Bio::Search::HSP GenericHSP
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Summary
Bio::Search::HSP::GenericHSP - A "Generic" implementation of a High Scoring Pair
Package variables
No package variables defined.
Included modules
Bio::Root::Root
Bio::Search::HSP::HSPI
Bio::SeqFeature::Similarity
Inherit
Bio::Root::Root Bio::Search::HSP::HSPI
Synopsis
    my $hsp = new Bio::Search::HSP::GenericHSP( -algorithm => 'blastp',
-evalue => '1e-30',
);
$r_type = $hsp->algorithm $pvalue = $hsp->p(); $evalue = $hsp->evalue(); $frac_id = $hsp->frac_identical( ['query'|'hit'|'total'] ); $frac_cons = $hsp->frac_conserved( ['query'|'hit'|'total'] ); $gaps = $hsp->gaps( ['query'|'hit'|'total'] ); $qseq = $hsp->query_string; $hseq = $hsp->hit_string; $homo_string = $hsp->homology_string; $len = $hsp->length( ['query'|'hit'|'total'] ); $len = $hsp->length( ['query'|'hit'|'total'] ); $rank = $hsp->rank;
Description
This implementation is "Generic", meaning it is is suitable for
holding information about High Scoring pairs from most Search reports
such as BLAST and FastA. Specialized objects can be derived from
this.
Methods
BEGIN Code
_calculate_seq_positionsDescriptionCode
algorithmDescriptionCode
bitsDescriptionCode
evalueDescriptionCode
frac_conservedDescriptionCode
frac_identicalDescriptionCode
frameDescriptionCode
gapsDescriptionCode
get_alnDescriptionCode
hit_stringDescriptionCode
homology_stringDescriptionCode
hsp_lengthDescriptionCode
lengthDescriptionCode
nDescriptionCode
newDescriptionCode
num_conservedDescriptionCode
num_identicalDescriptionCode
pvalueDescriptionCode
query_stringDescriptionCode
rangeDescriptionCode
rankDescriptionCode
scoreDescriptionCode
seq_indsDescriptionCode
Methods description
_calculate_seq_positionscode    nextTop
 Title   : _calculate_seq_positions
Usage : $self->_calculate_seq_positions
Function: Internal function
Returns :
Args :
algorithmcodeprevnextTop
 Title   : algorithm
Usage : my $r_type = $hsp->algorithm
Function: Obtain the name of the algorithm used to obtain the HSP
Returns : string (e.g., BLASTP)
Args : [optional] scalar string to set value
bitscodeprevnextTop
 Title   : bits
Usage : my $bits = $hsp->bits();
Function: Returns the bit value for this HSP or undef
Returns : numeric
Args : none
evaluecodeprevnextTop
 Title   : evalue
Usage : my $evalue = $hsp->evalue();
Function: Returns the e-value for this HSP
Returns : float or exponential (2e-10)
Args : [optional] numeric to set value
frac_conservedcodeprevnextTop
 Title    : frac_conserved
Usage : my $frac_cons = $hsp->frac_conserved( ['query'|'hit'|'total'] );
Function : Returns the fraction of conserved positions for this HSP.
This is the fraction of symbols in the alignment with a
positive score.
Returns : Float in range 0.0 -> 1.0
Args : arg 1: 'query' = num conserved / length of query seq (without gaps)
'hit' = num conserved / length of hit seq (without gaps)
'total' = num conserved / length of alignment (with gaps)
default = 'total'
arg 2: [optional] frac conserved value to set for the type requested
frac_identicalcodeprevnextTop
 Title   : frac_identical
Usage : my $frac_id = $hsp->frac_identical( ['query'|'hit'|'total'] );
Function: Returns the fraction of identitical positions for this HSP
Returns : Float in range 0.0 -> 1.0
Args : arg 1: 'query' = num identical / length of query seq (without gaps)
'hit' = num identical / length of hit seq (without gaps)
'total' = num identical / length of alignment (with gaps)
default = 'total'
arg 2: [optional] frac identical value to set for the type requested
framecodeprevnextTop
 Title   : frame
Usage : $hsp->frame($queryframe,$subjectframe)
Function: Set the Frame for both query and subject and insure that
they agree.
This overrides the frame() method implementation in
FeaturePair.
