/ 
bioperl-0.6
/ Bio::Search::Hit::HitI

NAME

Bio::Search::Hit::HitI - Abstract interface for Hit objects

SYNOPSIS

This is a abstract class meant to define an interface, and nothing more.

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.

vsns-bcd-perl@lists.uni-bielefeld.de          - General discussion
vsns-bcd-perl-guts@lists.uni-bielefeld.de     - Technically-oriented 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

Email amackey@virginia.edu

APPENDIX

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

get_hit_id

Title   : get_hit_id
Usage   : $id = $hit->get_hit_id();
Function: Used to obtain the id of the matched entity.
Returns : a scalar string
Args    : <none>

get_hit_desc

Title   : get_hit_desc
Usage   : $desc = $hit->get_hit_desc();
Function: Used to obtain the description of a matched entity
Returns : a scalar string
Args    : <none>

get_algorithm

Title   : get_algorithm
Usage   : $which = $hit->get_algorithm();
Function: Used to obtain the algorithm specification used to obtain the hit
Returns : a scalar string 
Args    : <none>

get_raw_score

Title   : get_raw_score
Usage   : $score = $hit->get_raw_score();
Function: Used to obtain 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>

get_expectation_value

Title   : get_expectation_value
Usage   : $evalue = $hit->get_expectation_value();
Function: Used to obtain the E() 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>

get_evalue

Title   : get_evalue
Usage   : $evalue = $hit->get_evalue();
Function: same as get_expectation_value (just an alias)
Returns : see above
Args    : <none>

get_alignments

Title   : get_alignments
Usage   : @aligns = $hit->get_alignments()
Function: Used to obtain an array of Bio::Alignment objects corresponding to
          the Hit.
Returns : an array of Alignment objects, if more than one Alignments exist and
          called in wantarray context.  In scalar context will return a
          reference to an array of Alignment objects, if more than one
          Alignment objects exist, otherwise will return the unique
          Alignment object.  If no Alignment objects exist, returns undef
Args    :