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::SeqFeature::Similarity
Inherit
Bio::Search::HSP::HSPI
Synopsis
    my $hsp = Bio::Search::HSP::GenericHSP->new( -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;
# TODO: Describe how to configure a SearchIO stream so that it generates
# GenericHSP objects.
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.
Unless you're writing a parser, you won't ever need to create a
GenericHSP or any other HSPI-implementing object. If you use
the SearchIO system, HSPI objects are created automatically from
a SearchIO stream which returns Bio::Search::Result::ResultI objects
and you get the HSPI objects via the ResultI API.
For documentation on what you can do with GenericHSP (and other HSPI
objects), please see the API documentation in
Bio::Search::HSP::HSPI.
Methods
newDescriptionCode
_logical_length
No description
Code
algorithmDescriptionCode
pvalueDescriptionCode
evalueDescriptionCode
frac_identicalDescriptionCode
frac_conservedDescriptionCode
gapsDescriptionCode
query_stringDescriptionCode
hit_stringDescriptionCode
homology_stringDescriptionCode
lengthDescriptionCode
hsp_lengthDescriptionCode
percent_identityDescriptionCode
frameDescriptionCode
get_alnDescriptionCode
num_conservedDescriptionCode
num_identicalDescriptionCode
rankDescriptionCode
seq_indsDescriptionCode
ambiguous_seq_indsDescriptionCode
queryDescriptionCode
feature1
No description
Code
hitDescriptionCode
feature2
No description
Code
significanceDescriptionCode
_calculate_seq_positionsDescriptionCode
_calculate_seq_offsets
No description
Code
nDescriptionCode
rangeDescriptionCode
linksDescriptionCode
hsp_groupDescriptionCode
hit_featuresDescriptionCode
cigar_stringDescriptionCode
generate_cigar_stringDescriptionCode
_sub_cigar_string
No description
Code
_pre_seq_feature
No description
Code
_query_seq_feature
No description
Code
_subject_seq_feature
No description
Code
_pre_similar_stats
No description
Code
_pre_frac
No description
Code
_pre_gaps
No description
Code
_pre_pi
No description
Code
Methods description
newcode    nextTop
 Title   : new
Usage : my $obj = Bio::Search::HSP::GenericHSP->new();
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
-percent_identity => (optional) percent identity
-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)
-query_length=> total length of the query sequence
-query_seq => query sequence portion of the HSP
-query_desc => textual description of the query
-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
-hit_seq => hit sequence portion of the HSP
-hit_desc => textual description of the hit
-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
-links => HSP links information (WU-BLAST only)
-hsp_group => HSP Group informat (WU-BLAST only)
-gap_symbol => symbol representing a gap (default = '-')
-hit_features=> string of features found in or near HSP hit
region (reported in some BLAST text output,
v. 2.2.13 and up)
-stranded => If the algorithm isn't known (i.e. defaults to
'generic'), setting this will indicate start/end
coordinates are to be used to determine the strand
for 'query', 'subject', 'hit', 'both', or 'none'
(default = 'none')
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
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
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_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)
synonyms: 'sbjct', 'subject'
'total' = num identical / length of alignment (with gaps)
synonyms: 'hsp'
default = 'total'
arg 2: [optional] frac identical value to set for the type requested
Note : for translated sequences, this adjusts the length accordingly
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)
synonyms: 'sbjct', 'subject'
'total' = num conserved / length of alignment (with gaps)
synonyms: 'hsp'
default = 'total'
arg 2: [optional] frac conserved value to set for the type requested
gapscodeprevnextTop
 Title    : gaps
Usage : my $gaps = $hsp->gaps( ['query'|'hit'|'total'] );
Function : Get the number of gap characters in the query, hit, or total alignment.
Returns : Integer, number of gaps or 0 if none
Args : arg 1: 'query' = num gap characters in query seq
'hit' = num gap characters in hit seq; synonyms: 'sbjct', 'subject'
'total' = num gap characters in whole alignment; synonyms: 'hsp'
default = 'total'
arg 2: [optional] integer gap value to set for the type requested
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
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
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) (synonyms: sbjct, subject)
'total' = length of alignment (with gaps)
default = 'total'
arg 2: [optional] integer length value to set for specific type
hsp_lengthcodeprevnextTop
 Title   : hsp_length
Usage : my $len = $hsp->hsp_length()
Function: shortcut length('hsp')
Returns : floating point between 0 and 100
Args : none
percent_identitycodeprevnextTop
 Title   : percent_identity
Usage : my $percentid = $hsp->percent_identity()
Function: Returns the calculated percent identity for an HSP
Returns : floating point between 0 and 100
Args : none
framecodeprevnextTop
 Title   : frame
Usage : my ($qframe, $hframe) = $hsp->frame('list',$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 subject frame if return type wants an array
or query frame if defined or subject frame if not defined
Args : 'hit' or 'subject' or 'sbjct' to retrieve the frame of the subject (default)
'query' to retrieve the query frame
'list' or 'array' to retrieve both query and hit frames together
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)
get_alncodeprevnextTop
 Title   : get_aln
Usage : my $aln = $hsp->gel_aln
Function: Returns a Bio::SimpleAlign object representing the HSP alignment
Returns : Bio::SimpleAlign
Args : none
num_conservedcodeprevnextTop
 Title   : num_conserved
Usage : $obj->num_conserved($newval)
Function: returns the number of conserved residues in the alignment
Returns : integer
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)
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.
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' - identical positions
: 'conserved' - conserved positions
: 'nomatch' - mismatched residue or gap positions
: 'mismatch' - mismatched residue positions (no gaps)
: 'gap' - gap positions only
: 'frameshift'- frameshift positions only
: 'conserved-not-identical' - conserved positions w/o
: identical residues
: The name can be shortened to 'id' or 'cons' unless
: the name is . The default value is
: '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 : For HSPs partially or completely derived from translated sequences
: (TBLASTN, BLASTX, TBLASTX, or similar), some positional data
: cannot easily be attributed to a single position (i.e. the
: positional data is ambiguous). In these cases all three codon
: positions are reported. Under these conditions you can check
: ambiguous_seq_inds() to determine whether the query, subject,
: or both are ambiguous.
:
See Also : Bio::Search::SearchUtils::collapse_nums(),
Bio::Search::Hit::HitI::seq_inds()
ambiguous_seq_indscodeprevnextTop
 Title     : ambiguous_seq_inds
Purpose : returns a string denoting whether sequence indices for query,
: subject, or both are ambiguous
Returns : String; 'query', 'subject', 'query/subject', or empty string ''
Argument : none
Comments : For HSPs partially or completely derived from translated sequences
: (TBLASTN, BLASTX, TBLASTX, or similar), some positional data
: cannot easily be attributed to a single position (i.e. the
: positional data is ambiguous). In these cases all three codon
: positions are reported when using seq_inds(). Under these
: conditions you can check ambiguous_seq_inds() to determine whether
: the query, subject, or both are ambiguous.
See Also : Bio::Search::Hit::HSPI::seq_inds()
querycodeprevnextTop
 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
hitcodeprevnextTop
 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
significancecodeprevnextTop
 Title   : significance
Usage : $evalue = $obj->significance();
$obj->significance($evalue);
Function: Get/Set the significance value
Returns : numeric
Args : [optional] new value to set
_calculate_seq_positionscodeprevnextTop
 Title   : _calculate_seq_positions
Usage : $self->_calculate_seq_positions
Function: Internal function
Returns :
Args :
ncodeprevnextTop
See documentation in Bio::Search::HSP::HSPI::n()
rangecodeprevnextTop
See documentation in Bio::Search::HSP::HSPI::range()
linkscodeprevnextTop
 Title   : links
Usage : $obj->links($newval)
Function: Get/Set the Links value (from WU-BLAST)
Indicates the placement of the alignment in the group of HSPs
Returns : Value of links
Args : On set, new value (a scalar or undef, optional)
hsp_groupcodeprevnextTop
 Title   : hsp_group
Usage : $obj->hsp_group($newval)
Function: Get/Set the Group value (from WU-BLAST)
Indicates a grouping of HSPs
Returns : Value of group
Args : On set, new value (a scalar or undef, optional)
hit_featurescodeprevnextTop
 Title   : hit_features
Usage : $obj->hit_features($newval)
Function: Get/Set the HSP hit feature string (from some BLAST 2.2.13 text
output), which is a string of overlapping or nearby features in HSP
hit
Returns : Value of hit features, if present
Args : On set, new value (a scalar or undef, optional)
cigar_stringcodeprevnextTop
  Name:     cigar_string
Usage: $cigar_string = $hsp->cigar_string
Function: Generate and return cigar string for this HSP alignment
Args: No input needed
Return: a cigar string
generate_cigar_stringcodeprevnextTop
  Name:     generate_cigar_string
Usage: my $cigar_string = Bio::Search::HSP::GenericHSP::generate_cigar_string ($qstr, $hstr);
Function: generate cigar string from a simple sequence of alignment.
Args: the string of query and subject
Return: cigar string
Methods code
newdescriptionprevnextTop
sub new {
    my($class,%args) = @_;

