Christopher Fields > BioPerl > Bio::Search::Result::hmmer3Result

Download:
BioPerl-1.6.924.tar.gz

Dependencies

Annotate this POD

CPAN RT

New  12
Open  4
View/Report Bugs
Module Version: 1.006924   Source  

NAME ^

Bio::Search::Result::hmmer3Result - 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 = new Bio::Search::Result::hmmer3Result.pm();
 Function: Builds a new Bio::Search::Result::hmmer3Result.pm object 
 Returns : an instance of Bio::Search::Result::hmmer3Result.pm
 Args    : -hmm_name => string, name of hmm file
           -sequence_file => name of the sequence file

hmm_name

 Title   : hmm_name
 Usage   : $obj->hmm_name($newval)
 Function: Get/Set the value of hmm_name
 Returns : value of hmm_name
 Args    : newvalue (optional)

sequence_file

 Title   : sequence_file
 Usage   : $obj->sequence_file($newval)
 Function: Get/Set the value of sequence_file
 Returns : value of sequence_file
 Args    : newvalue (optional)

next_model

 Title   : next_model
 Usage   : my $domain = $result->next_model
 Function: Returns the next domain - this
           is an alias for next_hit
 Returns : L<Bio::Search::Hit::HitI> object
 Args    : none

models

 Title   : models
 Usage   : my @domains = $result->models;
 Function: Returns the list of HMM models seen - this
           is an alias for hits()
 Returns : Array of L<Bio::Search::Hit::HitI> objects
 Args    : none

rewind

 Title   : rewind
 Usage   : $result->rewind;
 Function: Allow one to reset the Hit iteration to the beginning
           Since this is an in-memory implementation
 Returns : none
 Args    : none
syntax highlighting: