Bio::Search::Hit PullHitI
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Summary
Bio::Search::Hit::PullHitI - Bio::Search::Hit::HitI interface for pull parsers.
Package variables
No package variables defined.
Included modules
Bio::Search::SearchUtils
Inherit
Bio::PullParserI Bio::Search::Hit::HitI
Synopsis
	# This is an interface and cannot be instantiated
# typically one gets HitI objects from a SearchIO stream via a ResultI use Bio::SearchIO; my $parser = Bio::SearchIO->new(-format => 'hmmer_pull', -file => 't/data/hmmpfam.out'); my $result = $parser->next_result; my $hit = $result->next_hit; $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
Description
This object handles the hit data from a database sequence search.
PullHitI is for fast implementations that only do parsing work on the hit
data when you actually request information by calling one of the HitI
methods.
Many methods of HitI are implemented in a way suitable for inheriting classes
that use Bio::PullParserI. It only really makes sense for PullHit modules to be
created by (and have as a -parent) PullResult modules.
In addition to the usual -chunk and -parent, -hit_data is all you should supply
when making a PullHit object. This will store that data and make it accessible
via _raw_hit_data, which you can access in your subclass. It would be best to
simply provide the data as the input -chunk instead, if the raw data is large
enough.
Methods
_setupDescriptionCode
_raw_hit_data
No description
Code
nameDescriptionCode
descriptionDescriptionCode
accessionDescriptionCode
locusDescriptionCode
lengthDescriptionCode
algorithmDescriptionCode
raw_scoreDescriptionCode
scoreDescriptionCode
significanceDescriptionCode
bitsDescriptionCode
next_hspDescriptionCode
hspsDescriptionCode
num_hspsDescriptionCode
seq_indsDescriptionCode
rewindDescriptionCode
overlapDescriptionCode
nDescriptionCode
pDescriptionCode
hspDescriptionCode
logical_lengthDescriptionCode
rankDescriptionCode
each_accession_numberDescriptionCode
tiled_hspsDescriptionCode
strandDescriptionCode
frameDescriptionCode
length_alnDescriptionCode
gapsDescriptionCode
matchesDescriptionCode
startDescriptionCode
endDescriptionCode
rangeDescriptionCode
frac_identicalDescriptionCode
frac_conservedDescriptionCode
frac_aligned_queryDescriptionCode
frac_aligned_hitDescriptionCode
num_unaligned_hitDescriptionCode
num_unaligned_queryDescriptionCode
Methods description
_setupcode    nextTop
 Title   : _setup
Usage : $self->_setup(@args)
Function: Implementers should call this to setup common fields and deal with
common arguments to new().
Returns : n/a
Args : @args received in new().
namecodeprevnextTop
 Title   : name
Usage : $hit_name = $hit->name();
Function: returns the name of the Hit sequence
Returns : a scalar string
Args : none
The name of a hit is unique within a Result or within an Iteration.
descriptioncodeprevnextTop
 Title   : description
Usage : $desc = $hit->description();
Function: Retrieve the description for the hit
Returns : a scalar string
Args : none
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
locuscodeprevnextTop
 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
lengthcodeprevnextTop
 Title   : length
Usage : my $len = $hit->length
Function: Returns the length of the hit
Returns : integer
Args : none
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 : none
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 : none
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 : none
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 double for FASTA reports
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 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 Blast hit.
Example : $nhsps = $hit_object->num_hsps();
Returns : Integer
Argument : n/a
Throws : Exception if the HSPs have not been collected.
See Also : 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' or 'nomatch' or 'gap'
: (default = 'identical')
: (can be shortened to 'id' or 'cons')
: Note that 'conserved' includes identical unless you use
: 'conserved-not-identical'
: [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::HSPI::seq_inds()
rewindcodeprevnextTop
 Title   : rewind
Usage : $hit->rewind;
Function: Allow one to reset the HSP iterator to the beginning if possible
Returns : none
Args : none
overlapcodeprevnextTop
 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 : Deprecated
Comments : This value isn't used for anything
ncodeprevnextTop
 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 : 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(), signif(),
Bio::Search::BlastUtils::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::HSPI object.
Argument : String (or no argument).
: No argument (default) = highest scoring HSP (same as 'best').
: 'best' = highest scoring HSP.
: 'worst' = lowest scoring HSP.
Throws : 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.
: 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 : length(), frac_aligned_query(),
frac_aligned_hit()
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)
each_accession_numbercodeprevnextTop
 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 (if there is one).
Returns : list of all accession numbers in the description
Args : none
tiled_hspscodeprevnextTop
 Usage     : $hit_object->tiled_hsps( [integer] );
Purpose : Gets/Sets an indicator for whether or not the HSPs in this Hit
: have been tiled.
Example : $hit_object->tiled_hsps(1);
: if( $hit_object->tiled_hsps ) { # do something }
Returns : Boolean (1 or 0)
Argument : integer (optional)
Throws : n/a
Status : Deprecated
Notes : This value is not used for anything
strandcodeprevnextTop
 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 : Bio::Search::HSP::HSPI::strand()
framecodeprevnextTop
 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 : hsps()
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, and excludes gaps.
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).
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')
Comments : If you need data for each HSP, use hsps() and then interate
: through each HSP object.
matchescodeprevnextTop
 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 : [0] class = 'id' | 'cons' OR none.
: [1] seq_type = 'query' or 'hit' or 'sbjct' (default = 'query')
: ('sbjct' is synonymous with 'hit')
: 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.)
startcodeprevnextTop
 Usage     : $sbjct->start( [seq_type] );
Purpose : Gets the start coordinate for the query, sbjct, or both sequences
: in the 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 : 'query' or 'hit' or 'sbjct' (default = 'query') ('sbjct' is
synonymous with 'hit')
endcodeprevnextTop
 Usage     : $sbjct->end( [seq_type] );
Purpose : Gets the end coordinate for the query, sbjct, or both sequences
: in the 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 : 'query' or 'hit' or 'sbjct' (default = 'query') ('sbjct' is
synonymous with 'hit')
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')
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')
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 : none
Comments : If you need data for each HSP, use hsps() and then interate
: through the HSP objects.
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 : none
Comments : If you need data for each HSP, use hsps() and then interate
: through the HSP objects.
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 : none
Comments : If you need data for each HSP, use hsps() and then interate
: through the HSP objects.
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 = $hit_object->num_unaligned_query();
Returns : Integer
Argument : none
Comments : If you need data for each HSP, use hsps() and then interate
: through the HSP objects.
Methods code
_setupdescriptionprevnextTop
sub _setup {
    my ($self, @args) = @_;
    
