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annotate lib/CPT/Util/CRC64.pm @ 1:d724f34e671d draft default tip

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planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
author cpt
date Mon, 05 Jun 2023 02:50:07 +0000
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1 package CPT::Util::CRC64;
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2
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3 # This was taken from Bio::GMOD::Bulkfiles::SWISS_CRC64
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4
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5 use Moose;
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6 use strict;
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7 use warnings;
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8 use autodie;
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9
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11 has 'POLY64REVh' => ( is => 'ro', isa => 'Any', default => 0xd8000000 );
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12 has 'CRCTableh' => ( is => 'rw', isa => 'ArrayRef', default => sub { [] });
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13 has 'CRCTablel' => ( is => 'rw', isa => 'ArrayRef', default => sub { [] });
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14 has 'initialized' => ( is => 'rw', isa => 'Bool', default => 0 );
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15 has 'size' => ( is => 'rw', isa => 'Int' );
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16 has 'crcl' => (is => 'rw', isa => 'Any', default => 0);
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17 has 'crch' => (is => 'rw', isa => 'Any', default => 0);
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18
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19 sub add {
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20 my ($self, $sequence) = @_;
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21 my $crcl = $self->crcl();
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22 my $crch = $self->crch();
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23 my $size = $self->size();
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24 my @CRCTableh = @{$self->CRCTableh()};
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25 my @CRCTablel = @{$self->CRCTablel()};
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26
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27 foreach (split //, $sequence){
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28 my $shr = ($crch & 0xFF) << 24;
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29 my $temp1h = $crch >> 8;
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30 my $temp1l = ($crcl >> 8) | $shr;
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31 my $tableindex = ($crcl ^ (unpack "C", $_)) & 0xFF;
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32 $crch = $temp1h ^ $CRCTableh[$tableindex];
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33 $crcl = $temp1l ^ $CRCTablel[$tableindex];
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34 $size++;
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35 }
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36 $self->crcl($crcl);
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37 $self->crch($crch);
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38 $self->size($size);
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39 }
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40
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41 sub hexsum {
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42 my ($self) = @_;
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43 my $crcl = $self->crcl();
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44 my $crch = $self->crch();
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45 return sprintf("%08X%08X", $crch, $crcl);
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46 }
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47
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48 sub init {
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49 my ($self) = @_;
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50 $self->crcl(0);
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51 $self->crch(0);
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52 $self->size(0);
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53 my @h;
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54 my @l;
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55 my $POLY64REVh = $self->POLY64REVh();
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56 if(! $self->initialized() ){
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57 $self->initialized(1);
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58 for (my $i=0; $i<256; $i++) {
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59 my $partl = $i;
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60 my $parth = 0;
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61 for (my $j=0; $j<8; $j++) {
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62 my $rflag = $partl & 1;
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63 $partl >>= 1;
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64 $partl |= (1 << 31) if $parth & 1;
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65 $parth >>= 1;
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66 $parth ^= $POLY64REVh if $rflag;
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67 }
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68 $h[$i] = $parth;
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69 $l[$i] = $partl;
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70 }
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71 $self->CRCTableh(\@h);
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72 $self->CRCTablel(\@l);
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73 }
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74 }
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75
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76 sub crc64 {
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77 my ($self, $sequence) = @_;
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78 $self->init();
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79 $self->add($sequence);
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80 return $self->hexsum();
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81 }
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82
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83 no Moose;
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84
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85 1;
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86
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87 __END__
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88
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89 =pod
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90
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91 =encoding UTF-8
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92
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93 =head1 NAME
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94
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95 CPT::Util::CRC64
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96
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97 =head1 VERSION
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98
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99 version 1.99.4
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100
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101 =head1 CRC64 perl module documentation
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102
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103 =head2 NAME
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104
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105 CRC64 - Calculate the cyclic redundancy check.
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106
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107 =head2 SYNOPSIS
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108
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109 use CPT::Util::CRC64;
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110
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111 my $crc = CPT::Util::CRC64->new();
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112 $crc = $crc->add("IHATEMATH");
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113 #returns the string "E3DCADD69B01ADD1"
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114
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115 =head2 DESCRIPTION
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116
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117 SWISS-PROT + TREMBL use a 64-bit Cyclic Redundancy Check for the
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118 amino acid sequences.
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119
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120 The algorithm to compute the CRC is described in the ISO 3309
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121 standard. The generator polynomial is x64 + x4 + x3 + x + 1.
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122 Reference: W. H. Press, S. A. Teukolsky, W. T. Vetterling, and B. P.
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123 Flannery, "Numerical recipes in C", 2nd ed., Cambridge University
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124 Press. Pages 896ff.
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125
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126 =head2 Functions
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127
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128 =over
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129
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130 =item crc64 string
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131
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132 Calculate the CRC64 (cyclic redundancy checksum) for B<string>.
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133
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134 In array context, returns two integers equal to the higher and lower
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135 32 bits of the CRC64. In scalar context, returns a 16-character string
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136 containing the CRC64 in hexadecimal format.
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137
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138 =back
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139
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140 =head1 AUTHOR
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141
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142 Alexandre Gattiker, gattiker@isb-sib.ch
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143
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144 Eric Rasche <rasche.eric@yandex.ru> (reworte for CPT framework)
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145
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146 =head1 ACKNOWLEDGEMENTS
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147
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148 Based on SPcrc, a C implementation by Christian Iseli, available at
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149 ftp://ftp.ebi.ac.uk/pub/software/swissprot/Swissknife/old/SPcrc.tar.gz
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150
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151 =head1 AUTHOR
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152
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153 Eric Rasche <rasche.eric@yandex.ru>
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154
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155 =head1 COPYRIGHT AND LICENSE
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156
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157 This software is Copyright (c) 2014 by Eric Rasche.
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158
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159 This is free software, licensed under:
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160
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161 The GNU General Public License, Version 3, June 2007
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162
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163 =cut