/ 
bioperl-1.0.2
/ Bio::Search::HSP::HSPI

NAME

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

SYNOPSIS

$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;

$homo_string = $hsp->homology_string;

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

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/MailList.shtml  - About the mailing lists

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 email or the web:

bioperl-bugs@bioperl.org
http://bioperl.org/bioperl-bugs/

AUTHOR - Steve Chervitz, Jason Stajich

Email sac@bioperl.org Email jason@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'

gaps

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     : '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->gel_aln
Function: Returns a Bio::SimpleAlign representing the HSP alignment
Returns : Bio::SimpleAlign
Args    : none

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: 
Returns : 
Args    :

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