| line |
stmt |
bran |
cond |
sub |
pod |
time |
code |
|
1
|
|
|
|
|
|
|
package App::Greple::Regions; |
|
2
|
|
|
|
|
|
|
|
|
3
|
2
|
|
|
2
|
|
114571
|
use v5.14; |
|
|
2
|
|
|
|
|
15
|
|
|
4
|
2
|
|
|
2
|
|
11
|
use warnings; |
|
|
2
|
|
|
|
|
4
|
|
|
|
2
|
|
|
|
|
48
|
|
|
5
|
2
|
|
|
2
|
|
9
|
use Carp; |
|
|
2
|
|
|
|
|
4
|
|
|
|
2
|
|
|
|
|
96
|
|
|
6
|
2
|
|
|
2
|
|
11
|
use Data::Dumper; |
|
|
2
|
|
|
|
|
4
|
|
|
|
2
|
|
|
|
|
117
|
|
|
7
|
|
|
|
|
|
|
$Data::Dumper::Sortkeys = 1; |
|
8
|
|
|
|
|
|
|
|
|
9
|
2
|
|
|
2
|
|
14
|
use Exporter 'import'; |
|
|
2
|
|
|
|
|
6
|
|
|
|
2
|
|
|
|
|
210
|
|
|
10
|
|
|
|
|
|
|
our @EXPORT = qw(REGION_INSIDE REGION_OUTSIDE |
|
11
|
|
|
|
|
|
|
REGION_UNION REGION_INTERSECT |
|
12
|
|
|
|
|
|
|
match_regions |
|
13
|
|
|
|
|
|
|
classify_regions |
|
14
|
|
|
|
|
|
|
select_regions |
|
15
|
|
|
|
|
|
|
filter_regions |
|
16
|
|
|
|
|
|
|
merge_regions |
|
17
|
|
|
|
|
|
|
reverse_regions |
|
18
|
|
|
|
|
|
|
match_borders |
|
19
|
|
|
|
|
|
|
borders_to_regions |
|
20
|
|
|
|
|
|
|
); |
|
21
|
|
|
|
|
|
|
our %EXPORT_TAGS = ( ); |
|
22
|
|
|
|
|
|
|
our @EXPORT_OK = qw(); |
|
23
|
|
|
|
|
|
|
|
|
24
|
|
|
|
|
|
|
use constant { |
|
25
|
|
|
|
|
|
|
|
|
26
|
2
|
|
|
|
|
1381
|
REGION_AREA_MASK => 1, |
|
27
|
|
|
|
|
|
|
REGION_INSIDE => 0, |
|
28
|
|
|
|
|
|
|
REGION_OUTSIDE => 1, |
|
29
|
|
|
|
|
|
|
|
|
30
|
|
|
|
|
|
|
REGION_SET_MASK => 2, |
|
31
|
|
|
|
|
|
|
REGION_INTERSECT => 0, |
|
32
|
|
|
|
|
|
|
REGION_UNION => 2, |
|
33
|
2
|
|
|
2
|
|
14
|
}; |
|
|
2
|
|
|
|
|
4
|
|
|
34
|
|
|
|
|
|
|
|
|
35
|
|
|
|
|
|
|
sub new { |
|
36
|
0
|
|
|
0
|
0
|
0
|
my $class = shift; |
|
37
|
|
|
|
|
|
|
|
|
38
|
0
|
|
|
|
|
0
|
my $obj = bless { |
|
39
|
|
|
|
|
|
|
FLAG => undef, |
|
40
|
|
|
|
|
|
|
SPEC => undef, |
|
41
|
|
|
|
|
|
|
}, $class; |
|
42
|
|
|
|
|
|
|
|
|
43
|
0
|
0
|
|
|
|
0
|
$obj->configure(@_) if @_; |
|
44
|
|
|
|
|
|
|
|
|
45
|
0
|
|
|
|
|
0
|
$obj; |
|
46
|
|
|
|
|
|
|
} |
|
47
|
|
|
|
|
|
|
|
|
48
|
|
|
|
|
|
|
sub configure { |
|
49
|
0
|
|
|
0
|
0
|
0
|
my $obj = shift; |
|
50
|
0
|
|
|
|
|
0
|
while (@_ >= 2) { |
|
51
|
0
|
|
|
|
|
0
|
$obj->{$_[0]} = $_[1]; |
|
52
|
