/i;
    return $hsps[$#hsps] if $option =~ /worst|last/i;

    $self->throw("Can't get HSP for: $option\n" .
                 "Valid arguments: 'best', 'worst'");
}
logical_lengthdescriptionprevnextTop
sub logical_length {
    my $self = shift;
    my $seqType = shift || 'query';
    $seqType = 'sbjct' if $seqType eq 'hit';

    my ($length, $logical);
    my $algo = $self->algorithm;

    # For the sbjct, return logical sbjct length
if( $seqType eq 'sbjct' ) { $length = $self->length; } else { # Otherwise, return logical query length
$length = $self->query_length(); $self->throw("Must have defined query_len") unless ( $length ); } $logical = Bio::Search::SearchUtils::logical_length($algo, $seqType, $length); return int($logical);
}
length_alndescriptionprevnextTop
sub length_aln {
    my( $self, $seqType, $num ) = @_;

    $seqType ||= 'query';
    $seqType = 'sbjct' if $seqType eq 'hit';

    # Setter:
if( defined $num) { return $self->{'_length_aln_'.$seqType} = $num; } unless ($self->{'_hsps'}) { #return wantarray ? ('-','-') : '-';
Bio::Search::SearchUtils::_warn_about_no_hsps($self); return '-'; } Bio::Search::SearchUtils::tile_hsps($self) unless $self->tiled_hsps; my $data = $self->{'_length_aln_'.$seqType}; ## If we don't have data, figure out what went wrong.
if(!$data) { $self->throw("Can't get length aln for sequence type\" $seqType\". " . "Valid types are 'query', 'hit', 'sbjct' ('sbjct' = 'hit')"); } return $data;
}
gapsdescriptionprevnextTop
sub gaps {
    my( $self, $seqType, $num ) = @_;

    $seqType ||= (wantarray ? 'list' : 'total');
    $seqType = 'sbjct' if $seqType eq 'hit';

    unless ($self->{'_hsps'}) {
        Bio::Search::SearchUtils::_warn_about_no_hsps($self);
        return wantarray ? ('-','-') : '-';
        #return '-';
} Bio::Search::SearchUtils::tile_hsps($self) unless $self->tiled_hsps; $seqType = lc($seqType); if( defined $num ) { $self->throw("Can't set gaps for seqType '$seqType'. Must be 'query' or 'hit'\n") unless ($seqType eq 'sbjct' or $seqType eq 'query'); return $self->{'_gaps_'.$seqType} = $num; } elsif($seqType =~ /list|array/i) { return ($self->{'_gaps_query'}, $self->{'_gaps_sbjct'}); } elsif($seqType eq 'total') { return ($self->{'_gaps_query'} + $self->{'_gaps_sbjct'}) || 0; } else { return $self->{'_gaps_'.$seqType} || 0; }
}
matchesdescriptionprevnextTop
sub matches {
    my( $self, $arg1, $arg2) = @_;
    my(@data,$data);

    unless ($self->{'_hsps'}) {
        Bio::Search::SearchUtils::_warn_about_no_hsps($self);
        return wantarray ? ('-','-') : '-';
    }

    Bio::Search::SearchUtils::tile_hsps($self) unless $self->tiled_hsps;

    unless( $arg1 ) {
        @data = ($self->{'_totalIdentical'}, $self->{'_totalConserved'});

        return @data;
    } else {

        if( defined $arg2 ) {
            $self->{'_totalIdentical'} = $arg1;
            $self->{'_totalConserved'} = $arg2;
            return ( $arg1, $arg2 );
        }
        elsif($arg1 =~ /^id/i) { 
            $data = $self->{'_totalIdentical'};
        } else {
            $data = $self->{'_totalConserved'};
        }
        #print STDERR "\nmatches(): id=$self->{'_totalIdentical'}, cons=$self->{'_totalConserved'}\n\n";
return $data; } ## If we make it to here, it is likely the case that
## the parser constructed a minimal hit object from the summary line only.
## It either delibrately skipped parsing the alignment section,
## or was not able to because it was absent (due to blast executable parameter
## setting such as -b 0 (B=0 for WU-BLAST) )
#$self->throw("Can't get identical or conserved data: no data.");
}
startdescriptionprevnextTop
sub start {
    my ($self, $seqType, $num) = @_;

    unless ($self->{'_hsps'}) {
        Bio::Search::SearchUtils::_warn_about_no_hsps($self);
        return wantarray ? ('-','-') : '-';
    }

