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stmt |
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cond |
sub |
pod |
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package Finnigan::Profile; |
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use strict; |
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use warnings FATAL => qw( all ); |
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our $VERSION = 0.0206; |
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use Carp; |
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use Finnigan; |
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use base 'Finnigan::Decoder'; |
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3485
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my $preamble = [ |
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"first value" => ['d<', 'Float64'], |
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"step" => ['d<', 'Float64'], |
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"peak count" => ['V', 'UInt32'], |
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"nbins" => ['V', 'UInt32'], |
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]; |
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sub decode { |
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my $self = bless Finnigan::Decoder->read($_[1], $preamble), $_[0]; |
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return $self->iterate_object($_[1], $self->{data}->{"peak count"}->{value}, chunks => 'Finnigan::ProfileChunk', $_[2]); # the last arg is layout |
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} |
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sub nchunks { # in place of the erroneous "peak_count" |
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shift->{data}->{"peak count"}->{value}; |
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} |
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sub peak_count { # deprecated |
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shift->{data}->{"peak count"}->{value}; |
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} |
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sub nbins { |
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shift->{data}->{"nbins"}->{value}; |
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} |
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36
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sub first_value { |
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1
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shift->{data}->{"first value"}->{value}; |
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} |
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40
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sub step { |
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1
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401
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my $self = shift; |
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1
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50
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10
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confess "undefined" unless $self; |
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1
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8
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$self->{data}->{"step"}->{value}; |
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} |
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46
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sub chunks { |
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0
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1
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shift->{data}->{"chunks"}->{value}; |
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} |
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50
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sub chunk { # a syntactic eye-sore remover |
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5
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5
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1
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833
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shift->{data}->{"chunks"}->{value}; |
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} |
53
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54
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sub set_converter { |
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1
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1
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1
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400
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$_[0]->{converter} = $_[1]; |
56
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} |
57
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58
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sub set_inverse_converter { |
59
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0
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0
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1
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$_[0]->{"inverse converter"} = $_[1]; |
60
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} |
61
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62
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sub bins { |
63
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1
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1
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1
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8
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my ($self, $range, $add_zeroes) = @_; |
64
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1
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2
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my @list; |
65
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1
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5
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my $start = $self->{data}->{"first value"}->{value}; |
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1
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4
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my $step = $self->{data}->{step}->{value}; |
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1
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50
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5
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unless ( $range ) { |
68
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1
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50
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6
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unless ( exists $self->{converter} ) { |
69
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0
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0
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$range = [$start, $start + $self->{data}->{nbins}->{value} * $step]; |
70
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} |
71
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} |
72
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73
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1
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50
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6
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push @list, [$range->[0], 0] if $add_zeroes; |
74
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1
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2
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my $last_bin_written = 0; |
75
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76
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1
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3
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my $shift = 0; # this is declared outside the chunk loop to allow |
77
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# writing the empty bin following the last chunk with |
78
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# the same amount of shift as in the last chunk |
79
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80
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1
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7
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foreach my $i ( 0 .. $self->{data}->{"peak count"}->{value} - 1 ) { # each chunk |
81
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580
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1746
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my $chunk = $self->{data}->{chunks}->{value}->[$i]; |
82
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580
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1653
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my $first_bin = $chunk->{data}->{"first bin"}->{value}; |
83
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580
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50
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1749
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$shift = $chunk->{data}->{fudge} ? $chunk->{data}->{fudge}->{value} : 0; |
84
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580
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1337
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my $x = $start + $first_bin * $step; |