0
|
|
|
|
|
0
|
splice @_, 0, 2; |
|
53
|
|
|
|
|
|
|
} |
|
54
|
|
|
|
|
|
|
} |
|
55
|
|
|
|
|
|
|
|
|
56
|
0
|
|
|
0
|
0
|
0
|
sub spec { $_[0]->{SPEC} } |
|
57
|
0
|
|
|
0
|
0
|
0
|
sub flag { $_[0]->{FLAG} } |
|
58
|
|
|
|
|
|
|
sub is_x { |
|
59
|
0
|
|
|
0
|
0
|
0
|
my($p, $mask, $set) = @_; |
|
60
|
0
|
0
|
|
|
|
0
|
((ref $p ? $p->flag : $p) & $mask) == $set; |
|
61
|
|
|
|
|
|
|
} |
|
62
|
0
|
|
|
0
|
0
|
0
|
sub is_union { is_x $_[0], REGION_SET_MASK, REGION_UNION } |
|
63
|
0
|
|
|
0
|
0
|
0
|
sub is_intersect { is_x $_[0], REGION_SET_MASK, REGION_INTERSECT } |
|
64
|
0
|
|
|
0
|
0
|
0
|
sub is_inside { is_x $_[0], REGION_AREA_MASK, REGION_INSIDE } |
|
65
|
0
|
|
|
0
|
0
|
0
|
sub is_outside { is_x $_[0], REGION_AREA_MASK, REGION_OUTSIDE } |
|
66
|
|
|
|
|
|
|
|
|
67
|
|
|
|
|
|
|
package App::Greple::Regions::Holder { |
|
68
|
|
|
|
|
|
|
|
|
69
|
|
|
|
|
|
|
sub new { |
|
70
|
0
|
|
|
0
|
|
0
|
my $class = shift; |
|
71
|
0
|
|
|
|
|
0
|
bless [], $class; |
|
72
|
|
|
|
|
|
|
} |
|
73
|
|
|
|
|
|
|
|
|
74
|
|
|
|
|
|
|
sub append { |
|
75
|
0
|
|
|
0
|
|
0
|
my $obj = shift; |
|
76
|
0
|
|
|
|
|
0
|
push @$obj, App::Greple::Regions->new(@_); |
|
77
|
|
|
|
|
|
|
} |
|
78
|
|
|
|
|
|
|
|
|
79
|
|
|
|
|
|
|
sub regions { |
|
80
|
0
|
|
|
0
|
|
0
|
my $obj = shift; |
|
81
|
0
|
|
|
|
|
0
|
@$obj; |
|
82
|
|
|
|
|
|
|
} |
|
83
|
|
|
|
|
|
|
|
|
84
|
|
|
|
|
|
|
sub union { |
|
85
|
0
|
|
|
0
|
|
0
|
grep { $_->is_union } shift->regions; |
|
|
0
|
|
|
|
|
0
|
|
|
86
|
|
|
|
|
|
|
} |
|
87
|
|
|
|
|
|
|
|
|
88
|
|
|
|
|
|
|
sub intersect { |
|
89
|
0
|
|
|
0
|
|
0
|
grep { $_->is_intersect } shift->regions; |
|
|
0
|
|
|
|
|
0
|
|
|
90
|
|
|
|
|
|
|
} |
|
91
|
|
|
|
|
|
|
} |
|
92
|
|
|
|
|
|
|
|
|
93
|
|
|
|
|
|
|
sub match_regions { |
|
94
|
0
|
|
|
0
|
0
|
0
|
my %arg = @_; |
|
95
|
0
|
|
0
|
|
|
0
|
my $pattern = $arg{pattern} // croak "Parameter error"; |
|
96
|
0
|
0
|
|
|
|
0
|
my $regex = ref $pattern eq 'Regexp' ? $pattern : qr/$pattern/m; |
|
97
|
0
|
0
|
|
|
|
0
|
return &match_regions_by_group($regex) if $arg{group}; |
|
98
|
|
|
|
|
|
|
|
|
99
|
0
|
|
|
|
|
0
|
my @regions; |
|
100
|
|
|
|
|
|
|
|
|
101
|
2
|
|
|
2
|
|
16
|
no warnings 'utf8'; |
|
|
2
|
|
|
|
|
4
|
|
|
|
2
|
|
|
|
|
285
|
|
|
102
|
|
|
|
|
|
|
|
|
103
|
0
|
|
|
|
|
0
|
while (/$regex/gp) { |
|
104
|
|
|
|
|
|
|
## |
|
105
|
|
|
|
|
|
|
## this is much faster than: |
|
106
|
|
|
|
|
|
|
## my($s, $e) = ($-[0], $+[0]); |
|
107
|
|
|
|
|
|
|
## |
|
108
|
|
|
|
|
|
|
## calling pos() cost is not neglective, either. |
|
109
|
|
|
|
|
|
|
## |
|
110
|
0
|
|
|
|
|
0
|
my $pos = pos(); |
|
111
|
0
|
|
|
|
|
0
|
push @regions, [ $pos - length(${^MATCH}), $pos ]; |
|
112
|
|
|
|
|
|
|
} |
|
113
|
0
|
|
|
|
|
0
|
@regions; |
|
114
|
|
|
|
|
|
|
} |
|
115
|
|
|
|
|
|
|
|
|
116
|
|
|
|
|
|
|
sub match_regions_by_group { |
|
117
|
0
|
|
|
0
|
0
|
0
|
my $regex = shift; |
|
118
|
0
|
|
|
|
|
0
|
my @regions; |
|
119
|
|
|
|
|
|
|
|
|
120
|
2
|
|
|
2
|
|
16
|
no warnings 'utf8'; |
|
|
2
|
|
|
|
|
4
|
|
|
|
2
|
|
|
|
|
2406
|
|
|
121
|
|
|
|
|
|
|
|
|
122
|
0
|
|
|
|
|
0
|
while (/$regex/g) { |
|
123
|
0
|
0
|
|
|
|
0
|
if (@- == 1) { |
|
124
|
0
|
|
|
|
|
0
|
push @regions, [ $-[0], $+[0], 0 ]; |
|
125
|
|
|
|
|
|
|
} else { |
|
126
|
0
|
|
|
|
|
0
|
for my $i (1 .. $#-) { |
|
127
|
0
|
|
|
|
|
0
|
push @regions, [ $-[$i], $+[$i], $i]; |
|
128
|
|
|
|
|
|
|
} |
|
129
|
|
|
|
|
|
|
} |
|
130
|
|
|
|
|
|
|
} |
|
131
|
0
|
|
|
|
|
0
|
@regions; |
|
132
|
|
|
|
|
|
|
} |
|
133
|
|
|
|
|
|
|
|
|
134
|
|
|
|
|
|
|
sub classify_regions { |
|
135
|
0
|
0
|
|
0
|
0
|
0
|
my $opt = ref $_[0] eq 'HASH' ? shift : {}; |
|
136
|
|
|
|
|
|
|
|
|
137
|
0
|
0
|
|
|
|
0
|
$opt->{strict} and goto &classify_regions_strict; |
|
138
|
|
|
|
|
|
|
|
|
139
|
0
|
|
|
|
|
0
|
my @list = @{+shift}; |
|
|
0
|
|
|
|
|
0
|
|
|
140
|
0
|
|
|
|
|
0
|
my @by = @{+shift}; |
|
|
0
|
|
|
|
|
0
|
|
|
141
|
0
|
|
|
|
|
0
|
my @table; |
|
142
|
0
|
|
|
|
|
0
|
for (my $i = 0; $i < @by; $i++) { |
|
143
|
0
|
|
|
|
|
0
|
my($from, $to) = @{$by[$i]}; |
|
|
0
|
|
|
|
|
0
|
|
|
144
|
0
|
|
0
|
|
|
0
|
while (@list and $list[0][1] < $from) { |
|
145
|
0
|
|
|
|
|
0
|
shift @list; |
|
146
|
|
|
|
|
|
|
} |
|
147
|
0
|
|
0
|
|
|
0
|
while (@list and $list[0][1] == $from and $list[0][0] < $from) { |
|
|
|
|
0
|
|
|
|
|
|
148
|
0
|
|
|
|
|
