Bio::Tools::HMMER::Set - Set of identical domains from HMMER matches

BioPerl documentation Contained in the BioPerl distribution.

Index

Code Index:

NAME

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Bio::Tools::HMMER::Set - Set of identical domains from HMMER matches

SYNOPSIS

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    # get a Set object probably from the results object
    print "Bits score over set ",$set->bits," evalue ",$set->evalue,"\n";

    foreach $domain ( $set->each_Domain ) {
	print "Domain start ",$domain->start," end ",$domain->end,"\n";
    }

DESCRIPTION

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Represents a set of HMMER domains hitting one sequence. HMMER reports two different scores, a per sequence total score (and evalue) and a per domain score and evalue. This object represents a collection of the same domain with the sequence bits score and evalue. (these attributes are also on the per domain scores, which you can get there).

FEEDBACK

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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://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 the bugs and their resolution.Bug reports can be submitted via the web: 

 https://redmine.open-bio.org/projects/bioperl/

AUTHOR - Ewan Birney

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Email birney-at-ebi.ac.uk

APPENDIX

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

add_Domain

 Title   : add_Domain
 Usage   : $set->add_Domain($domain)
 Function: adds the domain to the list
 Returns : nothing
 Args    : A Bio::Tools::HMMER::Domain object

each_Domain

 Title   : each_Domain
 Usage   : foreach $domain ( $set->each_Domain() )
 Function: returns an array of domain objects in this set
 Returns : array
 Args    : none

name

 Title   : name
 Usage   : $obj->name($newval)
 Function:
 Example :
 Returns : value of name
 Args    : newvalue (optional)

desc

 Title   : desc
 Usage   : $obj->desc($newval)
 Function:
 Example :
 Returns : value of desc
 Args    : newvalue (optional)

accession

 Title   : accession
 Usage   : $obj->accession($newval)
 Function:
 Example :
 Returns : value of accession
 Args    : newvalue (optional)

bits

 Title   : bits
 Usage   : $obj->bits($newval)
 Function:
 Example :
 Returns : value of bits
 Args    : newvalue (optional)

evalue

 Title   : evalue
 Usage   : $obj->evalue($newval)
 Function:
 Example :
 Returns : value of evalue
 Args    : newvalue (optional)
BioPerl documentation Contained in the BioPerl distribution. 
#
# BioPerl module for Bio::Tools::HMMER::Set
#
# Please direct questions and support issues to <bioperl-l@bioperl.org> 
#
# Cared for by Ewan Birney <birney@sanger.ac.uk>
#
# Copyright Ewan Birney
#
# You may distribute this module under the same terms as perl itself

# POD documentation - main docs before the code



# Let the code begin...


package Bio::Tools::HMMER::Set;
use strict;

use Bio::Tools::HMMER::Domain;

use base qw(Bio::Root::Root);

sub new {
    my($class,@args) = @_;
    my $self = $class->SUPER::new(@args);
    my ($name,$acc,$desc) = $self->_rearrange([qw(NAME ACCESSION DESC)],
					      @args);
    $name && $self->name($name);
    $acc  && $self->accession($acc);
    $desc && $self->desc($desc);


    $self->{'domains'} = [];
    $self->{'domainnames'} = {};
    return $self;
}


sub add_Domain{
   my ($self,$domain) = @_;


   if( ! defined $domain || ! $domain->isa("Bio::Tools::HMMER::Domain") ) {
       $self->throw("[$domain] is not a Bio::Tools::HMMER::Domain. aborting");
   }
   return if $self->{'domainnames'}->{$domain->get_nse}++;
   push(@{$self->{'domains'}},$domain);

}


sub each_Domain{
   my ($self,@args) = @_;

   return @{$self->{'domains'}};
}


sub name{
   my ($obj,$value) = @_;
   if( defined $value) {
      $obj->{'name'} = $value;
    }
    return $obj->{'name'};

}


sub desc{
   my ($self,$value) = @_;
   if( defined $value) {
      $self->{'desc'} = $value;
    }
    return $self->{'desc'};

}


sub accession{
   my ($self,$value) = @_;
   if( defined $value) {
      $self->{'accession'} = $value;
    }
    return $self->{'accession'};
}



sub bits{
   my ($obj,$value) = @_;

   if( defined $value) {
      $obj->{'bits'} = $value;
    }
    return $obj->{'bits'};

}


sub evalue{
   my ($obj,$value) = @_;
   if( defined $value) {
      $obj->{'evalue'} = $value;
    }
    return $obj->{'evalue'};

}


sub addHMMUnit {
    my $self = shift;
    my $unit = shift;

    $self->warn("Using old addHMMUnit call on Bio::Tools::HMMER::Set. Should replace with add_Domain");
    return $self->add_Domain($unit);
}

sub eachHMMUnit {
    my $self = shift;
    $self->warn("Using old eachHMMUnit call on Bio::Tools::HMMER::Set. Should replace with each_Domain");
    return $self->each_Domain();
}

1;  # says use was ok
__END__