85
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86
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580
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50
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33
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1966
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if ( $add_zeroes and $last_bin_written < $first_bin - 1) { |
87
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# add an empty bin ahead of the chunk, unless there is no gap |
88
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# between this and the previous chunk |
89
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0
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0
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my $x0 = $x - $step; |
90
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0
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0
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0
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my $x_conv = exists $self->{converter} ? &{$self->{converter}}($x0) + $shift : $x0; |
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0
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0
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91
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0
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0
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push @list, [$x_conv, 0]; |
92
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} |
93
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94
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580
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1674
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foreach my $j ( 0 .. $chunk->{data}->{nbins}->{value} - 1) { |
95
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3878
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50
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8767
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my $x_conv = exists $self->{converter} ? &{$self->{converter}}($x) + $shift : $x; |
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3878
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13554
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96
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3878
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6684
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$x += $step; |
97
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3878
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50
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8884
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if ( $range ) { |
98
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0
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0
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0
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if ( exists $self->{converter} ) { |
99
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0
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0
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0
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0
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next unless $x_conv >= $range->[0] and $x_conv <= $range->[1]; |
100
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} |
101
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else { |
102
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# frequencies have the reverse order |
103
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0
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0
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0
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0
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next unless $x_conv <= $range->[0] and $x_conv >= $range->[1]; |
104
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} |
105
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} |
106
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3878
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5915
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my $bin = $first_bin + $j; |
107
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3878
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15246
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push @list, [$x_conv, $chunk->{data}->{signal}->{value}->[$j]]; |
108
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3878
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7620
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$last_bin_written = $first_bin + $j; |
109
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} |
110
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111
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580
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0
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33
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2008
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if ( $add_zeroes |
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33
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112
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and |
113
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$i < $self->{data}->{"peak count"}->{value} - 1 |
114
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and |
115
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$last_bin_written < $self->{data}->{chunks}->{value}->[$i+1]->{data}->{"first bin"}->{value} - 1 |
116
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) { |
117
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# add an empty bin following the chunk, unless there is no gap |
118
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# between this and the next chunk |
119
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0
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0
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my $bin = $last_bin_written + 1; |
120
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# $x has been incremented inside the chunk loop |
121
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0
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0
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0
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my $x_conv = exists $self->{converter} ? &{$self->{converter}}($x) + $shift: $x; |
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0
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0
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122
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0
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0
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push @list, [$x_conv, 0]; |
123
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0
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0
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$last_bin_written++; |
124
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} |
125
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} |
126
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127
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1
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50
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33
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8
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if ( $add_zeroes and $last_bin_written < $self->{data}->{nbins}->{value} - 1 ) { |
128
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# add an empty bin following the last chunk, unless there is no gap |
129
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# left between it and the end of the range ($self->nbins - 1) |
130
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0
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0
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my $x = $start + ($last_bin_written + 1) * $step; |
131
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0
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0
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0
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my $x_conv = exists $self->{converter} ? &{$self->{converter}}($x) + $shift: $x; |
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0
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0
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132
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0
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0
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push @list, [$x_conv, 0]; |
133
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0
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0
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0
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push @list, [$range->[1], 0] if $add_zeroes; |
134
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} |
135
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1
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9
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return \@list; |
136
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} |
137
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138
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sub print_bins { |
139
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0
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0