Returns : array of query and subjects if return type wants an array
or query frame if defined or subject frame
Args : none
Note : Frames are stored in the GFF way (0-2) not 1-3
as they are in BLAST (negative frames are deduced by checking
the strand of the query or hit)
gapscodeprevnextTop
 Title    : gaps
Usage : my $gaps = $hsp->gaps( ['query'|'hit'|'total'] );
Function : Get the number of gaps in the query, hit, or total alignment.
Returns : Integer, number of gaps or 0 if none
Args : arg 1: 'query' = num gaps in query seq
'hit' = num gaps in hit seq
'total' = num gaps in whole alignment
default = 'total'
arg 2: [optional] integer gap value to set for the type requested
get_alncodeprevnextTop
 Title   : get_aln
Usage : my $aln = $hsp->gel_aln
Function: Returns a Bio::SimpleAlign representing the HSP alignment
Returns : Bio::SimpleAlign
Args : none
hit_stringcodeprevnextTop
 Title   : hit_string
Usage : my $hseq = $hsp->hit_string;
Function: Retrieves the hit sequence of this HSP as a string
Returns : string
Args : [optional] string to set for hit sequence
homology_stringcodeprevnextTop
 Title   : homology_string
Usage : my $homo_string = $hsp->homology_string;
Function: Retrieves the homology sequence for this HSP as a string.
: The homology sequence is the string of symbols in between the
: query and hit sequences in the alignment indicating the degree
: of conservation (e.g., identical, similar, not similar).
Returns : string
Args : [optional] string to set for homology sequence
hsp_lengthcodeprevnextTop
 Title   : hsp_length
Usage : my $len = $hsp->hsp_length()
Function: shortcut length('hsp')
Returns : floating point between 0 and 100
Args : none
lengthcodeprevnextTop
 Title    : length
Usage : my $len = $hsp->length( ['query'|'hit'|'total'] );
Function : Returns the length of the query or hit in the alignment
(without gaps)
or the aggregate length of the HSP (including gaps;
this may be greater than either hit or query )
Returns : integer
Args : arg 1: 'query' = length of query seq (without gaps)
'hit' = length of hit seq (without gaps)
'total' = length of alignment (with gaps)
default = 'total'
arg 2: [optional] integer length value to set for specific type
ncodeprevnextTop
See documentation in Bio::Search::HSP::HSPI::n()
newcodeprevnextTop
 Title   : new
Usage : my $obj = new Bio::Search::HSP::GenericHSP();
Function: Builds a new Bio::Search::HSP::GenericHSP object
Returns : Bio::Search::HSP::GenericHSP
Args : -algorithm => algorithm used (BLASTP, TBLASTX, FASTX, etc)
-evalue => evalue
-pvalue => pvalue
-bits => bit value for HSP
-score => score value for HSP (typically z-score but depends on
analysis)
-hsp_length=> Length of the HSP (including gaps)
-identical => # of residues that that matched identically
-conserved => # of residues that matched conservatively
(only protein comparisions;
conserved == identical in nucleotide comparisons)
-hsp_gaps => # of gaps in the HSP
-query_gaps => # of gaps in the query in the alignment
-hit_gaps => # of gaps in the subject in the alignment
-query_name => HSP Query sequence name (if available)
-query_start => HSP Query start (in original query sequence coords)
-query_end => HSP Query end (in original query sequence coords)
-hit_name => HSP Hit sequence name (if available)
-hit_start => HSP Hit start (in original hit sequence coords)
-hit_end => HSP Hit end (in original hit sequence coords)
-hit_length => total length of the hit sequence
-query_length=> total length of the query sequence
-query_seq => query sequence portion of the HSP
-hit_seq => hit sequence portion of the HSP
-homology_seq=> homology sequence for the HSP
-hit_frame => hit frame (only if hit is translated protein)
-query_frame => query frame (only if query is translated protein)
-rank => HSP rank
num_conservedcodeprevnextTop
 Title   : num_conserved
Usage : $obj->num_conserved($newval)
Function: returns the number of conserved residues in the alignment
Returns : inetger
Args : integer (optional)
num_identicalcodeprevnextTop
 Title   : num_identical
Usage : $obj->num_identical($newval)
Function: returns the number of identical residues in the alignment
Returns : integer
Args : integer (optional)
pvaluecodeprevnextTop
 Title   : pvalue
Usage : my $pvalue = $hsp->pvalue();
Function: Returns the P-value for this HSP or undef
Returns : float or exponential (2e-10)
P-value is not defined with NCBI Blast2 reports.
