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Bio/Align/ProteinStatistics.pm  view on Meta::CPAN

	   # are fraction of amino acids differing, as also in the
	   # case of the PAM distance. If the fraction of amino acids
	   # differing gets larger than 0.8541 the distance becomes
	   # infinite.

	   my $D = 1 - ( $match / $scored );
	   if( $D < 0.8541 ) {
	       $D = - log ( 1 - $D - (0.2 * ($D ** 2)));
	       $values[$j][$i] = $values[$i][$j] = sprintf($precisionstr,$D);
	   } else { 
	       $values[$j][$i] = $values[$i][$j] = '    NaN';
	   }
	   # fwd and rev lookup
	   $dist{$names[$i]}->{$names[$j]} = [$i,$j];
	   $dist{$names[$j]}->{$names[$i]} = [$i,$j];	   

           # (diagonals) distance is 0 for same sequence
	   $dist{$names[$j]}->{$names[$j]} = [$j,$j];	   
	   $values[$j][$j] = sprintf($precisionstr,0); 

       }

Bio/MapIO/fpc.pm  view on Meta::CPAN

            else {
                $_contigs{$ctgname}{'group'}  = "?";
            }
        }
        elsif ($line =~ /^User_remark\s+"(.+)"/) {
            $_contigs{$ctgname}{'usr_remark'} = $1;
        }
        elsif ($line =~ /^Trace_remark\s+"(.+)"/) {
            $_contigs{$ctgname}{'trace_remark'} = $1;
        }
        elsif ($grpabbr && $line =~ /^Chr_remark\s+"(\W|$grpabbr((\d+)|(\w+)|([.\w\d]+)))\s*(\{(.*)\}|\[(.*)\])?"\s+(Pos\s+((\d.)+|NaN))(NOEDIT)?/)
        {
            my $grpmatch = $2;
            my $pos = $10;
            if ($pos eq "NaN") {
                $pos = 0;
                print "Warning: Nan encountered for Contig position \n";
            }
            $_contigs{$ctgname}{'chr_remark'}   = $6;
            $_contigs{$ctgname}{'position'} = $pos;
            $_contigs{$ctgname}{'subgroup'} = 0;

            if (defined($grpmatch)) {
                $_contigs{$ctgname}{'anchor'} = 1;