    # don't pass anything to SUPER; complex hierarchy results in lots of work
# for nothing
my $self = $class->SUPER::new(); # for speed, don't use _rearrange and just store all input data directly
# with no method calls and no work done. work can be carried
# out just-in-time later if desired
while (my ($arg, $value) = each %args) { $arg =~ tr/a-z\055/A-Z/d; $self->{$arg} = $value; } my $bits = $self->{BITS}; defined $self->{VERBOSE} && $self->verbose($self->{VERBOSE}); if (exists $self->{GAP_SYMBOL}) { # not checking anything else but the length (must be 1 as only one gap
# symbol allowed currently); can add in support for symbol checks or
# multiple symbols later if needed
$self->throw("Gap symbol must be of length 1") if CORE::length($self->{GAP_SYMBOL}) != 1; } else { # dafault
$self->{GAP_SYMBOL} = '-'; } $self->{ALGORITHM} ||= 'GENERIC'; $self->{STRANDED} ||= 'NONE'; if (! defined $self->{QUERY_LENGTH} || ! defined $self->{HIT_LENGTH}) { $self->throw("Must define hit and query length"); } $self->{'_sequenceschanged'} = 1; $self->{_finished_new} = 1; return $self;
}
_logical_lengthdescriptionprevnextTop
sub _logical_length {
    my ($self, $type) = @_;
    if (!defined($self->{_sbjct_offset}) || !defined($self->{_query_offset})) {
        $self->_calculate_seq_offsets();
    }    
    my $key = $type =~ /sbjct|hit|tot/i ? 'sbjct' : 'query';
    
    my $offset = $self->{"_${key}_offset"};
    return $self->length($type) / $offset ;
}
algorithmdescriptionprevnextTop
sub algorithm {
    my ($self,$value) = @_;
    my $previous = $self->{'ALGORITHM'};
    if( defined $value || ! defined $previous ) {
        $value = $previous = '' unless defined $value;
        $self->{'ALGORITHM'} = $value;
    }