Args : [optional] numeric to set value
query_stringcodeprevnextTop
 Title   : query_string
Usage : my $qseq = $hsp->query_string;
Function: Retrieves the query sequence of this HSP as a string
Returns : string
Args : [optional] string to set for query sequence
rangecodeprevnextTop
See documentation in Bio::Search::HSP::HSPI::range()
rankcodeprevnextTop
 Usage     : $hsp->rank( [string] );
Purpose : Get the rank of the HSP within a given Blast hit.
Example : $rank = $hsp->rank;
Returns : Integer (1..n) corresponding to the order in which the HSP
appears in the BLAST report.
scorecodeprevnextTop
 Title   : score
Usage : my $score = $hsp->score();
Function: Returns the score for this HSP or undef
Returns : numeric
Args : [optional] numeric to set value
seq_indscodeprevnextTop
 Title   : seq_inds
Purpose : Get a list of residue positions (indices) for all identical
: or conserved residues in the query or sbjct sequence.
Example : @s_ind = $hsp->seq_inds('query', 'identical');
: @h_ind = $hsp->seq_inds('hit', 'conserved');
@h_ind = $hsp->seq_inds('hit', 'conserved-not-identical');
: @h_ind = $hsp->seq_inds('hit', 'conserved', 1);
Returns : List of integers
: May include ranges if collapse is true.
Argument : seq_type = 'query' or 'hit' or 'sbjct' (default = query)
: ('sbjct' is synonymous with 'hit')
: class = 'identical' or 'conserved' or 'nomatch' or 'gap'
: (default = identical)
: (can be shortened to 'id' or 'cons')
: or 'conserved-not-identical'
: collapse = boolean, if true, 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.
Comments :
See Also : Bio::Search::SearchUtils::collapse_nums(),
Bio::Search::Hit::HitI::seq_inds()
Methods code
BEGINTop
BEGIN {
    $GAP_SYMBOL = '-';
}
_calculate_seq_positionsdescriptionprevnextTop
sub _calculate_seq_positions {
    my ($self,@args) = @_;
    return unless ( $self->{'_sequenceschanged'} );
    $self->{'_sequenceschanged'} = 0;
    my ($mchar, $schar, $qchar);
    my ($seqString, $qseq,$sseq) = ( $self->homology_string(),
				     $self->query_string(),
				     $self->hit_string() );

    # Using hashes to avoid saving duplicate residue numbers.
my %identicalList_query = (); my %identicalList_sbjct = (); my %conservedList_query = (); my %conservedList_sbjct = (); my %gapList_query = (); my %gapList_sbjct = (); my %nomatchList_query = (); my %nomatchList_sbjct = (); my $qdir = $self->query->strand || 1; my $sdir = $self->hit->strand || 1; my $resCount_query = ($qdir >=0) ? $self->query->end : $self->query->start; my $resCount_sbjct = ($sdir >=0) ? $self->hit->end : $self->hit->start; my $prog = $self->algorithm; if( $prog =~ /FAST/i ) { # fasta reports some extra 'regional' sequence information
# we need to clear out first
# this seemed a bit insane to me at first, but it appears to
# work --jason
# we infer the end of the regional sequence where the first
# non space is in the homology string
# then we use the HSP->length to tell us how far to read
# to cut off the end of the sequence
# one possible problem is the sequence which
my ($start) = (0); if( $seqString =~ /^(\s+)/ ) { $start = CORE::length($1); } $seqString = substr($seqString, $start,$self->length('total')); $qseq = substr($qseq, $start,$self->length('total')); $sseq = substr($sseq, $start,$self->length('total')); $qseq =~ s![\\\/]!!g; $sseq =~ s![\\\/]!!g; } if($prog =~ /^(PSI)?T(BLAST|FAST)N/oi ) { $resCount_sbjct = int($resCount_sbjct / 3);
