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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 Bugs

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algorithm

 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    : none

pvalue

 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    : none

evalue

 Title   : evalue
 Usage   : my $evalue = $hsp->evalue();
 Function: Returns the e-value for this HSP
 Returns : float or exponential (2e-10)
 Args    : none

frac_identical

 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    : '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'

frac_conserved

 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    : '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'

num_identical

 Title   : num_identical
 Usage   : $obj->num_identical($newval)
 Function: returns the number of identical residues in the alignment
 Returns : integer
 Args    : integer (optional)

num_conserved

 Title   : num_conserved
 Usage   : $obj->num_conserved($newval)
 Function: returns the number of conserved residues in the alignment
 Returns : inetger
 Args    : integer (optional)

gaps

 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 gap characters or 0 if none
 Args     : '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'

query_string

 Title   : query_string
 Usage   : my $qseq = $hsp->query_string;
 Function: Retrieves the query sequence of this HSP as a string
 Returns : string
 Args    : none

hit_string

 Title   : hit_string
 Usage   : my $hseq = $hsp->hit_string;
 Function: Retrieves the hit sequence of this HSP as a string
 Returns : string
 Args    : none

homology_string

 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    : none

length

 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     : 'query' = length of query seq (without gaps)
            'hit'   = length of hit seq (without gaps)
            'total' = length of alignment (with gaps)
            default = 'total' 
 Args    : none

percent_identity

 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

get_aln

 Title   : get_aln
 Usage   : my $aln = $hsp->get_aln
 Function: Returns a Bio::SimpleAlign representing the HSP alignment
 Returns : Bio::SimpleAlign
 Args    : none

seq_inds

 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', 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')

             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::BlastUtils::collapse_nums(), Bio::Search::Hit::HitI::seq_inds()

Inherited from Bio::SeqFeature::SimilarityPair

query

 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

hit

 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

significance

 Title   : significance
 Usage   : $evalue = $obj->significance();
           $obj->significance($evalue);
 Function: Get/Set the significance value (see Bio::SeqFeature::SimilarityPair)
 Returns : significance value (scientific notation string)
 Args    : significance value (sci notation string)

score

 Title   : score
 Usage   : my $score = $hsp->score();
 Function: Returns the score for this HSP or undef 
 Returns : numeric           
 Args    : [optional] numeric to set value

bits

 Title   : bits
 Usage   : my $bits = $hsp->bits();
 Function: Returns the bit value for this HSP or undef 
 Returns : numeric
 Args    : none

strand

 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)
           'list' or 'array' to retrieve both query and hit together

start

 Title   : start
 Usage   : $hsp->start('query')
 Function: Retrieves the start for the HSP component requested
 Returns : integer
 Args    : 'hit' or 'subject' or 'sbjct' to retrieve the start of the subject
           'query' to retrieve the query start (default)

end

 Title   : end
 Usage   : $hsp->end('query')
 Function: Retrieves the end for the HSP component requested
 Returns : integer
 Args    : 'hit' or 'subject' or 'sbjct' to retrieve the end of the subject
           'query' to retrieve the query end (default)

seq

 Usage     : $hsp->seq( [seq_type] );
 Purpose   : Get the query or sbjct sequence as a Bio::Seq.pm object.
 Example   : $seqObj = $hsp->seq('query');
 Returns   : Object reference for a Bio::Seq.pm object.
 Argument  : seq_type = 'query' or 'hit' or 'sbjct' (default = 'query').
           :  ('sbjct' is synonymous with 'hit') 
           : default is 'query'
 Throws    : Propagates any exception that occurs during construction
           : of the Bio::Seq.pm object.
 Comments  : The sequence is returned in an array of strings corresponding
           : to the strings in the original format of the Blast alignment.
           : (i.e., same spacing).

See Also : "seq_str", "seq_inds", Bio::Seq

seq_str

 Usage     : $hsp->seq_str( seq_type );
 Purpose   : Get the full query, sbjct, or 'match' sequence as a string.
           : The 'match' sequence is the string of symbols in between the 
           : query and sbjct sequences.
 Example   : $str = $hsp->seq_str('query');
 Returns   : String
 Argument  : seq_Type = 'query' or 'hit' or 'sbjct' or 'match'
           :  ('sbjct' is synonymous with 'hit')
           : default is 'query'
 Throws    : Exception if the argument does not match an accepted seq_type.
 Comments  :

See Also : "seq", "seq_inds", "_set_match_seq"

rank

 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.

matches

 Usage     : $hsp->matches(-seq   => 'hit'|'query', 
                           -start => $start, 
                           -stop  => $stop);
 Purpose   : Get the total number of identical and conservative matches 
           : in the query or sbjct sequence for the given HSP. Optionally can
           : report data within a defined interval along the seq.
           : (Note: 'conservative' matches are called 'positives' in the
           : Blast report.)
 Example   : ($id,$cons) = $hsp_object->matches(-seq   => 'hit');
           : ($id,$cons) = $hsp_object->matches(-seq   => 'query',
                                                -start => 300,
                                                -stop  => 400);
 Returns   : 2-element array of integers 
 Argument  : (1) seq_type = 'query' or 'hit' or 'sbjct' (default = query)
           :  ('sbjct' is synonymous with 'hit') 
           : (2) start = Starting coordinate (optional)
           : (3) stop  = Ending coordinate (optional)
 Throws    : Exception if the supplied coordinates are out of range.
 Comments  : Relies on seq_str('match') to get the string of alignment symbols
           : between the query and sbjct lines which are used for determining
           : the number of identical and conservative matches.

See Also : "length", "gaps", "seq_str", Bio::Search::Hit::BlastHit::_adjust_contigs()

n

 Usage     : $hsp_obj->n()
 Purpose   : Get the N value (num HSPs on which P/Expect is based).
           : This value is not defined with NCBI Blast2 with gapping.
 Returns   : Integer or null string if not defined.
 Argument  : n/a
 Throws    : n/a
 Comments  : The 'N' value is listed in parenthesis with P/Expect value:
           : e.g., P(3) = 1.2e-30  ---> (N = 3).
           : Not defined in NCBI Blast2 with gaps.
           : This typically is equal to the number of HSPs but not always.
           : To obtain the number of HSPs, use Bio::Search::Hit::HitI::num_hsps().

See Also : Bio::SeqFeature::SimilarityPair::score()

range

 Usage     : $hsp->range( [seq_type] );
 Purpose   : Gets the (start, end) coordinates for the query or sbjct sequence
           : in the HSP alignment.
 Example   : ($query_beg, $query_end) = $hsp->range('query');
           : ($hit_beg, $hit_end) = $hsp->range('hit');
 Returns   : Two-element array of integers 
 Argument  : seq_type = string, 'query' or 'hit' or 'sbjct'  (default = 'query')
           :  ('sbjct' is synonymous with 'hit') 
 Throws    : n/a
 Comments  : This is a convenience method for constructions such as
             ($hsp->query->start, $hsp->query->end)