    return $previous;
}
pvaluedescriptionprevnextTop
sub pvalue {
    my ($self,$value) = @_;
    my $previous = $self->{'PVALUE'};
    if( defined $value  ) {
        $self->{'PVALUE'} = $value;
    }
    return $previous;
}
evaluedescriptionprevnextTop
sub evalue {
    my ($self,$value) = @_;
    my $previous = $self->{'EVALUE'};
    if( defined $value  ) {
        $self->{'EVALUE'} = $value;
    }
    return $previous;
}
frac_identicaldescriptionprevnextTop
sub frac_identical {
   my ($self, $type,$value) = @_;

    unless ($self->{_did_prefrac}) {
        $self->_pre_frac;
    }

   $type = lc $type if defined $type;
   $type = 'hit' if( defined $type &&
		     $type =~ /subject|sbjct/);
   $type = 'total' if( ! defined $type || $type eq 'hsp' ||
                        $type !~ /query|hit|subject|sbjct|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 $previous;
}
frac_conserveddescriptionprevnextTop
sub frac_conserved {
    my ($self, $type,$value) = @_;

    unless ($self->{_did_prefrac}) {
        $self->_pre_frac;
    }

    $type = lc $type if defined $type;
    $type = 'hit' if( defined $type && $type =~ /subject|sbjct/);
    $type = 'total' if( ! defined $type || $type eq 'hsp' ||
                        $type !~ /query|hit|subject|sbjct|total/);
    my $previous = $self->{'_frac_conserved'}->{$type};
    if( defined $value || ! defined $previous ) {
        $value = $previous = '' unless defined $value;
        $self->{'_frac_conserved'}->{$type} = $value;
    }
    return $previous;
}
gapsdescriptionprevnextTop
sub gaps {
    my ($self, $type, $value) = @_;

    unless ($self->{_did_pregaps}) {
        $self->_pre_gaps;
    }

    $type = lc $type if defined $type;
    $type = 'total' if( ! defined $type || $type eq 'hsp' ||
                        $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 $previous || 0;
}
query_stringdescriptionprevnextTop
sub query_string {
    my ($self,$value) = @_;
    my $previous = $self->{QUERY_SEQ};
    if( defined $value || ! defined $previous ) {
        $value = $previous = '' unless defined $value;
        $self->{QUERY_SEQ} = $value;
        # do some housekeeping so we know when to
# re-run _calculate_seq_positions
$self->{'_sequenceschanged'} = 1; } return $previous;
}
hit_stringdescriptionprevnextTop
sub hit_string {
    my ($self,$value) = @_;
    my $previous = $self->{HIT_SEQ};
    if( defined $value || ! defined $previous ) {
        $value = $previous = '' unless defined $value;
        $self->{HIT_SEQ} = $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_SEQ};
    if( defined $value || ! defined $previous ) {
        $value = $previous = '' unless defined $value;
        $self->{HOMOLOGY_SEQ} = $value;
        # do some housekeeping so we know when to
# re-run _calculate_seq_positions
$self->{'_sequenceschanged'} = 1; } return $previous;
}
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->{HSP_LENGTH} = $v;
        }
        return $self->{HSP_LENGTH};
   }
    return 0; # should never get here
}
hsp_lengthdescriptionprevnextTop
sub hsp_length {
 return shift->length('hsp', shift);
}
percent_identitydescriptionprevnextTop
sub percent_identity {
    my $self = shift;

    unless ($self->{_did_prepi}) {
        $self->_pre_pi;
    }

    return $self->SUPER::percent_identity(@_);
}
framedescriptionprevnextTop
sub frame {
    my $self = shift;
    my $val = shift;
    if (!defined $val) {
        # unfortunately, w/o args we need to warn about API changes
$self->warn("API for frame() has changed.\n". "Please refer to documentation for Bio::Search::HSP::GenericHSP;\n". "returning query frame"); $val = 'query'; } $val =~ s/^\s+//; if( $val =~ /^q/i ) { return $self->query->frame(@_); } elsif( $val =~ /^hi|^s/i ) { return $self->hit->frame(@_); } elsif ( $val =~ /^list|array/i ) { return ($self->query->frame($_[0]), $self->hit->frame($_[1]) ); } elsif ( $val =~ /^\d+$/) { # old API i.e. frame($query_frame, $hit_frame). This catches all but one
# case, where no arg is passed (so the hit is wanted).
$self->warn("API for frame() has changed.\n". "Please refer to documentation for Bio::Search::HSP::GenericHSP"); wantarray ? return ($self->query->frame($val), $self->hit->frame(@_) ) : return $self->hit->frame($val,@_); } else { $self->warn("unrecognized component '$val' requested\n"); } return 0;
}
get_alndescriptionprevnextTop
sub get_aln {
    my ($self) = @_;
    require Bio::LocatableSeq;
    require Bio::SimpleAlign;
    my $aln = Bio::SimpleAlign->new();
    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()); # Should we silently change the name of the query or hit if it isn't
# defined? May need revisiting... cjfields 2008-12-3 (commented out below)
#unless( defined $q_nm && CORE::length ($q_nm) ) {
# $q_nm = 'query';
#}
#unless( defined $s_nm && CORE::length ($s_nm) ) {
# $s_nm = 'hit';
#}
# mapping: 1 residues for every x coordinate positions
my $query = Bio::LocatableSeq->new('-seq' => $qs, '-id' => $q_nm, '-start' => $self->query->start, '-end' => $self->query->end, '-strand' => $self->query->strand, '-force_nse' => $q_nm ? 0 : 1, '-mapping' => [1, $self->{_query_mapping}] ); $seqonly = $hs; $seqonly =~ s/[\-\s]//g; my $hit = Bio::LocatableSeq->new('-seq' => $hs, '-id' => $s_nm, '-start' => $self->hit->start, '-end' => $self->hit->end, '-strand' => $self->hit->strand, '-force_nse' => $s_nm ? 0 : 1, '-mapping' => [1, $self->{_hit_mapping}] ); $aln->add_seq($query); $aln->add_seq($hit); return $aln;
}
num_conserveddescriptionprevnextTop
sub num_conserved {
    my ($self,$value) = @_;