} elsif($prog =~ /^(BLAST|FAST)(X|Y|XY)/oi ) { $resCount_query = int($resCount_query / 3);
} elsif($prog =~ /^T(BLAST|FAST)(X|Y|XY)/oi ) { $resCount_query = int($resCount_query / 3);
$resCount_sbjct = int($resCount_sbjct / 3);
} while( $mchar = chop($seqString) ) { ($qchar, $schar) = (chop($qseq), chop($sseq)); if( $mchar eq '+' || $mchar eq '.' || $mchar eq ':' ) { $conservedList_query{ $resCount_query } = 1; $conservedList_sbjct{ $resCount_sbjct } = 1; } elsif( $mchar ne ' ' ) { $identicalList_query{ $resCount_query } = 1; $identicalList_sbjct{ $resCount_sbjct } = 1; } elsif( $mchar eq ' ') { $nomatchList_query{ $resCount_query } = 1; $nomatchList_sbjct{ $resCount_sbjct } = 1; } if( $qchar eq $GAP_SYMBOL ) { $gapList_query{ $resCount_query } ++; } else { $resCount_query -= $qdir; } if( $schar eq $GAP_SYMBOL ) { $gapList_sbjct{ $resCount_query } ++; } else { $resCount_sbjct -=$sdir; } } $self->{'_identicalRes_query'} =\% identicalList_query; $self->{'_conservedRes_query'} =\% conservedList_query; $self->{'_nomatchRes_query'} =\% nomatchList_query; $self->{'_gapRes_query'} =\% gapList_query; $self->{'_identicalRes_sbjct'} =\% identicalList_sbjct; $self->{'_conservedRes_sbjct'} =\% conservedList_sbjct; $self->{'_nomatchRes_sbjct'} =\% nomatchList_sbjct; $self->{'_gapRes_sbjct'} =\% gapList_sbjct; return 1;
}
algorithmdescriptionprevnextTop
sub algorithm {
    my ($self,$value) = @_;
    my $previous = $self->{'_algorithm'};
    if( defined $value || ! defined $previous ) { 
	$value = $previous = '' unless defined $value;
	$self->{'_algorithm'} = $value;
    } 

    return $previous;
}
bitsdescriptionprevnextTop
sub bits {
    my ($self,$value) = @_;
    my $previous = $self->{'_bits'};
    if( defined $value ) { 
        $self->{'_bits'} = $value;
    } 
    return $previous;
}
evaluedescriptionprevnextTop
sub evalue {
 shift->significance(@_)
}
frac_conserveddescriptionprevnextTop
sub frac_conserved {
    my ($self, $type,$value) = @_;
    $type = lc $type if defined $type;
    $type = 'total' if( ! defined $type ||
			$type !~ /query|hit|total/);
    my $previous = $self->{'_frac_conserved'}->{$type};
    if( defined $value || ! defined $previous ) { 
	$value = $previous = '' unless defined $value;
	$self->{'_frac_conserved'}->{$type} = $value;
    } 
    return $previous;
}
frac_identicaldescriptionprevnextTop
sub frac_identical {
   my ($self, $type,$value) = @_;

   $type = lc $type if defined $type;
   $type = 'total' if( ! defined $type ||
		       $type !~ /query|hit|total/); 
   my $previous = $self->{'_frac_identical'}->{$type};
   if( defined $value || ! defined $previous ) { 
       $value = $previous = '' unless defined $value;
       if( $type eq 'hit' || $type eq 'query' ) {
	   $self->$type()->frac_identical( $value);
       }
       $self->{'_frac_identical'}->{$type} = $value;
   } 
   return $previous;
}
framedescriptionprevnextTop
sub frame {
    my ($self, $qframe, $sframe) = @_;
    if( defined $qframe ) {
	if( $qframe == 0 ) {
	    $qframe = 0;
	} elsif( $qframe !~ /^([+-])?([1-3])/ ) {
	    $self->warn("Specifying an invalid query frame ($qframe)");
	    $qframe = undef;
	} else {
	    my $dir = $1;
	    $dir = '+' unless defined $dir;
	    if( ($dir eq '-' && $self->query->strand >= 0) ||
		($dir eq '+' && $self->query->strand <= 0) ) {
		$self->warn("Query frame ($qframe) did not match strand of query (". $self->query->strand() . ")");
