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Summary

Bio::Align::PairwiseStatistics - Base statistic object for Pairwise Alignments

Package variables

Included modules

Inherit

Bio::Align::StatisticsI Bio::Root::Root

Synopsis

Give standard usage here

Description

Describe the object here

Methods

Methods description

 Title   : number_of_comparable_bases
 Usage   : my $bases = $stat->number_of_comparable_bases($aln);
 Function: Returns the count of the number of bases that can be
           compared (L) in this alignment ( length - gaps)
 Returns : integer
 Args    : Bio::Align::AlignI

 Title   : number_of_differences
 Usage   : my $nd = $stat->number_of_distances($aln);
 Function: Returns the number of differences between two  
 Returns : integer
 Args    : Bio::Align::AlignI

 Title   : number_of_gaps
 Usage   : my $nd = $stat->number_of_gaps($aln);
 Function: Returns the number of differences between two  
 Example :
 Returns : 
 Args    :

Methods code

BEGIN {

 $GapChars = '(\.|\-)';

}

sub number_of_comparable_bases {

   my ($self,$aln) = @_;
   if( ! defined $aln || ! $aln->isa('Bio::Align::AlignI') ) {
       $self->warn("Must provide a Bio::Align::AlignI compliant object to Bio::Align::PairwiseStatistics");
       return 0;
   } elsif( $aln->no_sequences != 2 ) { 
       $self->warn("only pairwise calculations currently supported");
   }
   my $L = $aln->length - $self->number_of_gaps($aln);
   return $L;

}

sub number_of_differences {

   my ($self,$aln) = @_;
    if( ! defined $aln || ! $aln->isa('Bio::Align::AlignI') ) {
	$self->warn("Must provide a Bio::Align::AlignI compliant object to Bio::Align::PairwiseStatistics");
	return 0;
    } elsif( $aln->no_sequences != 2 ) { 
	$self->warn("only pairwise calculations currently supported");
    }
   my (@seqs);
   foreach my $seq ( $aln->each_seq) {
       push @seqs, [ split(//,$seq->seq())];
   }
   my $firstseq = shift @seqs;
#    my $secondseq = shift @seqs;
   my $diffcount = 0;
   for (my $i = 0;$i<$aln->length; $i++ ) {
       next if( $firstseq->[$i]  =~ /^$GapChars$/);
       foreach my $seq ( @seqs ) {
	   next if( $seq->[$i]  =~ /^$GapChars$/);
	   if( $firstseq->[$i] ne $seq->[$i] ) {
	       $diffcount++;
	   }
       }
   }
   return $diffcount;

}

sub number_of_gaps {

   my ($self,$aln) = @_;
    if( ! defined $aln || ! $aln->isa('Bio::Align::AlignI') ) {
	$self->warn("Must provide a Bio::Align::AlignI compliant object to Bio::Align::PairwiseStatistics");
	return 0;
    } elsif( $aln->no_sequences != 2 ) { 
	$self->warn("only pairwise calculations currently supported");
    }
    my (@seqs);
    foreach my $seq ( $aln->each_seq) {
	push @seqs, [ split(//,$seq->seq())];
    }
    my $firstseq = shift @seqs;
#    my $secondseq = shift @seqs;
   my $gapcount = 0;
    for (my $i = 0;$i<$aln->length; $i++ ) { 
	($gapcount++) && next if( $firstseq->[$i]  =~ /^$GapChars$/);
	foreach my $seq ( @seqs ) {
	    ($gapcount++) && next if( $seq->[$i]  =~ /^$GapChars$/);
	}
    }
    return $gapcount;
}

1;

}

General documentation

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