    $seqType ||= (wantarray ? 'list' : 'query');
    $seqType = 'sbjct' if $seqType eq 'hit';

    if( defined $num ) {
        $seqType = "_\L$seqType\E";
        return $self->{$seqType.'Start'} = $num;
    }

    # If there is only one HSP, defer this call to the solitary HSP.
if($self->num_hsps == 1) { return $self->hsp->start($seqType); } else { # Tiling normally generates $self->{'_queryStart'} and
# $self->{'_sbjctStart'}, but is very slow. If we haven't tiled,
# find the answer quickly without tiling.
unless (defined $self->{'_queryStart'}) { my $earliest_query_start; my $earliest_sbjct_start; foreach my $hsp ($self->hsps) { my $this_query_start = $hsp->start('query'); if (! defined $earliest_query_start || $this_query_start < $earliest_query_start) { $earliest_query_start = $this_query_start; } my $this_sbjct_start = $hsp->start('sbjct'); if (! defined $earliest_sbjct_start || $this_sbjct_start < $earliest_sbjct_start) { $earliest_sbjct_start = $this_sbjct_start; } } $self->{'_queryStart'} = $earliest_query_start; $self->{'_sbjctStart'} = $earliest_sbjct_start; } if ($seqType =~ /list|array/i) { return ($self->{'_queryStart'}, $self->{'_sbjctStart'}); } else { ## Sensitive to member name changes.
$seqType = "_\L$seqType\E"; return $self->{$seqType.'Start'}; } }
}
enddescriptionprevnextTop
sub end {
    my ($self, $seqType, $num) = @_;

    unless ($self->{'_hsps'}) {
        return wantarray ? ('-','-') : '-';
    }

    $seqType ||= (wantarray ? 'list' : 'query');
    $seqType = 'sbjct' if $seqType eq 'hit';

    if( defined $num ) {
        $seqType = "_\L$seqType\E";
        return $self->{$seqType.'Stop'} = $num;
    }

    # If there is only one HSP, defer this call to the solitary HSP.
if($self->num_hsps == 1) { return $self->hsp->end($seqType); } else { # Tiling normally generates $self->{'_queryStop'} and
# $self->{'_sbjctStop'}, but is very slow. If we haven't tiled,
# find the answer quickly without tiling.
unless (defined $self->{'_queryStop'}) { my $latest_query_end; my $latest_sbjct_end; foreach my $hsp ($self->hsps) { my $this_query_end = $hsp->end('query'); if (! defined $latest_query_end || $this_query_end > $latest_query_end) { $latest_query_end = $this_query_end; } my $this_sbjct_end = $hsp->end('sbjct'); if (! defined $latest_sbjct_end || $this_sbjct_end > $latest_sbjct_end) { $latest_sbjct_end = $this_sbjct_end; } } $self->{'_queryStop'} = $latest_query_end; $self->{'_sbjctStop'} = $latest_sbjct_end; } if($seqType =~ /list|array/i) { return ($self->{'_queryStop'}, $self->{'_sbjctStop'}); } else { ## Sensitive to member name changes.
$seqType = "_\L$seqType\E"; return $self->{$seqType.'Stop'}; } }
}
rangedescriptionprevnextTop
sub range {
    my ($self, $seqType) = @_;
    $seqType ||= 'query';
    $seqType = 'sbjct' if $seqType eq 'hit';
    return ($self->start($seqType), $self->end($seqType));
}
frac_identicaldescriptionprevnextTop
sub frac_identical {
    my ($self, $seqType) = @_;
    $seqType ||= 'query';
    $seqType = 'sbjct' if $seqType eq 'hit';

