lib/Bio/SecreTary/Helix.pm

   1 package Bio::SecreTary::Helix;
   2 use Moose;
   3 use namespace::autoclean;
   4
   5 has center => (
   6     isa     => 'ArrayRef[Maybe[Num]]',
   7     is      => 'rw',
   8     default => sub { [ undef, undef ] }
   9 );
  10 has nterm => (
  11     isa     => 'ArrayRef[Maybe[Num]]',
  12     is      => 'rw',
  13     default => sub { [ undef, undef ] }
  14 );
  15 has cterm => (
  16     isa     => 'ArrayRef[Maybe[Num]]',
  17     is      => 'rw',
  18     default => sub { [ undef, undef ] }
  19 );
  20 has sh_nterm => (
  21     isa     => 'ArrayRef[Maybe[Num]]',
  22     is      => 'rw',
  23     default => sub { [ undef, undef ] }
  24 );
  25 has sh_cterm => (
  26     isa     => 'ArrayRef[Maybe[Num]]',
  27     is      => 'rw',
  28     default => sub { [ undef, undef ] }
  29 );
  30 has score => ( isa => 'Maybe[Num]', is => 'rw', default => undef );
  31 has nt_in => ( isa => 'Bool',       is => 'rw', default => undef );
  32
  33 sub get_descriptor_string {
  34     my $self   = shift;
  35     my $string = '';
  36     my $offset = 1;       # add this to 0-based positions to get unit-based
  37     if (0) {
  38         $string .= 'nt_in: ' . $self->nt_in() . "\n";
  39         $string .= 'score: ' . $self->score() . "\n";
  40         $string .= 'center: ' . join( ', ', @{ $self->center() } ) . "\n";
  41         $string .= 'nterm: ' . join( ', ', @{ $self->nterm() } ) . "\n";
  42         $string .= 'cterm: ' . join( ', ', @{ $self->cterm() } ) . "\n";
  43         $string .= 'sh_nterm: ' . join( ', ', @{ $self->sh_nterm() } ) . "\n";
  44         $string .= 'sh_cterm: ' . join( ', ', @{ $self->sh_cterm() } ) . "\n";
  45     }
  46     else {
  47         my $npos       = $self->nterm()->[0] + $offset;
  48         my $npos_core  = $self->sh_nterm()->[0] + $offset;
  49         my $cpos       = $self->cterm()->[0] + $offset;
  50         my $cpos_core  = $self->sh_cterm()->[0] + $offset;
  51         my $center_pos = $self->center()->[0] + $offset;
  52         $string .=
  53             $npos . '  ('
  54           . $npos_core . ')    '
  55           . $cpos . '  ('
  56           . $cpos_core . ')    '
  57           . $self->score() . '     '
  58           . $center_pos;
  59     }
  60
  61     return $string;
  62 }
  63
  64 sub short_description {
  65     my $self = shift;
  66     my $npos = $self->nterm()->[0] + 1;
  67     my $cpos = $self->cterm()->[0] + 1;
  68     return '[' . $self->score() . ",$npos,$cpos]";
  69 }
  70
  71 __PACKAGE__->meta->make_immutable;
  72
  73 1;