    unless ($self->{_did_presimilar}) {
        $self->_pre_similar_stats;
    }

    if (defined $value) {
        $self->{CONSERVED} = $value;
    }
    return $self->{CONSERVED};
}
num_identicaldescriptionprevnextTop
sub num_identical {
   my ($self,$value) = @_;

   unless ($self->{_did_presimilar}) {
        $self->_pre_similar_stats;
    }

   if( defined $value) {
       $self->{IDENTICAL} = $value;
   }
   return $self->{IDENTICAL};
}
rankdescriptionprevnextTop
sub rank {
    my ($self,$value) = @_;
    if( defined $value) {
        $self->{RANK} = $value;
    }
    return $self->{RANK};
}
seq_indsdescriptionprevnextTop
sub seq_inds {
   my ($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 'm' ) { $class = 'mismatch'; } elsif( $t eq 'g' ) { $class = 'gap'; } elsif( $t eq 'f' ) { $class = 'frameshift'; } 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.
# changing this; since the index is the position prior to the insertion,
# repeat the position based on the number of gaps inserted
@ary = map { my @tmp; # position holds number of gaps inserted
for my $g (1..$self->{seqinds}{"${class}Res$seqType"}->{$_}) { push @tmp, $_ ; } @tmp} sort { $a <=> $b } keys %{ $self->{seqinds}{"${class}Res$seqType"}}; } elsif( $class eq '_conservedall' ) { @ary = sort { $a <=> $b } keys %{ $self->{seqinds}{"_conservedRes$seqType"}}, keys %{ $self->{seqinds}{"_identicalRes$seqType"}}, } else { @ary = sort { $a <=> $b } keys %{ $self->{seqinds}{"${class}Res$seqType"}}; } require Bio::Search::BlastUtils if $collapse; return $collapse ? &Bio::Search::SearchUtils::collapse_nums(@ary) : @ary;
}
ambiguous_seq_indsdescriptionprevnextTop
sub ambiguous_seq_inds {
    my $self = shift;
    $self->_calculate_seq_positions();
    my $type = ($self->{_query_offset} == 3 && $self->{_sbjct_offset} == 3) ?
        'query/subject' :
        ($self->{_query_offset} == 3) ? 'query' :
        ($self->{_sbjct_offset} == 3) ? 'subject' : '';
    return $type;
}
querydescriptionprevnextTop
sub query {
    my $self = shift;
    unless ($self->{_created_qff}) {
        $self->_query_seq_feature;
    }
    return $self->SUPER::query(@_);
}
feature1descriptionprevnextTop
sub feature1 {
    my $self = shift;
    if (! $self->{_finished_new} || $self->{_making_qff}) {
        return $self->{_sim1} if $self->{_sim1};
        $self->{_sim1} = Bio::SeqFeature::Similarity->new();
        return $self->{_sim1};
    }
    unless ($self->{_created_qff}) {
        $self->_query_seq_feature;
    }
    return $self->SUPER::feature1(@_);
}
hitdescriptionprevnextTop
sub hit {
    my $self = shift;
    unless ($self->{_created_sff}) {
        $self->_subject_seq_feature;
    }
    return $self->SUPER::hit(@_);
}
feature2descriptionprevnextTop
sub feature2 {
    my $self = shift;
    if (! $self->{_finished_new} || $self->{_making_sff}) {
        return $self->{_sim2} if $self->{_sim2};
        $self->{_sim2} = Bio::SeqFeature::Similarity->new();
        return $self->{_sim2};
    }
    unless ($self->{_created_sff}) {
        $self->_subject_seq_feature;
    }
    return $self->SUPER::feature2(@_);
}
significancedescriptionprevnextTop
sub significance {
    my ($self, $val) = @_;
    if (!defined $self->{SIGNIFICANCE} || defined $val) {
        $self->{SIGNIFICANCE} = defined $val ? $val :
                                defined $self->evalue ?  $self->evalue :
                                defined $self->pvalue ? $$self->pvalue :
                                undef;        
        $self->query->significance($self->{SIGNIFICANCE});
    }
    return $self->{SIGNIFICANCE};
}
_calculate_seq_positionsdescriptionprevnextTop
sub _calculate_seq_positions {
    my ($self,@args) = @_;
    return unless ( $self->{'_sequenceschanged'} );
    $self->{'_sequenceschanged'} = 0;
    my ($seqString, $qseq,$sseq) = ( $self->homology_string(),
                                     $self->query_string(),
                                     $self->hit_string() );
    my ($mlen, $qlen, $slen) = (CORE::length($seqString), CORE::length($qseq), CORE::length($sseq));
    my $qdir = $self->query->strand || 1;
    my $sdir = $self->hit->strand || 1;
    my ($resCount_query, $endpoint_query) = ($qdir <=0) ? ($self->query->end, $self->query->start)
        : ($self->query->start, $self->query->end);
    my ($resCount_sbjct, $endpoint_sbjct) = ($sdir <=0) ? ($self->hit->end, $self->hit->start)
        : ($self->hit->start, $self->hit->end);
    