    ## Sensitive to member name format.
$seqType = lc($seqType); unless ($self->{'_hsps'}) { Bio::Search::SearchUtils::_warn_about_no_hsps($self); #return wantarray ? ('-','-') : '-';
return '-'; } Bio::Search::SearchUtils::tile_hsps($self) unless $self->tiled_hsps; my $ident = $self->matches('id'); my $total = $self->length_aln($seqType); my $ratio = $ident / $total;
my $ratio_rounded = sprintf( "%.3f", $ratio); # Round down iff normal rounding yields 1 (just like blast)
$ratio_rounded = 0.999 if (($ratio_rounded == 1) && ($ratio < 1)); return $ratio_rounded;
}
frac_conserveddescriptionprevnextTop
sub frac_conserved {
    my ($self, $seqType) = @_;
    $seqType ||= 'query';
    $seqType = 'sbjct' if $seqType eq 'hit';

    ## Sensitive to member name format.
$seqType = lc($seqType); unless ($self->{'_hsps'}) { Bio::Search::SearchUtils::_warn_about_no_hsps($self); #return wantarray ? ('-','-') : '-';
return '-'; } Bio::Search::SearchUtils::tile_hsps($self) unless $self->tiled_hsps; my $consv = $self->matches('cons'); my $total = $self->length_aln($seqType); my $ratio = $consv / $total;
my $ratio_rounded = sprintf( "%.3f", $ratio); # Round down iff normal rounding yields 1 (just like blast)
$ratio_rounded = 0.999 if (($ratio_rounded == 1) && ($ratio < 1)); return $ratio_rounded;
}
frac_aligned_querydescriptionprevnextTop
sub frac_aligned_query {
    my $self = shift;

    unless ($self->{'_hsps'}) {
        Bio::Search::SearchUtils::_warn_about_no_hsps($self);
        #return wantarray ? ('-','-') : '-';
return '-'; } Bio::Search::SearchUtils::tile_hsps($self) unless $self->tiled_hsps; sprintf( "%.2f", $self->length_aln('query') /
$self->logical_length('query'));
}
frac_aligned_hitdescriptionprevnextTop
sub frac_aligned_hit {
    my $self = shift;

    unless ($self->{'_hsps'}) {
        Bio::Search::SearchUtils::_warn_about_no_hsps($self);
        #return wantarray ? ('-','-') : '-';
return '-'; } Bio::Search::SearchUtils::tile_hsps($self) unless $self->tiled_hsps; sprintf( "%.2f", $self->length_aln('sbjct') / $self->logical_length('sbjct'));
} ## These methods are being maintained for backward compatibility.
}
num_unaligned_hitdescriptionprevnextTop
sub num_unaligned_hit {
    my $self = shift;

    unless ($self->{'_hsps'}) {
        Bio::Search::SearchUtils::_warn_about_no_hsps($self);
        #return wantarray ? ('-','-') : '-';
return '-'; } Bio::Search::SearchUtils::tile_hsps($self) unless $self->tiled_hsps; my $num = $self->logical_length('sbjct') - $self->length_aln('sbjct'); ($num < 0 ? 0 : $num );
}
num_unaligned_querydescriptionprevnextTop
sub num_unaligned_query {
    my $self = shift;

    unless ($self->{'_hsps'}) {
        Bio::Search::SearchUtils::_warn_about_no_hsps($self);
        #return wantarray ? ('-','-') : '-';
return '-'; } Bio::Search::SearchUtils::tile_hsps($self) unless $self->tiled_hsps; my $num = $self->logical_length('query') - $self->length_aln('query'); ($num < 0 ? 0 : $num );
}
seq_indsdescriptionprevnextTop
sub seq_inds {
    my ($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; } $collapse ? &Bio::Search::SearchUtils::collapse_nums(@inds) : @inds;
}
stranddescriptionprevnextTop
sub strand {
    my ($self, $seqType, $strnd) = @_;