0
|
shift @list; |
|
149
|
|
|
|
|
|
|
} |
|
150
|
0
|
|
|
|
|
0
|
my $t = $table[$i] = []; |
|
151
|
0
|
|
0
|
|
|
0
|
for (my $i = 0; ($i < @list) and ($list[$i][0] < $to); $i++) { |
|
152
|
0
|
|
|
|
|
0
|
push @$t, [ @{$list[$i]} ]; |
|
|
0
|
|
|
|
|
0
|
|
|
153
|
|
|
|
|
|
|
} |
|
154
|
|
|
|
|
|
|
} |
|
155
|
0
|
|
|
|
|
0
|
@table; |
|
156
|
|
|
|
|
|
|
} |
|
157
|
|
|
|
|
|
|
|
|
158
|
|
|
|
|
|
|
sub classify_regions_strict { |
|
159
|
0
|
|
|
0
|
0
|
0
|
my @list = @{+shift}; |
|
|
0
|
|
|
|
|
0
|
|
|
160
|
0
|
|
|
|
|
0
|
my @by = @{+shift}; |
|
|
0
|
|
|
|
|
0
|
|
|
161
|
0
|
|
|
|
|
0
|
my @table; |
|
162
|
0
|
|
|
|
|
0
|
for (my $i = 0; $i < @by; $i++) { |
|
163
|
0
|
|
|
|
|
0
|
my($from, $to) = @{$by[$i]}; |
|
|
0
|
|
|
|
|
0
|
|
|
164
|
0
|
|
0
|
|
|
0
|
while (@list and $list[0][0] < $from) { |
|
165
|
0
|
|
|
|
|
0
|
shift @list; |
|
166
|
|
|
|
|
|
|
} |
|
167
|
0
|
|
|
|
|
0
|
my $t = $table[$i] = []; |
|
168
|
0
|
|
0
|
|
|
0
|
while (@list and $list[0][0] < $to and $list[0][1] <= $to) { |
|
|
|
|
0
|
|
|
|
|
|
169
|
0
|
|
|
|
|
0
|
push @$t, shift @list; |
|
170
|
|
|
|
|
|
|
} |
|
171
|
|
|
|
|
|
|
} |
|
172
|
0
|
|
|
|
|
0
|
@table; |
|
173
|
|
|
|
|
|
|
} |
|
174
|
|
|
|
|
|
|
|
|
175
|
|
|
|
|
|
|
sub select_regions { |
|
176
|
0
|
0
|
|
0
|
0
|
0
|
my $opt = ref $_[0] eq 'HASH' ? shift : {}; |
|
177
|
0
|
|
|
|
|
0
|
my($list, $by, $flag) = @_; |
|
178
|
0
|
|
|
|
|
0
|
my($inside, $outside) = ([], []); |
|
179
|
0
|
0
|
|
|
|
0
|
my $target = is_inside($flag) ? $inside : $outside; |
|
180
|
0
|
0
|
|
|
|
0
|
my $overlap = $opt->{strict} ? [] : $target; |
|
181
|
0
|
|
|
|
|
0
|
filter_regions($list, $by, $inside, $overlap, $outside); |
|
182
|
0
|
|
|
|
|
0
|
@$target; |
|
183
|
|
|
|
|
|
|
} |
|
184
|
|
|
|
|
|
|
|
|
185
|
|
|
|
|
|
|
## |
|
186
|
|
|
|
|
|
|
## Split @input into @inside, @overlap, @outside by @filter and return |
|
187
|
|
|
|
|
|
|
## their pointers. |
|
188
|
|
|
|
|
|
|
## |
|
189
|
|
|
|
|
|
|
## 4th and 5th result is corresponding entry of @filter for @inside |
|
190
|
|
|
|
|
|
|
## and @overlap. |
|
191
|
|
|
|
|
|
|
## |
|
192
|
|
|
|
|
|
|
sub filter_regions { |
|
193
|
0
|
|
