Provided by: libbio-perl-perl_1.7.6-3_all bug

NAME

       Bio::Search::HSP::HSPI - Interface for a High Scoring Pair in a similarity search result

SYNOPSIS

           # Bio::Search::HSP::HSPI objects cannot be instantiated since this
           # module defines a pure interface.

           # Given an object that implements the Bio::Search::HSP::HSPI  interface,
           # you can do the following things with it:

           $r_type = $hsp->algorithm;

           $pvalue = $hsp->pvalue();

           $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;

           $homology_string = $hsp->homology_string;

           $len = $hsp->length( ['query'|'hit'|'total'] );

           $rank = $hsp->rank;

DESCRIPTION

       Bio::Search::HSP::HSPI objects cannot be instantiated since this module defines a pure
       interface.

       Given an object that implements the Bio::Search::HSP::HSPI interface, you can do the
       following things with it:

SEE ALSO

       This interface inherits methods from these other modules:

       Bio::SeqFeatureI, Bio::SeqFeature::FeaturePair Bio::SeqFeature::SimilarityPair

       Please refer to these modules for documentation of the many additional inherited methods.

FEEDBACK

   Mailing Lists
       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
       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 Bugs
       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://github.com/bioperl/bioperl-live/issues

AUTHOR - Steve Chervitz, Jason Stajich

       Email sac-at-bioperl.org Email jason-at-bioperl.org

COPYRIGHT

       Copyright (c) 2001 Steve Chervitz, Jason Stajich. All Rights Reserved.

DISCLAIMER

       This software is provided "as is" without warranty of any kind.

APPENDIX

       The rest of the documentation details each of the object methods.  Internal methods are
       usually preceded with a _

   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
       These methods come 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)