	    }
	    # Set frame to GFF [0-2] -
# what if someone tries to put in a GFF frame!
$qframe = $2 - 1; } $self->query->frame($qframe); } if( defined $sframe ) { if( $sframe == 0 ) { $sframe = 0; } elsif( $sframe !~ /^([+-])?([1-3])/ ) { $self->warn("Specifying an invalid subject frame ($sframe)"); $sframe = undef; } else { my $dir = $1; $dir = '+' unless defined $dir; if( ($dir eq '-' && $self->hit->strand >= 0) || ($dir eq '+' && $self->hit->strand <= 0) ) { $self->warn("Subject frame ($sframe) did not match strand of subject (". $self->hit->strand() . ")"); } # Set frame to GFF [0-2]
$sframe = $2 - 1; } $self->hit->frame($sframe); } if (wantarray() && $self->algorithm =~ /^T(BLAST|FAST)(X|Y|XY)/oi) { return ($self->query->frame(), $self->hit->frame()); } elsif (wantarray()) { ($self->query->frame() && return ($self->query->frame(), undef)) || ($self->hit->frame() && return (undef, $self->hit->frame())); } else { ($self->query->frame() && return $self->query->frame()) || ($self->hit->frame() && return $self->hit->frame()); }
}
gapsdescriptionprevnextTop
sub gaps {
    my ($self, $type,$value) = @_;
    $type = lc $type if defined $type;
    $type = 'total' if( ! defined $type ||
			$type !~ /query|hit|subject|sbjct|total/);
    $type = 'hit' if $type =~ /sbjct|subject/;
    my $previous = $self->{'_gaps'}->{$type};
    if( defined $value || ! defined $previous ) { 
	$value = $previous = '' unless defined $value;
	$self->{'_gaps'}->{$type} = $value;
    }
    return $previous || 0;
}
get_alndescriptionprevnextTop
sub get_aln {
    my ($self) = @_;
    require Bio::LocatableSeq;
    require Bio::SimpleAlign;
    my $aln = new Bio::SimpleAlign;
    my $hs = $self->hit_string();
    my $qs = $self->query_string();
    # FASTA specific stuff moved to the FastaHSP object
my $seqonly = $qs; $seqonly =~ s/[\-\s]//g; my ($q_nm,$s_nm) = ($self->query->seq_id(), $self->hit->seq_id()); unless( defined $q_nm && CORE::length ($q_nm) ) { $q_nm = 'query'; } unless( defined $s_nm && CORE::length ($s_nm) ) { $s_nm = 'hit'; } my $query = new Bio::LocatableSeq('-seq' => $qs, '-id' => $q_nm, '-start' => 1, '-end' => CORE::length($seqonly), ); $seqonly = $hs; $seqonly =~ s/[\-\s]//g; my $hit = new Bio::LocatableSeq('-seq' => $hs, '-id' => $s_nm, '-start' => 1, '-end' => CORE::length($seqonly), ); $aln->add_seq($query); $aln->add_seq($hit); return $aln;
}
hit_stringdescriptionprevnextTop
sub hit_string {
    my ($self,$value) = @_;
    my $previous = $self->{'_hit_string'};
    if( defined $value || ! defined $previous ) { 
	$value = $previous = '' unless defined $value;
	$self->{'_hit_string'} = $value;
	# do some housekeeping so we know when to 
# re-run _calculate_seq_positions
$self->{'_sequenceschanged'} = 1; } return $previous;
}
homology_stringdescriptionprevnextTop
sub homology_string {
    my ($self,$value) = @_;
    my $previous = $self->{'_homology_string'};
    if( defined $value || ! defined $previous ) { 
	$value = $previous = '' unless defined $value;
	$self->{'_homology_string'} = $value;
	# do some housekeeping so we know when to 
# re-run _calculate_seq_positions
$self->{'_sequenceschanged'} = 1; } return $previous;
}
hsp_lengthdescriptionprevnextTop
sub hsp_length {
 return shift->length('hsp', shift);
}
lengthdescriptionprevnextTop
sub length {
    my $self = shift;
    my $type = shift;

    $type = 'total' unless defined $type;
    $type = lc $type;

    if( $type =~ /^q/i ) {
	return $self->query()->length(shift);
    } elsif( $type =~ /^(hit|subject|sbjct)/ ) {
	return $self->hit()->length(shift);
    } else { 
	my $v = shift;
