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Summary

Bio::Search::HSP::WABAHSP - HSP object suitable for describing WABA alignments

Package variables

Included modules

Inherit

Bio::Search::HSP::GenericHSP

Synopsis

# use this object as you would a GenericHSP
# a few other methods have been added including state

Description

This object implements a few of the extra methods such as
hmmstate_string which returns the HMM state representation for the
WABA alignment. We also must implement a method to calculate
homology_string since it is not returned by the algorithm in the
machine readable format.

Methods

Methods description

 Title   : hmmstate_string
 Usage   : my $hmmseq = $wabahsp->hmmstate_string();
 Function: Get/Set the WABA HMM stateseq
 Returns : string
 Args    : [optional] string

 Title   : homolgy_string
 Usage   : my $homology_str = $hsp->homology_string();
 Function: Homology string must be calculated for a WABA HSP so we can do
           so here and cache the result so it is only done once
 Returns : string
 Args    : none

 Title   : new
 Usage   : my $obj = new Bio::Search::HSP::WABAHSP();
 Function: Builds a new Bio::Search::HSP::WABAHSP object 
 Returns : Bio::Search::HSP::WABAHSP
 Args    : -hmmstate_seq => the string representing the state output from WABA

Methods code

sub hmmstate_string {

   my ($self,$val) = @_;
   if( defined $val ) { 
       $self->{'_hmmstate_string'} = $val;
   }
   return $self->{'_hmmstate_string'};

}

sub homolgy_string {

   my ($self) = @_;
   return '';
}


1;

}

sub new {

  my($class,@args) = @_;

  # gotta do some preprocessing before we send the arguments to the superclass
  my ($len,$qs,$hs) = Bio::Root::RootI->_rearrange([qw(HSP_LENGTH
						       QUERY_SEQ 
						       HIT_SEQ)],@args);  
  if( $len != length($qs) ) {
    Bio::Root::RootI->warn("HSP_LENGTH must equal length of query_seq string, using value from QUERY_SEQ\n");
      $len = length($qs);
  }
  my( $homol_seq,$gapct,$identical) = ('',0,0);
  
  for(my $i=0;$i<$len;$i++) {
      my $q = substr($qs,$i,1);
      my $h = substr($hs,$i,1);
      if( $q eq '-' || $h eq '-' ) {
	  $homol_seq .= ' ';
	  $gapct ++;
      } elsif( $q eq $h ) { 
	  $homol_seq .= '|';
	  $identical++;
      } else { 
	  $homol_seq .= ' ';
      }
  }
  my $self = $class->SUPER::new('-conserved' => $identical,
				'-identical' => $identical,
				'-gaps'      => $gapct,
				'-homology_seq' => $homol_seq,
				@args);
    
  my ($hmmst) = $self->_rearrange([qw(HMMSTATE_SEQ)],@args);
  defined $hmmst && $self->hmmstate_string($hmmst);
  
  $self->add_tag_value('Target' , join(" ","Sequence:".$self->hit->seq_id, 
				       $self->hit->start, $self->hit->end));

  return $self;

}

General documentation

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.

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  bioperl-bugs@bioperl.org
  http://bugzilla.bioperl.org/

Email jason@bioperl.org
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Additional contributors names and emails here

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