    my $prog = $self->algorithm;
    
    if( $prog  =~ /FAST|SSEARCH|SMITH-WATERMAN/i ) {
    
        # we infer the end of the regional sequence where the first and last
# non spaces are 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
my ($start, $rest) = (0,0); if( $seqString =~ /^(\s+)?(.*?)\s*$/ ) { ($start, $rest) = ($1 ? CORE::length($1) : 0, CORE::length($2)); } $seqString = substr($seqString, $start, $rest); $qseq = substr($qseq, $start, $rest); $sseq = substr($sseq, $start, $rest); # commented out 10/29/08
# removing frameshift symbols doesn't take into account the following:
# 1) does not remove the same point in the homology string (get
# positional errors)
# 2) adjustments to the overall position in the string due to the
# frameshift must be taken into consideration (get balancing errors)
#
# Frameshifts will be handled directly in the main loop.
# --chris
# fasta reports some extra 'regional' sequence information
# we need to clear out first
# this seemed a bit insane to me at first, but it appears to
# work --jason
#$qseq =~ s![\\\/]!!g;
#$sseq =~ s![\\\/]!!g;
} if (!defined($self->{_sbjct_offset}) || !defined($self->{_query_offset})) { $self->_calculate_seq_offsets(); } my ($qfs, $sfs) = (0,0); CHAR_LOOP: for my $pos (0..CORE::length($seqString)-1) { my @qrange = (0 - $qfs)..($self->{_query_offset} - 1); my @srange = (0 - $sfs)..($self->{_sbjct_offset} - 1); # $self->debug("QRange:@qrange SRange:@srange\n") if ($qfs || $sfs);
($qfs, $sfs) = (0,0); my ($mchar, $qchar, $schar) = ( unpack("x$pos A1",$seqString) || ' ', $pos < CORE::length($qseq) ? unpack("x$pos A1",$qseq) : '-', $pos < CORE::length($sseq) ? unpack("x$pos A1",$sseq) : '-' ); my $matchtype = ''; my ($qgap, $sgap) = (0,0); if( $mchar eq '+' || $mchar eq '.') { # conserved
$self->{seqinds}{_conservedRes_query}{ $resCount_query + ($_ * $qdir) } = 1 for @qrange; $self->{seqinds}{_conservedRes_sbjct}{ $resCount_sbjct + ($_ * $sdir) } = 1 for @srange; $matchtype = 'conserved'; } elsif( $mchar eq ':' || $mchar ne ' ' ) { # identical
$self->{seqinds}{_identicalRes_query}{ $resCount_query + ($_ * $qdir) } = 1 for @qrange; $self->{seqinds}{_identicalRes_sbjct}{ $resCount_sbjct + ($_ * $sdir) } = 1 for @srange; $matchtype = 'identical'; } elsif( $mchar eq ' ' ) { # possible mismatch/nomatch/frameshift
$qfs = $qchar eq '/' ? -1 : # base inserted to match frame
$qchar eq '\\' ? 1 : # base deleted to match frame
0; $sfs = $schar eq '/' ? -1 : $schar eq '\\' ? 1 : 0; if ($qfs) { # Frameshifts are tricky.
# '/' indicates that the next residue is shifted back one
# (-1) frame position and is a deletion of one base (so to
# correctly align, a base is inserted). That residue should only
# occupy two sequence positions instead of three.
# '\' indicates that the next residue is shifted forward
# one (+1) frame position and is an insertion of one base (so to
# correctly align, a base is removed). That residue should
# occupy four sequence positions instead of three.
# Note that gaps are not counted across from frameshifts.
# Frameshift indices are a range of positions starting in the
# previous sequence position in which the frameshift occurs;
# they are ambiguous by nature.
$self->{seqinds}{_frameshiftRes_query}{ $resCount_query - ($_ * $qdir * $qfs) } = $qfs for @qrange; $matchtype = "$qfs frameshift-query"; $sgap = $qgap = 1; } elsif ($sfs) { $self->{seqinds}{_frameshiftRes_sbjct}{ $resCount_sbjct - ($_ * $sdir * $sfs) } = $sfs for @srange; $matchtype = "$sfs frameshift-sbcjt"; $sgap = $qgap = 1; } elsif ($qchar eq $self->{GAP_SYMBOL}) { # gap are counted as being in the immediately preceeding residue
# position; for translated sequences this is not the start of
# the previous codon, but the third codon position
$self->{seqinds}{_gapRes_query}{ $resCount_query - $qdir }++ for @qrange; $matchtype = 'gap-query'; $qgap++; } elsif ($schar eq $self->{GAP_SYMBOL}) { $self->{seqinds}{_gapRes_sbjct}{ $resCount_sbjct - $sdir }++ for @srange; $matchtype = 'gap-sbjct'; $sgap++; } else { # if not a gap or frameshift in either seq, must be mismatch
$self->{seqinds}{_mismatchRes_query}{ $resCount_query + ($_ * $qdir) } = 1 for @qrange; $self->{seqinds}{_mismatchRes_sbjct}{ $resCount_sbjct + ($_ * $sdir) } = 1 for @srange; $matchtype = 'mismatch'; } # always add a nomatch unless the current position in the seq is a gap
if (!$sgap) { $self->{seqinds}{_nomatchRes_sbjct}{ $resCount_sbjct + ($_ * $sdir) } = 1 for @srange; } if (!$qgap) { $self->{seqinds}{_nomatchRes_query}{ $resCount_query + ($_ * $qdir) } = 1 for @qrange; } } else { $self->warn("Unknown midline character: [$mchar]"); } # leave in and uncomment for future debugging
#$self->debug(sprintf("%7d %1s[%1s]%1s %-7d Type: %-20s QOff:%-2d SOff:%-2d\n",
# $resCount_query,
# $qchar,
# $mchar,
# $schar,
# $resCount_sbjct,
# $matchtype,
# ($self->{_query_offset} * $qdir),
# ($self->{_sbjct_offset} * $sdir)));
$resCount_query += ($qdir * (scalar(@qrange) + $qfs)) if !$qgap; $resCount_sbjct += ($sdir * (scalar(@srange) + $sfs)) if !$sgap; } return 1;
}
_calculate_seq_offsetsdescriptionprevnextTop
sub _calculate_seq_offsets {
    my $self = shift;
    my $prog = $self->algorithm;
    ($self->{_sbjct_offset}, $self->{_query_offset}) = (1,1);
    if($prog =~ /^(?:PSI)?T(BLAST|FAST)(N|X|Y)/oi ) {
        $self->{_sbjct_offset} = 3;
        if ($1 eq 'BLAST' && $2 eq 'X') { #TBLASTX
$self->{_query_offset} = 3; } } elsif($prog =~ /^(BLAST|FAST)(X|Y|XY)/oi ) { $self->{_query_offset} = 3; } 1;
}
ndescriptionprevnextTop
sub n {
    my $self = shift;
    if(@_) { $self->{'N'} = shift; }
    # note that returning 1 is completely an assumption
defined $self->{'N'} ? $self->{'N'} : 1;
}
rangedescriptionprevnextTop
sub range {
    my ($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);
}
linksdescriptionprevnextTop
sub links {
    my $self = shift;