	if( defined $v ) { 
	    $self->{'_hsplength'} = $v;
	}
	return $self->{'_hsplength'};
   }
    return 0; # should never get here
}
ndescriptionprevnextTop
sub n {
     my $self = shift; 
    if(@_) { $self->{'_n'} = shift; }
    defined $self->{'_n'} ? $self->{'_n'} : '';
}
newdescriptionprevnextTop
sub new {
    my($class,@args) = @_;

    my $self = $class->SUPER::new(@args);
    my ($algo, $evalue, $pvalue, $identical, $conserved, 
	$gaps, $query_gaps, $hit_gaps,
	$hit_seq, $query_seq, $homology_seq,
	$hsp_len, $query_len,$hit_len,
	$hit_name,$query_name,$bits,$score,
	$hs,$he,$qs,$qe,
	$qframe,$hframe,
	$rank) = $self->_rearrange([qw(ALGORITHM
				       EVALUE
				       PVALUE
				       IDENTICAL
				       CONSERVED
				       HSP_GAPS
				       QUERY_GAPS
				       HIT_GAPS
				       HIT_SEQ
				       QUERY_SEQ
				       HOMOLOGY_SEQ
				       HSP_LENGTH
				       QUERY_LENGTH
				       HIT_LENGTH
				       HIT_NAME
				       QUERY_NAME
				       BITS
				       SCORE
				       HIT_START
				       HIT_END
				       QUERY_START
				       QUERY_END
				       QUERY_FRAME
				       HIT_FRAME
				       RANK
				       )], @args);

    $algo = 'GENERIC' unless defined $algo;
    $self->algorithm($algo);

#    defined $evalue    && $self->evalue($evalue)
# $hsp->significance is initialized by the
# the SimilarityPair object - let's only keep one
# value, don't need 2 slots.
defined $pvalue && $self->pvalue($pvalue); defined $bits && $self->bits($bits); defined $score && $self->score($score); my ($queryfactor, $hitfactor) = (0,0); if( $algo =~ /^(PSI)?T(BLAST|FAST)[NY]/oi ) { $hitfactor = 1; } elsif ($algo =~ /^(FAST|BLAST)(X|Y|XY)/oi ) { $queryfactor = 1; } elsif ($algo =~ /^T(BLAST|FAST)(X|Y|XY)/oi || $algo =~ /^(BLAST|FAST)N/oi || $algo eq 'WABA' || $algo eq 'EXONERATE' || $algo eq 'MEGABLAST' || $algo eq 'SMITH-WATERMAN' ){ $hitfactor = 1; $queryfactor = 1; } elsif( $algo eq 'RPSBLAST' ) { $queryfactor = $hitfactor = 0; $qframe = $hframe = 0; } # Store the aligned query as sequence feature
my $strand; unless( defined $qe && defined $qs ) { $self->throw("Did not specify a Query End or Query Begin @args ($qs,$qe)"); } unless( defined $he && defined $hs ) { $self->throw("Did not specify a Hit End or Hit Begin"); } if ($qe > $qs) { # normal query: start < end
if ($queryfactor) { $strand = 1; } else { $strand = undef; } } else { # reverse query (i dont know if this is possible,
# but feel free to correct)
if ($queryfactor) { $strand = -1; } else { $strand = undef; } ($qs,$qe) = ($qe,$qs); } $self->query( new Bio::SeqFeature::Similarity ('-primary' => $self->primary_tag, '-start' => $qs, '-expect' => $evalue, '-bits' => $bits, '-end' => $qe, '-strand' => $strand, '-seq_id' => $query_name, '-seqlength'=> $query_len, '-source' => $algo, ) ); # to determine frame from something like FASTXY which doesn't
# report the frame
if( defined $strand && ! defined $qframe && $queryfactor ) { $qframe = ( $self->query->start % 3 ) * $strand; } elsif( ! defined $strand ) { $qframe = 0; } # store the aligned subject as sequence feature
if ($he > $hs) { # normal subject
if ($hitfactor) { $strand = 1; } else { $strand = undef; } } else { if ($hitfactor) { $strand = -1; } else { $strand = undef; } ($hs,$he) = ( $he,$hs); # reverse subject: start bigger than end