    unless ($self->{'_hsps'}) {
        Bio::Search::SearchUtils::_warn_about_no_hsps($self);
        return wantarray ? ('-','-') : '-';
        #return '-';
} Bio::Search::SearchUtils::tile_hsps($self) unless $self->tiled_hsps; $seqType ||= (wantarray ? 'list' : 'query'); $seqType = 'sbjct' if $seqType eq 'hit'; $seqType = lc($seqType); if( defined $strnd ) { $self->throw("Can't set strand for seqType '$seqType'. Must be 'query' or 'hit'\n") unless ($seqType eq 'sbjct' or $seqType eq 'query'); return $self->{'_strand_'.$seqType} = $strnd; } my ($qstr, $hstr); # If there is only one HSP, defer this call to the solitary HSP.
if($self->num_hsps == 1) { return $self->hsp->strand($seqType); } elsif( defined $self->{'_strand_query'}) { # Get the data computed during hsp tiling.
$qstr = $self->{'_strand_query'}; $hstr = $self->{'_strand_sbjct'} } else { # otherwise, iterate through all HSPs collecting strand info.
# This will return the string "-1/1" if there are HSPs on different strands.
# NOTE: This was the pre-10/21/02 procedure which will no longer be used,
# (unless the above elsif{} is commented out).
my (%qstr, %hstr); foreach my $hsp( $self->hsps ) { my ( $q, $h ) = $hsp->strand(); $qstr{ $q }++; $hstr{ $h }++; } $qstr = join( '/', sort keys %qstr); $hstr = join( '/', sort keys %hstr); } if($seqType =~ /list|array/i) { return ($qstr, $hstr); } elsif( $seqType eq 'query' ) { return $qstr; } else { return $hstr; }
}
framedescriptionprevnextTop
sub frame {
    my( $self, $frm ) = @_;

    unless ($self->{'_hsps'}) {
        Bio::Search::SearchUtils::_warn_about_no_hsps($self);
        #return wantarray ? ('-','-') : '-';
return '-'; } Bio::Search::SearchUtils::tile_hsps($self) unless $self->tiled_hsps; if( defined $frm ) { return $self->{'_frame'} = $frm; } # The check for $self->{'_frame'} is a remnant from the 'query' mode days
# in which the sbjct object would collect data from the description line only.
my ($frame); if(not defined($self->{'_frame'})) { $frame = $self->hsp->frame('hit'); } else { $frame = $self->{'_frame'}; } return $frame;
}
rankdescriptionprevnextTop
sub rank {
    my $self = shift;
    return $self->{'_rank'} = shift if @_;
    return $self->{'_rank'} || 1;
}
locusdescriptionprevnextTop
sub locus {
    my ($self,$value) = @_;
    my $previous = $self->{'_locus'};
    if( defined $value || ! defined $previous ) { 
      unless (defined $value) {
        if ($self->{'_name'} =~/(gb|emb|dbj|ref)\|(.*)\|(.*)/) {
                  $value = $previous = $3;
                } else {
          $value = $previous = '';
        }
      }
          $self->{'_locus'} = $value;
    } 
        return $previous;
}
each_accession_numberdescriptionprevnextTop
sub each_accession_number {
    my ($self,$value) = @_;
    my $desc = $self->{'_description'};
    #put primary accnum on the list
my @accnums; push (@accnums,$self->{'_accession'}); if( defined $desc ) { while ($desc =~ /(\b\S+\|\S*\|\S*\s?)/g) { my $id = $1; my ($acc, $version); if ($id =~ /(gb|emb|dbj|sp|pdb|bbs|ref|tp[gde])\|(.*)\|(.*)/) { ($acc, $version) = split /\./, $2; } elsif ($id =~ /(pir|prf|pat|gnl)\|(.*)\|(.*)/) { ($acc, $version) = split /\./, $3; } elsif( $id =~ /(gim|gi|bbm|bbs|lcl)\|(\d*)/) { $acc = $id; } elsif( $id =~ /(oth)\|(.*)\|(.*)\|(.*)/ ) { # discontinued...
($acc,$version) = ($2); } else { #punt, not matching the db's at ftp://ftp.ncbi.nih.gov/blast/db/README
#Database Name Identifier Syntax
#============================ ========================
#GenBank gb|accession|locus
#EMBL Data Library emb|accession|locus
#DDBJ, DNA Database of Japan dbj|accession|locus
#NBRF PIR pir||entry
#Protein Research Foundation prf||name
#SWISS-PROT sp|accession|entry name
#Brookhaven Protein Data Bank pdb|entry|chain
#Patents pat|country|number
#GenInfo Backbone Id bbs|number
#General database identifier gnl|database|identifier
#NCBI Reference Sequence ref|accession|locus
#Local Sequence identifier lcl|identifier
$acc=$id; } push(@accnums, $acc); } } return @accnums;
}
tiled_hspsdescriptionprevnextTop
sub tiled_hsps {
     my $self = shift;
    return $self->{'_tiled_hsps'} = shift if @_;
    return $self->{'_tiled_hsps'};
}
query_lengthdescriptionprevnextTop
sub query_length {
    my $self = shift;