    return $self->{LINKS} = shift if @_;
    return $self->{LINKS};
}
hsp_groupdescriptionprevnextTop
sub hsp_group {
    my $self = shift;

    return $self->{HSP_GROUP} = shift if @_;
    return $self->{HSP_GROUP};
}
hit_featuresdescriptionprevnextTop
sub hit_features {
    my $self = shift;

    return $self->{HIT_FEATURES} = shift if @_;
    return $self->{HIT_FEATURES};
}

# The cigar string code is written by Juguang Xiao <juguang@fugu-sg.org>
}
cigar_stringdescriptionprevnextTop
sub cigar_string {
    my ($self, $arg) = @_;
    $self->warn("this is not a setter") if(defined $arg);

    unless(defined $self->{_cigar_string}){ # generate cigar string
my $cigar_string = $self->generate_cigar_string($self->query_string, $self->hit_string); $self->{_cigar_string} = $cigar_string; } # end of unless
return $self->{_cigar_string};
}
generate_cigar_stringdescriptionprevnextTop
sub generate_cigar_string {
    my ($self, $qstr, $hstr) = @_;
    my @qchars = split //, $qstr;
    my @hchars = split //, $hstr;

    unless(scalar(@qchars) == scalar(@hchars)){
        $self->throw("two sequences are not equal in lengths");
    }

    $self->{_count_for_cigar_string} = 0;
    $self->{_state_for_cigar_string} = 'M';

    my $cigar_string = '';
    for(my $i=0; $i <= $#qchars; $i++){
        my $qchar = $qchars[$i];
        my $hchar = $hchars[$i];
        if($qchar ne $self->{GAP_SYMBOL} && $hchar ne $self->{GAP_SYMBOL}){ # Match
$cigar_string .= $self->_sub_cigar_string('M'); }elsif($qchar eq $self->{GAP_SYMBOL}){ # Deletion
$cigar_string .= $self->_sub_cigar_string('D'); }elsif($hchar eq $self->{GAP_SYMBOL}){ # Insertion
$cigar_string .= $self->_sub_cigar_string('I'); }else{ $self->throw("Impossible state that 2 gaps on each seq aligned"); } } $cigar_string .= $self->_sub_cigar_string('X'); # not forget the tail.
return $cigar_string; } # an internal method to help generate cigar string
}
_sub_cigar_stringdescriptionprevnextTop
sub _sub_cigar_string {
    my ($self, $new_state) = @_;

    my $sub_cigar_string = '';
    if($self->{_state_for_cigar_string} eq $new_state){
        $self->{_count_for_cigar_string} += 1; # Remain the state and increase the counter
}else{ $sub_cigar_string .= $self->{_count_for_cigar_string} unless $self->{_count_for_cigar_string} == 1; $sub_cigar_string .= $self->{_state_for_cigar_string}; $self->{_count_for_cigar_string} = 1; $self->{_state_for_cigar_string} = $new_state; } return $sub_cigar_string; } # needed before seqfeatures can be made
}
_pre_seq_featuredescriptionprevnextTop
sub _pre_seq_feature {
    my $self = shift;
    my $algo = $self->{ALGORITHM};

    my ($queryfactor, $hitfactor) = (0,0);
    my ($hitmap, $querymap) = (1,1);
    if( $algo =~ /^(?:PSI)?T(?:BLAST|FAST|SW)[NY]/oi ) {
        $hitfactor = 1;
        $hitmap = 3;
    }
    elsif ($algo =~ /^(?:FAST|BLAST)(?:X|Y|XY)/oi || $algo =~ /^P?GENEWISE/oi ) {
        $queryfactor = 1;
        $querymap = 3;
    }
    elsif ($algo =~ /^T(BLAST|FAST|SW)(X|Y|XY)/oi || $algo =~ /^(BLAST|FAST|SW)N/oi || $algo =~ /^WABA|AXT|BLAT|BLASTZ|PSL|MEGABLAST|EXONERATE|SW|SSEARCH|SMITH\-WATERMAN|SIM4$/){
        if ($2) {
            $hitmap = $querymap = 3;
        }
        $hitfactor = 1;
        $queryfactor = 1;
    }
    elsif ($algo =~ /^RPS-BLAST/) {
        if ($algo =~ /^RPS-BLAST\(BLASTX\)/) {
            $queryfactor = 1;
            $querymap  = 3;
        }
        $hitfactor = 0;
    }
    else {
        my $stranded = lc substr($self->{STRANDED}, 0,1);
        $queryfactor = ($stranded eq 'q' || $stranded eq 'b') ? 1 : 0;
        $hitfactor = ($stranded eq 'h' || $stranded eq 's' || $stranded eq 'b') ? 1 : 0;
    }
    $self->{_query_factor} = $queryfactor;
    $self->{_hit_factor} = $hitfactor;
    $self->{_hit_mapping} = $hitmap;
    $self->{_query_mapping} = $querymap;
}

# make query seq feature
}
_query_seq_featuredescriptionprevnextTop
sub _query_seq_feature {
    my $self = shift;
    $self->{_making_qff} = 1;
    my $qs = $self->{QUERY_START};
    my $qe = $self->{QUERY_END};
    unless (defined $self->{_query_factor}) {
        $self->_pre_seq_feature;
    }
    my $queryfactor = $self->{_query_factor};

    unless( defined $qe && defined $qs ) { $self->throw("Did not specify a Query End or Query Begin"); }

    my $strand;
    if ($qe > $qs) {  # normal query: start < end
if ($queryfactor) { $strand = 1; } else { $strand = undef; } } else { if ($queryfactor) { $strand = -1; } else { $strand = undef; } ($qs,$qe) = ($qe,$qs); } # Note: many of these data are not query- and hit-specific.
# Only start, end, name, length are.
# We could be more efficient by only storing this info once.
# steve chervitz --- Sat Apr 5 00:55:07 2003
my $sim1 = $self->{_sim1} || Bio::SeqFeature::Similarity->new(); $sim1->start($qs); $sim1->end($qe); $sim1->significance($self->{EVALUE}); $sim1->bits($self->{BITS}); $sim1->score($self->{SCORE}); $sim1->strand($strand); $sim1->seq_id($self->{QUERY_NAME}); $sim1->seqlength($self->{QUERY_LENGTH}); $sim1->source_tag($self->{ALGORITHM}); $sim1->seqdesc($self->{QUERY_DESC}); $sim1->add_tag_value('meta', $self->{META}) if $self->can('meta'); # to determine frame from something like FASTXY which doesn't
# report the frame
my $qframe = $self->{QUERY_FRAME}; if (defined $strand && !defined $qframe && $queryfactor) { $qframe = ( $qs % 3 ) * $strand; } elsif (!defined $strand) { $qframe = 0; } if( $qframe =~ /^([+-])?([0-3])/ ) { my $dir = $1 || '+'; if($qframe && (($dir eq '-' && $strand >= 0) || ($dir eq '+' && $strand <= 0)) ) { $self->warn("Query frame ($qframe) did not match strand of query ($strand)"); } $qframe = $2 != 0 ? $2 - 1 : $2; } else { $self->warn("Unknown query frame ($qframe)"); $qframe = 0; } $sim1->frame($qframe); $self->SUPER::feature1($sim1); $self->{_created_qff} = 1; $self->{_making_qff} = 0; } # make subject seq feature
}
_subject_seq_featuredescriptionprevnextTop
sub _subject_seq_feature {
    my $self = shift;
    $self->{_making_sff} = 1;
    my $hs = $self->{HIT_START};
    my $he = $self->{HIT_END};
    unless (defined $self->{_hit_factor}) {
        $self->_pre_seq_feature;
    }
    my $hitfactor = $self->{_hit_factor};

    unless( defined $he && defined $hs ) { $self->throw("Did not specify a Hit End or Hit Begin"); }

    my $strand;
    if ($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
} my $sim2 = $self->{_sim2} || Bio::SeqFeature::Similarity->new(); $sim2->start($hs); $sim2->end($he); $sim2->significance($self->{EVALUE}); $sim2->bits($self->{BITS}); $sim2->score($self->{SCORE}); $sim2->strand($strand); $sim2->seq_id($self->{HIT_NAME}); $sim2->seqlength($self->{HIT_LENGTH}); $sim2->source_tag($self->{ALGORITHM}); $sim2->seqdesc($self->{HIT_DESC}); $sim2->add_tag_value('meta', $self->{META}) if $self->can('meta'); my $hframe = $self->{HIT_FRAME}; if (defined $strand && !defined $hframe && $hitfactor) { $hframe = ( $hs % 3 ) * $strand; } elsif (!defined $strand) { $hframe = 0; } if( $hframe =~ /^([+-])?([0-3])/ ) { my $dir = $1 || '+'; if($hframe && (($dir eq '-' && $strand >= 0) || ($dir eq '+' && $strand <= 0)) ) { $self->warn("Subject frame ($hframe) did not match strand of subject ($strand)"); } $hframe = $2 != 0 ? $2 - 1 : $2; } else { $self->warn("Unknown subject frame ($hframe)"); $hframe = 0; } $sim2->frame($hframe); $self->SUPER::feature2($sim2); $self->{_created_sff} = 1; $self->{_making_sff} = 0; } # before calling the num_* methods
}
_pre_similar_statsdescriptionprevnextTop
sub _pre_similar_stats {
    my $self = shift;
    my $identical = $self->{IDENTICAL};
    my $conserved = $self->{CONSERVED};
    my $percent_id = $self->{PERCENT_IDENTITY};