    # fields most subclasses probably will want
$self->_fields( { ( next_hsp => undef, num_hsps => undef, hsps => undef, hit_start => undef, query_start => undef, hit_end => undef, query_end => undef, length => undef, name => undef , accession => undef ) } ); my ($parent, $chunk, $hit_data) = $self->_rearrange([qw(PARENT CHUNK HIT_DATA)], @args); $self->throw("Need -parent or -chunk to be defined") unless $parent || $chunk; $self->parent($parent) if $parent; if ($chunk) { my ($io, $start, $end) = (undef, 0, undef); if (ref($chunk) eq 'ARRAY') { ($io, $start, $end) = @{$chunk}; } else { $io = $chunk; } $self->chunk($io, -start => $start, -end => $end); } $self->_raw_hit_data($hit_data) if $hit_data;
}
_raw_hit_datadescriptionprevnextTop
sub _raw_hit_data {
	my $self = shift;
	if (@_) {
		$self->{_raw_hit_data} = shift;
	}
	return $self->{_raw_hit_data};
}

#
# Some of these methods are written explitely to avoid HitI throwing not
# implemented; if it didn't do that then PullParserI AUTOLOAD would have
# cought them.
#
}
namedescriptionprevnextTop
sub name {
    return shift->get_field('name');
}
descriptiondescriptionprevnextTop
sub description {
    return shift->get_field('description');
}
accessiondescriptionprevnextTop
sub accession {
    return shift->get_field('accession');
}
locusdescriptionprevnextTop
sub locus {
    return shift->get_field('locus');
}
lengthdescriptionprevnextTop
sub length {
   return shift->get_field('length');
}
algorithmdescriptionprevnextTop
sub algorithm {
    return shift->get_field('algorithm');
}
raw_scoredescriptionprevnextTop
sub raw_score {
    return shift->get_field('score');
}
scoredescriptionprevnextTop
sub score {
    return shift->get_field('score');
}
significancedescriptionprevnextTop
sub significance {
    return shift->get_field('significance');
}
bitsdescriptionprevnextTop
sub bits {
    return shift->get_field('bits');
}
next_hspdescriptionprevnextTop
sub next_hsp {
    return shift->get_field('next_hsp');
}
hspsdescriptionprevnextTop
sub hsps {
    return shift->get_field('hsps');
}
num_hspsdescriptionprevnextTop
sub num_hsps {
    return shift->get_field('num_hsps');
}

#
# HitI/ GenericHit methods that are unrelated to simply parsing information
# directly out of a file, but need more complex calculation; mostly not
# implemented here.
#
}
seq_indsdescriptionprevnextTop
sub seq_inds {
    my ($self, $seqType, $class, $collapse) = @_;
    
    $seqType  ||= 'query';
    $class ||= 'identical';
    $collapse ||= 0;
    
    $seqType = 'hit' if $seqType eq 'sbjct';
    
	my $storage_name = '_seq_inds_'.$seqType.'_'.$class;
	unless (defined $self->{$storage_name}) {
		my @inds;    
		foreach my $hsp ($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, unless gaps.
if (@inds && $class ne 'gap') { my %tmp = map { $_, 1 } @inds; @inds = sort {$a <=> $b} keys %tmp; } $self->{$storage_name} =\@ inds; } my @inds = @{$self->{$storage_name}}; $collapse ? &Bio::Search::SearchUtils::collapse_nums(@inds) : @inds;
}
rewinddescriptionprevnextTop
sub rewind {
    shift->throw_not_implemented();
}
overlapdescriptionprevnextTop
sub overlap {
    my $self = shift;
    if (@_) { $self->{_overlap} = shift }
    return $self->{_overlap} || 0;
}
ndescriptionprevnextTop
sub n {
    return shift->get_field('num_hsps');
}
pdescriptionprevnextTop
sub p {
    shift->throw_not_implemented;
}
hspdescriptionprevnextTop
sub hsp {
    shift->throw_not_implemented;
}
logical_lengthdescriptionprevnextTop
sub logical_length {
    my ($self, $type) = @_;
    $type ||= 'query';
    $type = lc($type);
	$type = 'hit' if $type eq 'sbjct';
    if ($type eq 'query') {
        return $self->get_field('query_length');
    }
    elsif ($type eq 'hit') {
        return $self->get_field('length');
    }
}
rankdescriptionprevnextTop
sub rank {
    return shift->get_field('rank');
}
each_accession_numberdescriptionprevnextTop
sub each_accession_number {
    my $self = shift;
    my $accession = $self->get_field('accession') if $self->has_field('accession');
    my $desc = $self->get_field('description') if $self->has_field('description');
    return unless $accession || $desc;
    
    my @accnums;
    push (@accnums, $accession) if $accession;
    
    if (defined $desc) { 
        while ($desc =~ /(\b\S+\|\S*\|\S*\s?)/g) {
            my $id = $1;
            my $acc;
            if ($id =~ /(?:gb|emb|dbj|sp|pdb|bbs|ref|tp[gde])\|(.*)\|(?:.*)/) {
                ($acc) = split /\./, $1; 
            }
            elsif ($id =~ /(?:pir|prf|pat|gnl)\|(?:.*)\|(.*)/) {
                ($acc) = split /\./, $1;  
            }
            elsif ($id =~ /(?:gim|gi|bbm|bbs|lcl)\|(?:\d*)/) {
                $acc = $id;
            }
            elsif ($id =~ /(?:oth)\|(.*)\|(?:.*)\|(?:.*)/ ) { # discontinued...
$acc = $1; } else { $acc = $id; } push(@accnums, $acc); } } return @accnums;
}
tiled_hspsdescriptionprevnextTop
sub tiled_hsps {
    my $self = shift;
    if (@_) { $self->{_hsps_are_tiled} = shift }
    return $self->{_hsps_are_tiled} || 0;
}
stranddescriptionprevnextTop
sub strand {
    shift->throw_not_implemented;
}
framedescriptionprevnextTop
sub frame {
    shift->throw_not_implemented;
}
length_alndescriptionprevnextTop
sub length_aln {
    my ($self, $seqType) = @_;
    $seqType ||= 'query';
    $seqType = 'hit' if $seqType eq 'sbjct';
    
	my %non_gaps = map { $_, 1 } $self->seq_inds($seqType, 'conserved'),
							     $self->seq_inds($seqType, 'no_match');
	return scalar(keys %non_gaps);
}
gapsdescriptionprevnextTop
sub gaps {
    my ($self, $seqType) = @_;
    
    $seqType ||= (wantarray ? 'list' : 'total');
    $seqType = 'hit' if $seqType eq 'sbjct';
    
    if ($seqType =~ /list|array/i) {
        return (scalar($self->seq_inds('query', 'gap')), scalar($self->seq_inds('hit', 'gap')));
    }
    elsif ($seqType eq 'total') {
        return (scalar($self->seq_inds('query', 'gap')) + scalar($self->seq_inds('hit', 'gap'))) || 0;
    }
    else {
        return scalar($self->seq_inds($seqType, 'gap')) || 0;
    }
}
matchesdescriptionprevnextTop
sub matches {
    my ($self, $class, $seqType) = @_;
    
