/ 
bioperl-1.0.2
/ Bio::Search::Hit::HitI

NAME

Bio::Search::Hit::HitI - Interface for a hit in a similarity search result

SYNOPSIS

Bio::Search::Hit::HitI objects should not be instantiated since this module defines a pure interface.

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

$hit_name = $hit->name();

$desc = $hit->description();

$len = $hit->length

$alg = $hit->algorithm();

$score = $hit->raw_score();

$significance = $hit->significance();

while( $hsp = $obj->next_hsp()) { ... }

DESCRIPTION

Bio::Search::Hit::* objects are data structures that contain information
about specific hits obtained during a library search.  Some information will
be algorithm-specific, but others will be generally defined.

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 one of the Bioperl mailing lists. Your participation is much appreciated.

bioperl-l@bioperl.org             - General discussion
http://bio.perl.org/MailList.html - About the mailing lists

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via email or the web:

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

AUTHOR - Aaron Mackey, Steve Chervitz

Email amackey@virginia.edu (original author) Email sac@bioperl.org

COPYRIGHT

Copyright (c) 1999-2001 Aaron Mackey, Steve Chervitz. 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 _

name

Title   : name
Usage   : $hit_name = $hit->name();
Function: returns the name of the Hit sequence
Returns : a scalar string
Args    : none

description

Title   : description
Usage   : $desc = $hit->description();
Function: Retrieve the description for the hit
Returns : a scalar string
Args    : none

accession

Title   : accession
Usage   : $acc = $hit->accession();
Function: Retrieve the accession (if available) for the hit
Returns : a scalar string (empty string if not set)
Args    : none

length

Title   : length
Usage   : my $len = $hit->length
Function: Returns the length of the hit 
Returns : integer
Args    : none

algorithm

Title   : algorithm
Usage   : $alg = $hit->algorithm();
Function: Gets the algorithm specification that was used to obtain the hit
          For BLAST, the algorithm denotes what type of sequence was aligned 
          against what (BLASTN: dna-dna, BLASTP prt-prt, BLASTX translated 
          dna-prt, TBLASTN prt-translated dna, TBLASTX translated 
          dna-translated dna).
Returns : a scalar string 
Args    : none

raw_score

Title   : raw_score
Usage   : $score = $hit->raw_score();
Function: Gets the "raw score" generated by the algorithm.  What
          this score is exactly will vary from algorithm to algorithm,
          returning undef if unavailable.
Returns : a scalar value
Args    : none

significance

Title   : significance
Usage   : $significance = $hit->significance();
Function: Used to obtain the E or P value of a hit, i.e. the probability that
          this particular hit was obtained purely by random chance.  If
          information is not available (nor calculatable from other
          information sources), return undef.
Returns : a scalar value or undef if unavailable
Args    : none

next_hsp

Title    : next_hsp
Usage    : while( $hsp = $obj->next_hsp()) { ... }
Function : Returns the next available High Scoring Pair
Example  : 
Returns  : Bio::Search::HSP::HSPI object or null if finished
Args     : none

hits

Title   : hits
Usage   :
Function:
Returns : 
Args    :