} $self->hit( Bio::SeqFeature::Similarity->new ('-start' => $hs, '-end' => $he, '-strand' => $strand, '-expect' => $evalue, '-bits' => $bits, '-source' => $algo, '-seq_id' => $hit_name, '-seqlength' => $hit_len, '-primary' => $self->primary_tag )); if( defined $strand && ! defined $hframe && $hitfactor ) { $hframe = ( $hs % 3 ) * $strand; } elsif( ! defined $strand ) { $hframe = 0; } $self->frame($qframe,$hframe); if( ! defined $query_len || ! defined $hit_len ) { $self->throw("Must defined hit and query length"); } if( ! defined $identical ) { $self->warn("Did not defined the number of identical matches in the HSP assuming 0"); $identical = 0; } if( ! defined $conserved ) { $self->warn("Did not defined the number of conserved matches in the HSP assuming conserved == identical ($identical)") if( $algo !~ /^((FAST|BLAST)N)|Exonerate/oi); $conserved = $identical; } # protect for divide by zero if user does not specify
# hsp_len, query_len, or hit_len
$self->num_identical($identical); $self->num_conserved($conserved); if( $hsp_len ) { $self->length('total', $hsp_len); $self->frac_identical( 'total', $identical / $self->length('total'));
$self->frac_conserved( 'total', $conserved / $self->length('total'));
} if( $hit_len ) { # $self->length('hit', $self->hit->length);
$self->frac_identical( 'hit', $identical / $self->length('hit'));
$self->frac_conserved( 'hit', $conserved / $self->length('hit'));
} if( $query_len ) { # $self->length('query', $self->query->length);
$self->frac_identical( 'query', $identical / $self->length('query')) ;
$self->frac_conserved( 'query', $conserved / $self->length('query'));
} $self->query_string($query_seq); $self->hit_string($hit_seq); $self->homology_string($homology_seq); if( defined $query_gaps ) { $self->gaps('query', $query_gaps); } elsif( defined $query_seq ) { $self->gaps('query', scalar ( $query_seq =~ tr/\-//)); } if( defined $hit_gaps ) { $self->gaps('hit', $hit_gaps); } elsif( defined $hit_seq ) { $self->gaps('hit', scalar ( $hit_seq =~ tr/\-//)); } if( ! defined $gaps ) { $gaps = $self->gaps("query") + $self->gaps("hit"); } $self->gaps('total', $gaps); $self->percent_identity($identical / $hsp_len ) if( $hsp_len > 0 );
$rank && $self->rank($rank); return $self;
}
num_conserveddescriptionprevnextTop
sub num_conserved {
   my ($self,$value) = @_;
   if( defined $value) {
       $self->{'num_conserved'} = $value;
   }
   return $self->{'num_conserved'};
}
num_identicaldescriptionprevnextTop
sub num_identical {
   my ($self,$value) = @_;
   if( defined $value) {
       $self->{'_num_identical'} = $value;
   }
   return $self->{'_num_identical'};
}
pvaluedescriptionprevnextTop
sub pvalue {
    my ($self,$value) = @_;
    my $previous = $self->{'_pvalue'};
    if( defined $value  ) { 	
	$self->{'_pvalue'} = $value;
    } 
    return $previous;
}
query_stringdescriptionprevnextTop
sub query_string {
    my ($self,$value) = @_;
    my $previous = $self->{'_query_string'};
    if( defined $value || ! defined $previous ) { 
	$value = $previous = '' unless defined $value;
	$self->{'_query_string'} = $value;
	# do some housekeeping so we know when to 
# re-run _calculate_seq_positions
$self->{'_sequenceschanged'} = 1; } return $previous;
}
rangedescriptionprevnextTop
sub range {
#----------
my ($self, $seqType) = @_; $seqType ||= 'query'; $seqType = 'sbjct' if $seqType eq 'hit'; my ($start, $end); if( $seqType eq 'query' ) { $start = $self->query->start; $end = $self->query->end; } else { $start = $self->hit->start; $end = $self->hit->end; } return ($start, $end); } 1;
}
rankdescriptionprevnextTop
sub rank {
     my ($self,$value) = @_;
    if( defined $value) {
	$self->{'_rank'} = $value;
    }
    return $self->{'_rank'};
}
scoredescriptionprevnextTop
sub score {
    my ($self,$value) = @_;
    my $previous = $self->{'_score'};
    if( defined $value ) { 
        $self->{'_score'} = $value;