	# no query/hit choice? The answer differs depending on sequence, since
# hsps could overlap on one sequence and not the other. Added an option,
# but otherwise will assume 'hit'
$seqType ||= 'hit'; $seqType = 'hit' if $seqType eq 'sbjct'; unless (exists $self->{_id_matches}) { $self->{_id_matches}->{hit} = scalar($self->seq_inds('hit', 'identical')); $self->{_id_matches}->{query} = scalar($self->seq_inds('query', 'identical')); } unless (exists $self->{_con_matches}) { foreach my $type ('hit', 'query') { # 'conserved-not-identical' can give us 'identical' matches if hsps
# overlapped so have to get the difference
my %identicals = map { $_ => 1 } $self->seq_inds($type, 'identical'); my @conserved = $self->seq_inds($type, 'conserved-not-identical'); my $real_conserved; foreach (@conserved) { unless (exists $identicals{$_}) { $real_conserved++; } } $self->{_con_matches}->{$type} = $real_conserved; } } unless ($class) { return ($self->{_id_matches}->{$seqType}, $self->{_con_matches}->{$seqType}); } else { if ($class =~ /^id/i) { return $self->{_id_matches}->{$seqType}; } else { return $self->{_con_matches}->{$seqType}; } } return;
}
startdescriptionprevnextTop
sub start {
    my ($self, $seqType) = @_;
    
    unless ($self->get_field('num_hsps')) {
        Bio::Search::SearchUtils::_warn_about_no_hsps($self);
        return;
    }
    
    $seqType ||= (wantarray ? 'list' : 'query');
    $seqType = 'hit' if $seqType eq 'sbjct';
    
    if ($seqType =~ /list|array/i) {
	    return ($self->get_field('query_start'), $self->get_field('hit_start'));
	}
    elsif ($seqType eq 'hit') {
        return $self->get_field('hit_start');
	}
    elsif ($seqType eq 'query') {
        return $self->get_field('query_start');
    }
    else {
        $self->throw("Unknown sequence type '$seqType'");
    }
}
enddescriptionprevnextTop
sub end {
    my ($self, $seqType) = @_;
    
    unless ($self->get_field('num_hsps')) {
        Bio::Search::SearchUtils::_warn_about_no_hsps($self);
        return;
    }
    
    $seqType ||= (wantarray ? 'list' : 'query');
    $seqType = 'hit' if $seqType eq 'sbjct';
    
    if ($seqType =~ /list|array/i) {
	    return ($self->get_field('query_end'), $self->get_field('hit_end'));
	}
    elsif ($seqType eq 'hit') {
        return $self->get_field('hit_end');
	}
    elsif ($seqType eq 'query') {
        return $self->get_field('query_end');
    }
    else {
        $self->throw("Unknown sequence type '$seqType'");
    }
}
rangedescriptionprevnextTop
sub range {
    my ($self, $seqType) = @_;
    $seqType ||= 'query';
    $seqType = 'hit' if $seqType eq 'sbjct';
    return ($self->start($seqType), $self->end($seqType));
}
frac_identicaldescriptionprevnextTop
sub frac_identical {
    my ($self, $seqType) = @_;
    $seqType ||= 'query';
    $seqType = lc($seqType);
    $seqType = 'hit' if $seqType eq 'sbjct';
    
    my $ident = $self->matches('id', $seqType);
    my $total = $self->length_aln($seqType);
    my $ratio = $ident / $total;
my $ratio_rounded = sprintf( "%.3f", $ratio); # Round down if 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';
    $seqType = lc($seqType);
    $seqType = 'hit' if $seqType eq 'sbjct';
    
    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;
    return sprintf("%.2f", $self->length_aln('query') / $self->logical_length('query'));
}
frac_aligned_hitdescriptionprevnextTop
sub frac_aligned_hit {
    my $self = shift;
    return sprintf( "%.2f", $self->length_aln('sbjct') / $self->logical_length('sbjct'));
}
num_unaligned_hitdescriptionprevnextTop
sub num_unaligned_hit {
    my $self = shift;
    # why does this method even exist?!
return $self->gaps('hit');
}
num_unaligned_querydescriptionprevnextTop
sub num_unaligned_query {
    my $self = shift;
	# why does this method even exist?!
return $self->gaps('query'); } # aliasing for Steve's method names
*hit_description =\& description; *hit_length =\& length; 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 one
of the Bioperl mailing lists. Your participation is much appreciated.
  bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
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
the bugs and their resolution. Bug reports can be submitted via the
web:
  https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Sendu BalaTop
Email bix@sendu.me.uk
COPYRIGHTTop
Copyright (c) 2006 Sendu Bala. All Rights Reserved.
DISCLAIMERTop
This software is provided "as is" without warranty of any kind.
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _