lib/Bio/SecreTary/Table.pm

   1 package Bio::SecreTary::Table;
   2 use strict;
   3 use warnings;
   4 use Carp;
   5 use Moose;
   6 use namespace::autoclean;
   7
   8 =head2 function new
   9
  10   Synopsis : my $table_obj =  Bio::SecreTary::Table->new(
  11         label => 'io_center',
  12         marked_position => 10,    # zero-based here
  13         table => [ [ 56.22, 63.83 ],[ 56.55, 56.78 ] ] );
  14
  15 =cut
  16
  17
  18 has label => (isa => 'Str', is => 'rw', required => 1 );
  19 has marked_position => (isa => 'Int', is => 'rw', required => 1 );
  20 has table => (isa => 'ArrayRef[ArrayRef[Num]]', is => 'rw', required => 1 );
  21
  22 # scale using aa frequency vector
  23 # the matrix should have 20 rows.
  24 # i.e. it is a ref to an array of 20 array refs.
  25 # each column is first normalized to sum to 1, then
  26 #
  27 sub scale {
  28     my $self = shift;
  29     my $v    = shift;
  30     my $m    = $self->table();
  31     ( scalar @$m == scalar @$v )
  32       || croak( "in Table::scale, sizes of m, v dont match:", scalar @$m, "  ", scalar @$v, "\n" );
  33
  34     my $ncols  = scalar @{$m->[0]};
  35     my @sums   = ( (0) x $ncols );
  36
  37     foreach my $row (@$m) {    # get the sums of each col; $row is an array ref
  38         for ( my $jcol = 0 ; $jcol < scalar @$row ; $jcol++ ) {
  39             $sums[$jcol] += $row->[$jcol];
  40         }
  41     }
  42     foreach my $row (@$m) {    # do something about elements which are zero
  43         for ( my $jcol = 0 ; $jcol < scalar @$row ; $jcol++ ) {
  44             my $element = $row->[$jcol];
  45             if ( $element == 0 ) {
  46                 $row->[$jcol] = 1 / $sums[$jcol]
  47                   ; # slavish imitation of pascal code - probably should be changed.
  48                  # $sums[$jcol] += $row->[$jcol]; # so sum reflects changed val of element
  49             }
  50         }
  51     }
  52     my $irow = 0;
  53     foreach my $row (@$m) {    #
  54         for ( my $jcol = 0 ; $jcol < scalar @$row ; $jcol++ ) {
  55             my $element = $row->[$jcol]/$sums[$jcol]; # normalize col sum to 1.
  56             $row->[$jcol] = log( $element / $v->[$irow] );
  57         }
  58         $irow++;
  59     }
  60     return $m;
  61 }
  62
  63 sub add_row{
  64     my $self = shift;
  65     my $new_row = shift; # array ref
  66     my $rows = $self->table(); # ref to array of array refs
  67     push @$rows, $new_row;
  68     return $self->table($rows);
  69 }
  70 sub table_as_string {
  71     my $self = shift;
  72     my $string = $self->label() . "\n";
  73     $string .= $self->marked_position . "\n";
  74     my $m = $self->table();
  75     foreach (@$m) {
  76         $string .=  join( ', ', @$_ ) . "\n";
  77     }
  78     return $string;
  79 }
  80
  81 __PACKAGE__->meta->make_immutable;
  82
  83 1;