    if (! defined $identical) {
        if (! defined $percent_id) {
            $self->warn("Did not defined the number of identical matches or overall percent identity in the HSP; assuming 0");
            $identical = 0;
        }
        else {
            $identical = sprintf("%.0f",$percent_id * $self->{HSP_LENGTH});
        }
    }

    if (! defined $conserved) {
        $self->warn("Did not define the number of conserved matches in the HSP; assuming conserved == identical ($identical)")
            if( $self->{ALGORITHM} !~ /^((FAST|BLAST)N)|EXONERATE|SIM4|AXT|PSL|BLAT|BLASTZ|WABA/oi);
        $conserved = $identical;
    }
    $self->{IDENTICAL} = $identical;
    $self->{CONSERVED} = $conserved;
    $self->{_did_presimilar} = 1;
}

# before calling the frac_* methods
}
_pre_fracdescriptionprevnextTop
sub _pre_frac {
    my $self = shift;
    
    my $hsp_len = $self->{HSP_LENGTH};
    my $hit_len = $self->{HIT_LENGTH};
    my $query_len = $self->{QUERY_LENGTH};

    my $identical = $self->num_identical;
    my $conserved = $self->num_conserved;

    $self->{_did_prefrac} = 1;
    my $logical;
    if( $hsp_len ) {
        $self->length('total', $hsp_len);
        $logical = $self->_logical_length('total');
        $self->frac_identical( 'total', $identical / $hsp_len);
$self->frac_conserved( 'total', $conserved / $hsp_len);
} if( $hit_len ) { $logical = $self->_logical_length('hit'); $self->frac_identical( 'hit', $identical / $logical);
$self->frac_conserved( 'hit', $conserved / $logical);
} if( $query_len ) { $logical = $self->_logical_length('query'); $self->frac_identical( 'query', $identical / $logical) ;
$self->frac_conserved( 'query', $conserved / $logical);
} } # before calling gaps()
# This relies first on passed parameters (parser-dependent), then on gaps
# calculated by seq_inds() (if set), then falls back to directly checking
# for '-' as a last resort
}
_pre_gapsdescriptionprevnextTop
sub _pre_gaps {
    my $self = shift;
    my $query_gaps = $self->{QUERY_GAPS};
    my $query_seq = $self->{QUERY_SEQ};
    my $hit_gaps = $self->{HIT_GAPS};
    my $hit_seq = $self->{HIT_SEQ};
    my $gaps = $self->{HSP_GAPS};

    $self->{_did_pregaps} = 1; # well, we're in the process; avoid recursion
if( defined $query_gaps ) { $self->gaps('query', $query_gaps); } elsif( defined $query_seq ) { my $qg = (defined $self->{'_query_offset'}) ? $self->seq_inds('query','gaps') : scalar( $query_seq =~ tr/\-//); my $offset = $self->{'_query_offset'} || 1; $self->gaps('query', $qg/$offset);
} if( defined $hit_gaps ) { $self->gaps('hit', $hit_gaps); } elsif( defined $hit_seq ) { my $hg = (defined $self->{'_sbjct_offset'}) ? $self->seq_inds('hit','gaps') : scalar( $hit_seq =~ tr/\-//); my $offset = $self->{'_sbjct_offset'} || 1; $self->gaps('hit', $hg/$offset);
} if( ! defined $gaps ) { $gaps = $self->gaps("query") + $self->gaps("hit"); } $self->gaps('total', $gaps); } # before percent_identity
}
_pre_pidescriptionprevnextTop
sub _pre_pi {
    my $self = shift;
    $self->{_did_prepi} = 1;
    $self->percent_identity($self->{PERCENT_IDENTITY} || $self->frac_identical('total')*100) if( $self->{HSP_LENGTH} > 0 );
}

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.org
Email sac-at-bioperl.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::HSP::HSPI methodsTop
Implementation of Bio::Search::HSP::HSPI methods follow
Inherited from Bio::SeqFeature::SimilarityPairTop
These methods come from Bio::SeqFeature::SimilarityPair
scoreTop
 Title   : score
Usage : $score = $obj->score();
$obj->score($value);
Function: Get/Set the score value
Returns : numeric
Args : [optional] new value to set
bitsTop
 Title   : bits
Usage : $bits = $obj->bits();
$obj->bits($value);
Function: Get/Set the bits value
Returns : numeric
Args : [optional] new value to set
strandTop
 Title   : strand
Usage : $hsp->strand('query')
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
Brief introduction on cigar stringTop
NOTE: the concept is originally from EnsEMBL docs at
http://may2005.archive.ensembl.org/Docs/wiki/html/EnsemblDocs/CigarFormat.html Please append to these docs if you have a better definition.
Sequence alignment hits can be stored in a database as ungapped alignments.
This imposes 2 major constraints on alignments:
a) alignments for a single hit record require multiple rows in the database,
and
b) it is not possible to accurately retrieve the exact original alignment.
Alternatively, sequence alignments can be stored as gapped alignments using
the CIGAR line format (where CIGAR stands for Concise Idiosyncratic Gapped
Alignment Report).
In the cigar line format alignments are stored as follows:
M: Match
D: Deletion
I: Insertion
An example of an alignment for a hypthetical protein match is shown below:
Query: 42 PGPAGLP----GSVGLQGPRGLRGPLP-GPLGPPL...
            PG    P    G     GP   R      PLGP
Sbjct: 1672 PGTP*TPLVPLGPWVPLGPSSPR--LPSGPLGPTD...
protein_align_feature table as the following cigar line:
7M4D12M2I2MD7M