    } 
    return $previous;
}
seq_indsdescriptionprevnextTop
sub seq_inds {
   my ($self, $seqType, $class, $collapse) = @_;

   # prepare the internal structures - this is cached so
# if the strings have not changed we're okay
$self->_calculate_seq_positions(); $seqType ||= 'query'; $class ||= 'identical'; $collapse ||= 0; $seqType = 'sbjct' if $seqType eq 'hit'; my $t = lc(substr($seqType,0,1)); if( $t eq 'q' ) { $seqType = 'query'; } elsif ( $t eq 's' || $t eq 'h' ) { $seqType = 'sbjct'; } else { $self->warn("unknown seqtype $seqType using 'query'"); $seqType = 'query'; } $t = lc(substr($class,0,1)); if( $t eq 'c' ) { if( $class =~ /conserved\-not\-identical/ ) { $class = 'conserved'; } else { $class = 'conservedall'; } } elsif( $t eq 'i' ) { $class = 'identical'; } elsif( $t eq 'n' ) { $class = 'nomatch'; } elsif( $t eq 'g' ) { $class = 'gap'; } else { $self->warn("unknown sequence class $class using 'identical'"); $class = 'identical'; } ## Sensitive to member name changes.
$seqType = "_\L$seqType\E"; $class = "_\L$class\E"; my @ary; if( $class eq '_gap' ) { # this means that we are remapping the gap length that is stored
# in the hash (for example $self->{'_gapRes_query'} )
# so we'll return an array which has the values of the position of the
# of the gap (the key in the hash) + the gap length (value in the
# hash for this key - 1.
@ary = map { $_ > 1 ? $_..($_ + $self->{"${class}Res$seqType"}->{$_} - 1) : $_ } sort { $a <=> $b } keys %{ $self->{"${class}Res$seqType"}}; } elsif( $class eq '_conservedall' ) { @ary = sort { $a <=> $b } keys %{ $self->{"_conservedRes$seqType"}}, keys %{ $self->{"_identicalRes$seqType"}}, } else { @ary = sort { $a <=> $b } keys %{ $self->{"${class}Res$seqType"}}; } require Bio::Search::BlastUtils if $collapse; return $collapse ? &Bio::Search::SearchUtils::collapse_nums(@ary) : @ary;
}
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/MailList.shtml - About the mailing lists
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
email or the web:
  bioperl-bugs@bioperl.org
http://bugzilla.bioperl.org/
AUTHOR - Jason Stajich and Steve ChervitzTop
Email jason@bioperl.org
Email sac@bioperl.org
Describe contact details here
CONTRIBUTORSTop
Additional contributors names and emails here
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
Bio::Search::HSP::HSPI methodsTop
Implementation of Bio::Search::HSP::HSPI methods follow
percent_identityTop
 Title   : percent_identity
Usage : my $percentid = $hsp->percent_identity()
Function: Returns the calculated percent identity for an HSP
Returns : floating point between 0 and 100
Args : none
Inherited from Bio::SeqFeature::SimilarityPairTop
These methods come from Bio::SeqFeature::SimilarityPair
queryTop
 Title   : query
Usage : my $query = $hsp->query
Function: Returns a SeqFeature representing the query in the HSP
Returns : Bio::SeqFeature::Similarity
Args : [optional] new value to set
hitTop
 Title   : hit
Usage : my $hit = $hsp->hit
Function: Returns a SeqFeature representing the hit in the HSP
Returns : Bio::SeqFeature::Similarity
Args : [optional] new value to set
significanceTop
 Title   : significance
Usage : $evalue = $obj->significance();
$obj->significance($evalue);
Function: Get/Set the significance value
Returns : numeric
Args : [optional] new value to set
strandTop
 Title   : strand
Usage : $hsp->strand('quer')
Function: Retrieves the strand for the HSP component requested
Returns : +1 or -1 (0 if unknown)
Args : 'hit' or 'subject' or 'sbjct' to retrieve the strand of the subject
'query' to retrieve the query strand (default)
Private methodsTop