    return $self->{'_query_length'} = shift if @_;
    return $self->{'_query_length'};
}
ncbi_gidescriptionprevnextTop
sub ncbi_gi {
    my ($self,$value) = @_;
    if( defined $value ) {
        $self->{'_ncbi_gi'} = $value;
    } else {
        $self->{'_ncbi_gi'} = $self->name =~ m{^gi\|(\d+)} ? $1 : '';
    } 
    return $self->{'_ncbi_gi'};
}


# sort method for HSPs
}
sort_hspsdescriptionprevnextTop
sub sort_hsps {
    my ($self, $coderef) = @_;
    my @sorted_hsps;

    if ($coderef)  {
	$self->throw('sort_hsps requires a sort function passed as a subroutine reference')
	    unless (ref($coderef) eq 'CODE');
    }
    else {
	$coderef =\& _default_sort_hsps;
	# throw a warning?
} my @hsps = $self->hsps(); eval {@sorted_hsps = sort $coderef @hsps }; if ($@) { $self->throw("Unable to sort hsps: $@"); } else { $self->{'_hsps'} =\@ sorted_hsps; 1; }
}
iterationdescriptionprevnextTop
sub iteration {
   my ($self,$value) = @_;
   if( defined $value) {
      $self->{'_psiblast_iteration'} = $value;
    }
    return $self->{'_psiblast_iteration'};
}
found_againdescriptionprevnextTop
sub found_again {
   my $self = shift;
   return $self->{'_found_again'} = shift if @_;
   return $self->{'_found_again'};
}

1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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 Top
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 BugsTop
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://redmine.open-bio.org/projects/bioperl/
AUTHOR - Jason Stajich and Steve ChervitzTop
Email jason-at-bioperl-dot-org
Email sac-at-bioperl-dot-org
CONTRIBUTORSTop
Sendu Bala, bix@sendu.me.uk
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
Bio::Search::Hit::HitI methodsTop
Implementation of Bio::Search::Hit::HitI methods
frac_aligned_sbjctTop
Same as frac_aligned_hit()
num_unaligned_sbjctTop
Same as num_unaligned_hit()
sort_hitsTop
 Title		: sort_hsps
Usage : $result->sort_hsps(\&sort_function)
Function : Sorts the available HSP 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::Hit::HitI namespace.
For example, use :
$hit->sort_hsps( sub{$Bio::Search::Result::HitI::a->length <=>
$Bio::Search::Result::HitI::b->length});
NOT $hit->sort_hsps($a->length <=> $b->length);