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lib/Bio/Trace/ABIF.pm  view on Meta::CPAN

		($self->{'_B1Pt2'}) = map { ($_ < $SHORT_MID) ? $_ : $_ - $SHORT_MAX }
			$self->get_data_item('B1Pt', 2, 'n');
	}
	return $self->{'_B1Pt2'};
}

=head2 peak1_location_orig()

  Usage     : $pl = peak1_location_orig();
  Returns   : The peak 1 location (orig);
              undef if the data item is not in the file.
  ABIF Tag  : B1Pt1
  ABIF Type : short
  File Type : ab1
  
This data item is from SeqScape(R) v2.5 and Sequencing Analysis v5.2 Software.

=cut

sub peak1_location_orig {
	my $self = shift;
	unless (defined $self->{'_B1Pt1'}) {
		($self->{'_B1Pt1'}) = map { ($_ < $SHORT_MID) ? $_ : $_ - $SHORT_MAX }
			$self->get_data_item('B1Pt', 1, 'n');
	}
	return $self->{'_B1Pt1'};
}

=head2 peak_area_ratio()

  Usage     : $par = $abif->peak_area_ratio();
  Returns   : The peak area ratio;
              undef if the data item is not in the file.
  ABIF Tag  : phAR1
  ABIF Type : float
  File Type : ab1

Returns the peak area ratio (equivalent to TRACE_PEAK_AREA_RATIO in phd1 file).

This data item is from SeqScape(R) v2.5 and Sequencing Analysis v5.2 Software.
  
=cut

sub peak_area_ratio {
	my $self = shift;
	unless (defined $self->{'_phAR1'}) {
		my $r = undef;
		($r) = $self->get_data_item('phAR', 1, 'B32');
		if (defined $r) {
			$self->{'_phAR1'} = $self->_ieee2decimal($r);
		}
	}
	return $self->{'_phAR1'};
}

=head2 peaks()

  Usage     : @pks = $abif->peaks(1);
  Returns   : An array of peak hashes. Each peak hash contains the following attributes:
              'position', 'height', 'beginPos', 'endPos', 'beginHI', 'endHI', 
              'area', 'volume', 'fragSize', 'isEdited', 'label';
              () if the data item is not in the file.
            
  ABIF Tag  : PEAK
  ABIF Type : user-defined structure
  File Type : fsa

Returns the data associated with PEAK data structures.

=cut

sub peaks {
	my ($self, $n) = @_;
	my $k = '_PEAK' . $n;
	my ($position, $height, $beginPos, $endPos, $beginHI, $endHI, $area, $volume, $fragSize, $isEdited, $label);
	my $s = undef;
	my @raw_data;
	my @peak_array;
	my $i;
	
	unless (defined $self->{$k}) {
		@raw_data = $self->get_data_item('PEAK', $n, '(NnNNnnNNB32nZ64)*');
		for ($i = 0; $i < @raw_data; $i += 11) {
			($position, $height, $beginPos, $endPos, $beginHI, $endHI, $area, $volume, $s, $isEdited, $label) = @raw_data[$i .. $i+10];
			$fragSize = $self->_ieee2decimal($s) if (defined $s);
			my $peak = {};
			$peak->{position} = $position;
			$peak->{height} = $height;
			$peak->{beginPos} = $beginPos;
			$peak->{endPos} = $endPos;
			$peak->{beginHI} = $beginHI;
			$peak->{endHI} = $endHI;
			$peak->{area} = $area;
			$peak->{volume} = $volume;
			$peak->{fragSize} = $fragSize;
			$peak->{isEdited} = $isEdited;
			$peak->{label} = $label;
			push @peak_array, $peak;
		}
	$self->{$k} = (@peak_array) ? [ @peak_array ] : [ ];
	}
	return @{$self->{$k}};
}

=head2 pixel_bin_size()

  Usage     : $n = $abif->pixel_bin_size();
  Returns   : The pixel bin size;
              undef if the data item is not in the file.
  ABIF Tag  : PXLB1
  ABIF Type : long
  File Type : ab1, fsa
  
=cut

sub pixel_bin_size {
	my $self = shift;
	unless (defined $self->{'_PXLB1'}) {
		($self->{'_PXLB1'}) = map { ($_ < $LONG_MID) ? $_ : $_ - $LONG_MAX }
			$self->get_data_item('PXLB', 1, 'N');
	}
	return $self->{'_PXLB1'};
}

=head2 pixels_lane()

  Usage     : $n = $abif->pixels_lane();
  Returns   : The pixels averaged per lane;
              undef if the data item is not in the file.
  ABIF Tag  : NAVG1
  ABIF Type : short
  File Type : ab1, fsa
  
=cut

sub pixels_lane {
	my $self = shift;
	unless (defined $self->{'_NAVG1'}) {
		($self->{'_NAVG1'}) =  map { ($_ < $SHORT_MID) ? $_ : $_ - $SHORT_MAX }
			$self->get_data_item('NAVG', 1, 'n');
	}
	return $self->{'_NAVG1'};
}

=head2 plate_type()

  Usage     : $s = $abif->plate_type();
  Returns   : The plate type;
              undef if the data item is not in the file.
  ABIF Tag  : PTYP1
  ABIF Type : cString
  File Type : ab1, fsa
  
Returns the plate type. Allowed values are 96-Well, 384-Well;