Bio::Tools::HMMER Set
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Summary
Bio::Tools::HMMER::Set - Set of identical domains from HMMER matches
Package variables
No package variables defined.
Included modules
Bio::Tools::HMMER::Domain
Inherit
Bio::Root::Root
Synopsis
    # 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
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).
Methods
new
No description
Code
add_DomainDescriptionCode
each_DomainDescriptionCode
nameDescriptionCode
descDescriptionCode
accessionDescriptionCode
bitsDescriptionCode
evalueDescriptionCode
addHMMUnit
No description
Code
eachHMMUnit
No description
Code
Methods description
add_Domaincode    nextTop
 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_DomaincodeprevnextTop
 Title   : each_Domain
Usage : foreach $domain ( $set->each_Domain() )
Function: returns an array of domain objects in this set
Returns : array
Args : none
namecodeprevnextTop
 Title   : name
Usage : $obj->name($newval)
Function:
Example :
Returns : value of name
Args : newvalue (optional)
desccodeprevnextTop
 Title   : desc
Usage : $obj->desc($newval)
Function:
Example :
Returns : value of desc
Args : newvalue (optional)
accessioncodeprevnextTop
 Title   : accession
Usage : $obj->accession($newval)
Function:
Example :
Returns : value of accession
Args : newvalue (optional)
bitscodeprevnextTop
 Title   : bits
Usage : $obj->bits($newval)
Function:
Example :
Returns : value of bits
Args : newvalue (optional)
evaluecodeprevnextTop
 Title   : evalue
Usage : $obj->evalue($newval)
Function:
Example :
Returns : value of evalue
Args : newvalue (optional)
Methods code
newdescriptionprevnextTop
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 $self;
}
add_DomaindescriptionprevnextTop
sub add_Domain {
   my ($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);
}
each_DomaindescriptionprevnextTop
sub each_Domain {
   my ($self,@args) = @_;

   return @{$self->{'domains'}};
}
namedescriptionprevnextTop
sub name {
   my ($obj,$value) = @_;
   if( defined $value) {
      $obj->{'name'} = $value;
    }
    return $obj->{'name'};
}
descdescriptionprevnextTop
sub desc {
   my ($self,$value) = @_;
   if( defined $value) {
      $self->{'desc'} = $value;
    }
    return $self->{'desc'};
}
accessiondescriptionprevnextTop
sub accession {
   my ($self,$value) = @_;
   if( defined $value) {
      $self->{'accession'} = $value;
    }
    return $self->{'accession'};
}
bitsdescriptionprevnextTop
sub bits {
   my ($obj,$value) = @_;

   if( defined $value) {
      $obj->{'bits'} = $value;
    }
    return $obj->{'bits'};
}
evaluedescriptionprevnextTop
sub evalue {
   my ($obj,$value) = @_;
   if( defined $value) {
      $obj->{'evalue'} = $value;
    }
    return $obj->{'evalue'};
}
addHMMUnitdescriptionprevnextTop
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);
}
eachHMMUnitdescriptionprevnextTop
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__
}
General documentation
FEEDBACKTop
Mailing ListsTop
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 Top
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 BugsTop
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 BirneyTop
Email birney-at-ebi.ac.uk
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _