| 1 | package Text::Levenshtein::Edlib; |
| 2 | |
| 3 | use 5.014000; |
| 4 | use strict; |
| 5 | use warnings; |
| 6 | use Carp; |
| 7 | use parent qw/Exporter/; |
| 8 | |
| 9 | my @constants = |
| 10 | qw/ |
| 11 | EDLIB_CIGAR_EXTENDED |
| 12 | EDLIB_CIGAR_STANDARD |
| 13 | EDLIB_EDOP_DELETE |
| 14 | EDLIB_EDOP_INSERT |
| 15 | EDLIB_EDOP_MATCH |
| 16 | EDLIB_EDOP_MISMATCH |
| 17 | EDLIB_MODE_HW |
| 18 | EDLIB_MODE_NW |
| 19 | EDLIB_MODE_SHW |
| 20 | EDLIB_STATUS_ERROR |
| 21 | EDLIB_STATUS_OK |
| 22 | EDLIB_TASK_DISTANCE |
| 23 | EDLIB_TASK_LOC |
| 24 | EDLIB_TASK_PATH/; |
| 25 | |
| 26 | our %EXPORT_TAGS = |
| 27 | (all => [ @constants, qw/align distance to_cigar/ ], constants => \@constants); |
| 28 | our @EXPORT_OK = ( @{ $EXPORT_TAGS{'all'} } ); |
| 29 | our @EXPORT = ( @{ $EXPORT_TAGS{'constants'} } ); |
| 30 | our $VERSION = '0.001'; |
| 31 | |
| 32 | require XSLoader; |
| 33 | XSLoader::load('Text::Levenshtein::Edlib', $VERSION); |
| 34 | |
| 35 | sub AUTOLOAD { |
| 36 | # This AUTOLOAD is used to 'autoload' constants from the constant() |
| 37 | # XS function. |
| 38 | |
| 39 | my $constname; |
| 40 | our $AUTOLOAD; |
| 41 | ($constname = $AUTOLOAD) =~ s/.*:://; |
| 42 | croak "&Text::Levenshtein::Edlib::constant not defined" if $constname eq 'constant'; |
| 43 | my ($error, $val) = constant($constname); |
| 44 | if ($error) { croak $error; } |
| 45 | { |
| 46 | no strict 'refs'; |
| 47 | *$AUTOLOAD = sub { $val }; |
| 48 | } |
| 49 | goto &$AUTOLOAD; |
| 50 | } |
| 51 | |
| 52 | sub align { |
| 53 | my ($q, $t, $k, $mode, $task) = @_; |
| 54 | $k //= -1; |
| 55 | $mode //= EDLIB_MODE_NW(); |
| 56 | $task //= EDLIB_TASK_PATH(); |
| 57 | my $result = edlibAlign($q, $t, $k, $mode, $task); |
| 58 | my ($dist, $alpha_len, $end, $start, $align) = @$result; |
| 59 | return {} if $dist == -1; |
| 60 | my %ret; |
| 61 | $ret{editDistance} = $dist; |
| 62 | $ret{alphabetLength} = $alpha_len; |
| 63 | $ret{endLocations} = $end if defined $end; |
| 64 | $ret{startLocations} = $start if defined $start; |
| 65 | $ret{alignment} = $align if defined $align; |
| 66 | \%ret |
| 67 | } |
| 68 | |
| 69 | sub distance { |
| 70 | my ($q, $t, $k, $mode) = @_; |
| 71 | align($q, $t, $k, $mode, EDLIB_TASK_DISTANCE())->{editDistance} |
| 72 | } |
| 73 | |
| 74 | sub to_cigar { |
| 75 | my ($align, $format) = @_; |
| 76 | $align = pack 'C*', @$align; |
| 77 | $format //= EDLIB_CIGAR_STANDARD(); |
| 78 | edlibAlignmentToCigar($align, $format); |
| 79 | } |
| 80 | |
| 81 | 1; |
| 82 | __END__ |
| 83 | |
| 84 | =encoding utf-8 |
| 85 | |
| 86 | =head1 NAME |
| 87 | |
| 88 | Text::Levenshtein::Edlib - XS edit distance and optimal alignment path calculation |
| 89 | |
| 90 | =head1 SYNOPSIS |
| 91 | |
| 92 | use feature 'say'; |
| 93 | |
| 94 | use Text::Levenshtein::Edlib qw/:all/; |
| 95 | say distance 'kitten', 'sitting'; # prints '3' |
| 96 | say 'Distance > 2!' |
| 97 | if !defined distance 'kitten', 'sitting', 2; # prints 'Distance > 2!' |
| 98 | |
| 99 | my $align = align('kitten', 'sitting'); |
| 100 | say "Edit distance is: $align->{editDistance}"; |
| 101 | say "Alphabet length is: $align->{alphabetLength}"; |
| 102 | say "Start locations are: @{$align->{startLocations}}"; |
| 103 | say "End locations are: @{$align->{endLocations}}"; |
| 104 | say "Alignment path is: @{$align->{alignment}}"; |
| 105 | say "Alignment path (in CIGAR format): ", to_cigar $align->{alignment}; |
| 106 | say "Alignment path (in extended CIGAR format): ", |
| 107 | to_cigar $align->{alignment}, EDLIB_CIGAR_EXTENDED; |
| 108 | |
| 109 | =head1 DESCRIPTION |
| 110 | |
| 111 | Text::Levenshtein::Edlib is a wrapper around the edlib library that |
| 112 | computes Levenshtein edit distance and optimal alignment path for a |
| 113 | pair of strings. |
| 114 | |
| 115 | It B<does not handle UTF-8 strings>, for those |
| 116 | L<Text::Levenshtein::XS> can compute edit distance but not alignment |
| 117 | path. |
| 118 | |
| 119 | This module has two functions: |
| 120 | |
| 121 | =over |
| 122 | |
| 123 | =item B<distance>(I<$query>, I<$target>, [I<$max_distance>, [I<$mode>]]) |
| 124 | |
| 125 | This is the basic interface to the library. It is compatible with the |
| 126 | function of the same name in L<Text::Levenshtein::XS>. |
| 127 | |
| 128 | It returns the edit distance between the two given strings. If the |
| 129 | third argument is specified, and the edit distance is greater than the |
| 130 | value of the third argument, then the function finishes the |
| 131 | computation early and returns undef. See below for the meaning of the |
| 132 | optional I<$mode> argument. |
| 133 | |
| 134 | =item B<align>(I<$query>, I<$target>, [I<$max_distance>, [I<$mode>, [I<$task>]]]) |
| 135 | |
| 136 | This is the full-featured interface to the library. |
| 137 | |
| 138 | It returns a hashref with the following keys: |
| 139 | |
| 140 | =over |
| 141 | |
| 142 | =item C<editDistance> |
| 143 | |
| 144 | The edit distance of the two strings. |
| 145 | |
| 146 | =item C<alphabetLength> |
| 147 | |
| 148 | The number of different characters in the query and target together. |
| 149 | |
| 150 | =item C<endLocations> |
| 151 | |
| 152 | Array of zero-based positions in target where optimal alignment paths |
| 153 | end. If gap after query is penalized, gap counts as part of query |
| 154 | (NW), otherwise not. |
| 155 | |
| 156 | =item C<startLocations> |
| 157 | |
| 158 | Array of zero-based positions in target where optimal alignment paths |
| 159 | start, they correspond to endLocations. If gap before query is |
| 160 | penalized, gap counts as part of query (NW), otherwise not. |
| 161 | |
| 162 | =item C<alignment> |
| 163 | |
| 164 | Alignment is found for first pair of start and end locations. |
| 165 | Alignment is sequence of numbers: 0, 1, 2, 3. 0 stands for match. 1 |
| 166 | stands for insertion to target. 2 stands for insertion to query. 3 |
| 167 | stands for mismatch. You can use the C<EDLIB_EDOP_*> constants instead |
| 168 | of 0, 1, 2, and 3. Alignment aligns query to target from begining of |
| 169 | query till end of query. If gaps are not penalized, they are not in |
| 170 | alignment. |
| 171 | |
| 172 | =back |
| 173 | |
| 174 | The third argument, I<$max_distance>, works similarly to the third |
| 175 | argument of B<distance>: if the distance is more than its value, this |
| 176 | function returns an empty hashref. Default value is -1, which disables |
| 177 | this optimization. |
| 178 | |
| 179 | The fourth argument, I<$mode>, chooses how Edlib should treat gaps |
| 180 | before and after query. The options are: |
| 181 | |
| 182 | =over |
| 183 | |
| 184 | =item C<EDLIB_MODE_NW> (default) |
| 185 | |
| 186 | Global method - gaps are not ignored. This is the standard Levenshtein |
| 187 | distance, and is the default if I<$mode> is not specified. |
| 188 | |
| 189 | =item C<EDLIB_MODE_SHW> |
| 190 | |
| 191 | Prefix method - gaps at query end are ignored. So the edit distance |
| 192 | between C<AACT> and C<AACTGGC> is 0, because we can ignore the C<GGC> |
| 193 | at the end. |
| 194 | |
| 195 | =item C<EDLIB_MODE_HW> |
| 196 | |
| 197 | Infix method - gaps at both query start and end are ignored. So the |
| 198 | edit distance between C<ACT> and C<CGACTGAC> is 0, because C<CG> at |
| 199 | the beginning and C<GAC> at the end of the target are ignored. |
| 200 | |
| 201 | =back |
| 202 | |
| 203 | The fifth argument, I<$task>, chooses what we want to compute. |
| 204 | If set to C<EDLIB_TASK_PATH> (default), all the keys described above will be computed. |
| 205 | If set to C<EDLIB_TASK_LOC>, all keys except for C<alignment> will be computed. |
| 206 | If set to C<EDLIB_TASK_DISTANCE>, all keys except for C<alignment> and C<startLocations> will be computed. |
| 207 | The less we compute, the faster the function will run. |
| 208 | |
| 209 | =back |
| 210 | |
| 211 | =head2 EXPORT |
| 212 | |
| 213 | All constants by default. You can export the functions C<align> and |
| 214 | C<distance> and any of the constants below. You can use the tags |
| 215 | C<:constants> to export every constant, and C<:all> to export every |
| 216 | constant, C<align> and C<distance>. |
| 217 | |
| 218 | =head2 Exportable constants |
| 219 | |
| 220 | EDLIB_CIGAR_EXTENDED |
| 221 | EDLIB_CIGAR_STANDARD |
| 222 | EDLIB_EDOP_DELETE |
| 223 | EDLIB_EDOP_INSERT |
| 224 | EDLIB_EDOP_MATCH |
| 225 | EDLIB_EDOP_MISMATCH |
| 226 | EDLIB_MODE_HW |
| 227 | EDLIB_MODE_NW |
| 228 | EDLIB_MODE_SHW |
| 229 | EDLIB_STATUS_ERROR |
| 230 | EDLIB_STATUS_OK |
| 231 | EDLIB_TASK_DISTANCE |
| 232 | EDLIB_TASK_LOC |
| 233 | EDLIB_TASK_PATH |
| 234 | |
| 235 | =head1 SEE ALSO |
| 236 | |
| 237 | L<https://github.com/Martinsos/edlib/>, L<http://martinsosic.com/edlib/edlib_8h.html> |
| 238 | |
| 239 | =head1 AUTHOR |
| 240 | |
| 241 | Marius Gavrilescu, E<lt>marius@ieval.roE<gt> |
| 242 | |
| 243 | =head1 COPYRIGHT AND LICENSE |
| 244 | |
| 245 | Copyright (C) 2017 by Marius Gavrilescu |
| 246 | |
| 247 | This library is free software; you can redistribute it and/or modify |
| 248 | it under the same terms as Perl itself, either Perl version 5.22.3 or, |
| 249 | at your option, any later version of Perl 5 you may have available. |
| 250 | |
| 251 | |
| 252 | =cut |