11-15-2001
echo "Hit return to continue"
read dummy_variable
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LEARN ABOUT DEBIAN
bio::search::hit::hmmer3hit
Bio::Search::Hit::hmmer3Hit(3pm) User Contributed Perl Documentation Bio::Search::Hit::hmmer3Hit(3pm)
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://redmine.open-bio.org/projects/bioperl/
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)
perl v5.14.2 2012-03-02 Bio::Search::Hit::hmmer3Hit(3pm)