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1
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my ($self, $range, $add_zeroes) = @_; |
140
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0
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my @list; |
141
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0
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my $data = $self->{data}; |
142
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0
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my $start = $data->{"first value"}->{value}; |
143
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0
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my $step = $data->{step}->{value}; |
144
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0
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my $chunks = $data->{chunks}->{value}; |
145
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146
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0
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0
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unless ( $range ) { |
147
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0
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0
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unless (exists $self->{converter} ) { |
148
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0
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$range = [$start, $start + $data->{nbins}->{value} * $step]; |
149
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} |
150
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} |
151
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152
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0
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0
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print "$range->[0]\t0\n" if $add_zeroes; |
153
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154
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0
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my $shift = 0; # this is declared outside the chunk loop to allow |
155
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# writing the empty bin following the last chunk with |
156
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# the same amount of shift as in the last chunk |
157
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158
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0
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foreach my $i ( 0 .. $data->{"peak count"}->{value} - 1 ) { # each chunk |
159
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0
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my $chunk = $chunks->[$i]->{data}; |
160
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0
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my $first_bin = $chunk->{"first bin"}->{value}; |
161
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0
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0
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$shift = $chunk->{fudge} ? $chunk->{fudge}->{value} : 0; |
162
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0
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my $x = $start + $first_bin * $step; |
163
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0
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0
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my $x_conv = exists $self->{converter} ? &{$self->{converter}}($x) + $shift : $x; |
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0
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164
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165
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# print all points in the chunk that fall within the specified range |
166
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0
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foreach my $j ( 0 .. $chunk->{nbins}->{value} - 1) { |
167
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0
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0
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my $x_conv = exists $self->{converter} ? &{$self->{converter}}($x) + $shift : $x; |
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0
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168
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0
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$x += $step; |
169
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0
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0
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if ( $range ) { |
170
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0
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0
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if ( exists $self->{converter} ) { |
171
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0
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0
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0
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next unless $x_conv >= $range->[0] and $x_conv <= $range->[1]; |
172
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} |
173
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else { |
174
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# frequencies have the reverse order |
175
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0
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0
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0
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next unless $x_conv <= $range->[0] and $x_conv >= $range->[1]; |
176
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} |
177
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} |
178
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0
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my $bin = $first_bin + $j; |
179
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0
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print "$x_conv\t" . $chunk->{signal}->{value}->[$j] . "\n"; |
180
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} |
181
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182
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0
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0
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0
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if ( $add_zeroes and $i < $data->{"peak count"}->{value} - 1 ) { |
183
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0
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my $from = $chunks->[$i]->first_bin + $chunks->[$i]->{data}->{nbins}->{value}; |
184
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0
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my $to = $chunks->[$i+1]->first_bin - 1; |
185
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0
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0
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if ($to >= $from) { |
186
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0
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foreach my $bin ( $from .. $to ) { |
187
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0
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|
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my $x = $start + $bin * $step; |
188
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0
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0
|
|
|
|
|
my $x_conv = exists $self->{converter} ? &{$self->{converter}}($x) + $shift: $x; |
|
0
|
|
|
|
|
|
|
189
|
0
|
0
|
|
|
|
|
if ( $range ) { |
190
|
0
|
0
|
|
|
|
|
if ( exists $self->{converter} ) { |
191
|
0
|
0
|
0
|
|
|
|
next unless $x_conv >= $range->[0] and $x_conv <= $range->[1]; |
192
|
|
|
|
|
|
|
} |
193
|
|
|
|
|
|
|
else { |
194
|
|
|
|
|
|
|
# frequencies have the reverse order |
195
|
0
|
0
|
0
|
|
|
|
next unless $x_conv <= $range->[0] and $x_conv >= $range->[1]; |
196
|
|
|
|
|
|
|
} |
197
|
|
|
|
|
|
|
} |
198
|
0
|
|
|
|
|
|
print "$x_conv\t0\n"; |
199
|
|
|
|
|
|
|
} |
200
|
|
|
|
|
|
|
} |
201
|
|
|
|
|
|
|
} |
202
|
|
|
|
|
|
|
} |
203
|
|
|
|
|
|
|
|
204
|
|
|
|
|
|
|
# get the last bin number in the last chunk |
205
|
0
|
0
|
|
|
|
|
if ( $add_zeroes ) { |
206
|
0
|
|
|
|
|
|
my $last_chunk = $chunks->[$data->{"peak count"}->{value} - 1]; |
207
|
0
|
|
|
|
|
|
my $first_trailer_bin = $last_chunk->{data}->{"first bin"}->{value} + $last_chunk->{data}->{nbins}->{value}; |
208
|
0
|
0
|
|
|
|
|
if ( $first_trailer_bin < $data->{nbins}->{value} ) { |
209
|
0
|
|
|
|
|
|
foreach my $bin ( $first_trailer_bin .. $self->{data}->{nbins}->{value} - 1 ) { |
210
|
0
|
|
|
|
|
|
my $x = $start + $bin * $step; |
211
|
0
|
0
|
|
|
|
|
my $x_conv = exists $self->{converter} ? &{$self->{converter}}($x) + $shift : $x; |
|
0
|
|
|
|
|
|
|
212
|
0
|
0
|
|
|
|
|
if ( $range ) { |
213
|
0
|
0
|
|
|
|
|
if ( exists $self->{converter} ) { |
214
|
0
|
0
|
0
|
|
|
|
next unless $x_conv >= $range->[0] and $x_conv <= $range->[1]; |
215
|
|
|
|
|
|
|
} |
216
|
|
|
|
|
|
|
else { |
217
|
|
|
|
|
|
|
# frequencies have the reverse order |
218
|
0
|
0
|
0
|
|
|
|
next unless $x_conv <= $range->[0] and $x_conv >= $range->[1]; |
219
|
|
|
|
|
|
|
} |
220
|
|
|
|
|
|
|
} |
221
|
0
|
|
|
|
|
|
print "$x_conv\t0\n"; |
222
|
|
|
|
|
|
|
} |
223
|
|
|
|
|
|
|
} |
224
|
0
|
|
|
|
|
|
print "$range->[1]\t0\n"; |
225
|
|
|
|
|
|
|
} |
226
|
|
|
|
|
|
|
} |
227
|
|
|
|
|
|
|
|
228
|
|
|
|
|
|
|
1; |
229
|
|
|
|
|
|
|
__END__ |