Bio::Search::HSP WABAHSP
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Summary
Bio::Search::HSP::WABAHSP - HSP object suitable for describing WABA alignments
Package variables
No package variables defined.
Included modules
Bio::Root::RootI
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
newDescriptionCode
hmmstate_stringDescriptionCode
homology_stringDescriptionCode
Methods description
newcode    nextTop
 Title   : new
Usage : my $obj = Bio::Search::HSP::WABAHSP->new();
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
hmmstate_stringcodeprevnextTop
 Title   : hmmstate_string
Usage : my $hmmseq = $wabahsp->hmmstate_string();
Function: Get/Set the WABA HMM stateseq
Returns : string
Args : [optional] string
homology_stringcodeprevnextTop
 Title   : homolgy_string
Usage : my $homology_str = $hsp->homology_string();
Function: Homology string must be calculated for a WABA HSP so we can do
so here and cache the result so it is only done once
Returns : string
Args : none
Methods code
newdescriptionprevnextTop
sub new {
  my($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 $self;
}
hmmstate_stringdescriptionprevnextTop
sub hmmstate_string {
   my ($self,$val) = @_;
   if( defined $val ) { 
       $self->{'_hmmstate_string'} = $val;
   }
   return $self->{'_hmmstate_string'};
}
homology_stringdescriptionprevnextTop
sub homology_string {
   my ($self) = @_;
   return '';
}


1;
}
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
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 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
of the bugs and their resolution. Bug reports can be submitted via the
web:
  https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Jason StajichTop
Email jason@bioperl.org
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _