/ 
BioPerl-1.007000
River stage two • 60 direct dependents • 65 total dependents
/ Bio::Search::Hit::hmmer3Hit

NAME

Bio::Search::Hit::hmmer3Hit - DESCRIPTION of Object

SYNOPSIS

Give standard usage here

DESCRIPTION

Describe the object here

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 - Thomas Sharpton

Email thomas.sharpton@gmail.com

Describe contact details here

CONTRIBUTORS

Additional contributors names and emails here

APPENDIX

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

new

Title   : new
Usage   : my $obj = Bio::Search::Hit::HMMERHit->new();
Function: Builds a new Bio::Search::Hit::HMMERHit object 
Returns : Bio::Search::Hit::HMMERHit
Args    : 

Plus the Bio::Search::Hit::GenericHit inherited params
          -name         => Name of Hit (required)
          -description  => Description (optional)
          -accession    => Accession number (optional)
          -length       => Length of the Hit (optional)
          -score        => Raw Score for the Hit (optional)
          -significance => Significance value for the Hit (optional)
          -algorithm    => Algorithm used (BLASTP, FASTX, etc...)
          -hsps         => Array ref of HSPs for this Hit.

next_domain

Title   : next_domain 
Usage   : my $domain = $hit->next_domain();
Function: An alias for L<next_hsp()>, this will return the next HSP
Returns : L<Bio::Search::HSP::HSPI> object
Args    : none

domains

Title   : domains
Usage   : my @domains = $hit->domains();
Function: An alias for L<hsps()>, this will return the full list of hsps
Returns : array of L<Bio::Search::HSP::HSPI> objects
Args    : none

bits

Usage     : $hit_object->bits();
Purpose   : Gets the bit score of the best HSP for the current hit.
Example   : $bits = $hit_object->bits();
Returns   : Integer or undef if bit score is not set
Argument  : n/a

See Also : score()

iteration

Title   : iteration
Usage   : $obj->iteration($newval)
Function: PSI-BLAST iteration
Returns : value of iteration
Args    : newvalue (optional)