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planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
author cpt
date Mon, 05 Jun 2023 02:47:24 +0000
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0:b8b8b52904a5 1:f093e08f21f3
1 package CPT::Util::CRC64;
2
3 # This was taken from Bio::GMOD::Bulkfiles::SWISS_CRC64
4
5 use Moose;
6 use strict;
7 use warnings;
8 use autodie;
9
10
11 has 'POLY64REVh' => ( is => 'ro', isa => 'Any', default => 0xd8000000 );
12 has 'CRCTableh' => ( is => 'rw', isa => 'ArrayRef', default => sub { [] });
13 has 'CRCTablel' => ( is => 'rw', isa => 'ArrayRef', default => sub { [] });
14 has 'initialized' => ( is => 'rw', isa => 'Bool', default => 0 );
15 has 'size' => ( is => 'rw', isa => 'Int' );
16 has 'crcl' => (is => 'rw', isa => 'Any', default => 0);
17 has 'crch' => (is => 'rw', isa => 'Any', default => 0);
18
19 sub add {
20 my ($self, $sequence) = @_;
21 my $crcl = $self->crcl();
22 my $crch = $self->crch();
23 my $size = $self->size();
24 my @CRCTableh = @{$self->CRCTableh()};
25 my @CRCTablel = @{$self->CRCTablel()};
26
27 foreach (split //, $sequence){
28 my $shr = ($crch & 0xFF) << 24;
29 my $temp1h = $crch >> 8;
30 my $temp1l = ($crcl >> 8) | $shr;
31 my $tableindex = ($crcl ^ (unpack "C", $_)) & 0xFF;
32 $crch = $temp1h ^ $CRCTableh[$tableindex];
33 $crcl = $temp1l ^ $CRCTablel[$tableindex];
34 $size++;
35 }
36 $self->crcl($crcl);
37 $self->crch($crch);
38 $self->size($size);
39 }
40
41 sub hexsum {
42 my ($self) = @_;
43 my $crcl = $self->crcl();
44 my $crch = $self->crch();
45 return sprintf("%08X%08X", $crch, $crcl);
46 }
47
48 sub init {
49 my ($self) = @_;
50 $self->crcl(0);
51 $self->crch(0);
52 $self->size(0);
53 my @h;
54 my @l;
55 my $POLY64REVh = $self->POLY64REVh();
56 if(! $self->initialized() ){
57 $self->initialized(1);
58 for (my $i=0; $i<256; $i++) {
59 my $partl = $i;
60 my $parth = 0;
61 for (my $j=0; $j<8; $j++) {
62 my $rflag = $partl & 1;
63 $partl >>= 1;
64 $partl |= (1 << 31) if $parth & 1;
65 $parth >>= 1;
66 $parth ^= $POLY64REVh if $rflag;
67 }
68 $h[$i] = $parth;
69 $l[$i] = $partl;
70 }
71 $self->CRCTableh(\@h);
72 $self->CRCTablel(\@l);
73 }
74 }
75
76 sub crc64 {
77 my ($self, $sequence) = @_;
78 $self->init();
79 $self->add($sequence);
80 return $self->hexsum();
81 }
82
83 no Moose;
84
85 1;
86
87 __END__
88
89 =pod
90
91 =encoding UTF-8
92
93 =head1 NAME
94
95 CPT::Util::CRC64
96
97 =head1 VERSION
98
99 version 1.99.4
100
101 =head1 CRC64 perl module documentation
102
103 =head2 NAME
104
105 CRC64 - Calculate the cyclic redundancy check.
106
107 =head2 SYNOPSIS
108
109 use CPT::Util::CRC64;
110
111 my $crc = CPT::Util::CRC64->new();
112 $crc = $crc->add("IHATEMATH");
113 #returns the string "E3DCADD69B01ADD1"
114
115 =head2 DESCRIPTION
116
117 SWISS-PROT + TREMBL use a 64-bit Cyclic Redundancy Check for the
118 amino acid sequences.
119
120 The algorithm to compute the CRC is described in the ISO 3309
121 standard. The generator polynomial is x64 + x4 + x3 + x + 1.
122 Reference: W. H. Press, S. A. Teukolsky, W. T. Vetterling, and B. P.
123 Flannery, "Numerical recipes in C", 2nd ed., Cambridge University
124 Press. Pages 896ff.
125
126 =head2 Functions
127
128 =over
129
130 =item crc64 string
131
132 Calculate the CRC64 (cyclic redundancy checksum) for B<string>.
133
134 In array context, returns two integers equal to the higher and lower
135 32 bits of the CRC64. In scalar context, returns a 16-character string
136 containing the CRC64 in hexadecimal format.
137
138 =back
139
140 =head1 AUTHOR
141
142 Alexandre Gattiker, gattiker@isb-sib.ch
143
144 Eric Rasche <rasche.eric@yandex.ru> (reworte for CPT framework)
145
146 =head1 ACKNOWLEDGEMENTS
147
148 Based on SPcrc, a C implementation by Christian Iseli, available at
149 ftp://ftp.ebi.ac.uk/pub/software/swissprot/Swissknife/old/SPcrc.tar.gz
150
151 =head1 AUTHOR
152
153 Eric Rasche <rasche.eric@yandex.ru>
154
155 =head1 COPYRIGHT AND LICENSE
156
157 This software is Copyright (c) 2014 by Eric Rasche.
158
159 This is free software, licensed under:
160
161 The GNU General Public License, Version 3, June 2007
162
163 =cut