|
0
|
0
|
0
|
my @input = @{+shift}; |
|
|
0
|
|
|
|
|
0
|
|
|
194
|
0
|
|
|
|
|
0
|
my @filter = @{+shift}; |
|
|
0
|
|
|
|
|
0
|
|
|
195
|
0
|
|
0
|
|
|
0
|
my($inside, $overlap, $outside) = (shift//[], shift//[], shift//[]); |
|
|
|
|
0
|
|
|
|
|
|
|
|
|
0
|
|
|
|
|
|
196
|
0
|
|
|
|
|
0
|
my($inside_match, $overlap_match) = ([], []); |
|
197
|
|
|
|
|
|
|
|
|
198
|
0
|
|
|
|
|
0
|
for (my $i = 0; $i < @filter; $i++) { |
|
199
|
0
|
|
|
|
|
0
|
my($from, $to) = @{$filter[$i]}; |
|
|
0
|
|
|
|
|
0
|
|
|
200
|
0
|
|
0
|
|
|
0
|
while (@input and $input[0][0] < $from and $input[0][1] <= $from) { |
|
|
|
|
0
|
|
|
|
|
|
201
|
0
|
|
|
|
|
0
|
push @$outside, shift @input; |
|
202
|
|
|
|
|
|
|
} |
|
203
|
0
|
|
0
|
|
|
0
|
while (@input and $input[0][0] < $from) { |
|
204
|
0
|
|
|
|
|
0
|
push @$overlap, shift @input; |
|
205
|
0
|
|
|
|
|
0
|
$overlap_match->[$#{$overlap}] = $filter[$i]; |
|
|
0
|
|
|
|
|
0
|
|
|
206
|
|
|
|
|
|
|
} |
|
207
|
0
|
|
0
|
|
|
0
|
while (@input and $input[0][0] < $to and $input[0][1] <= $to) { |
|
|
|
|
0
|
|
|
|
|
|
208
|
0
|
|
|
|
|
0
|
push @$inside, shift @input; |
|
209
|
0
|
|
|
|
|
0
|
$inside_match->[$#{$inside}] = $filter[$i]; |
|
|
0
|
|
|
|
|
0
|
|
|
210
|
|
|
|
|
|
|
} |
|
211
|
0
|
|
0
|
|
|
0
|
while (@input and $input[0][0] < $to) { |
|
212
|
0
|
|
|
|
|
0
|
push @$overlap, shift @input; |
|
213
|
0
|
|
|
|
|
0
|
$overlap_match->[$#{$overlap}] = $filter[$i]; |
|
|
0
|
|
|
|
|
0
|
|
|
214
|
|
|
|
|
|
|
} |
|
215
|
|
|
|
|
|
|
} |
|
216
|
0
|
|
|
|
|
0
|
push @$outside, splice @input; |
|
217
|
0
|
|
|
|
|
0
|
($inside, $overlap, $outside, $inside_match, $overlap_match); |
|
218
|
|
|
|
|
|
|
} |
|
219
|
|
|
|
|
|
|
|
|
220
|
|
|
|
|
|
|
sub merge_regions { |
|
221
|
0
|
0
|
|
0
|
0
|
0
|
my $option = ref $_[0] eq 'HASH' ? shift : {}; |
|
222
|
0
|
|
|
|
|
0
|
my $nojoin = $option->{nojoin}; |
|
223
|
0
|
0
|
|
|
|
0
|
my @in = $option->{destructive} ? @_ : map { [ @$_ ] } @_; |
|
|
0
|
|
|
|
|
0
|
|
|
224
|
0
|
0
|
|
|
|
0
|
unless ($option->{nosort}) { |
|
225
|
0
|
0
|
0
|
|
|
0
|
@in = sort({$a->[0] <=> $b->[0] || $b->[1] <=> $a->[1] |
|
|
0
|
0
|
|
|
|
0
|
|
|
226
|
|
|
|
|
|
|
|| (@$a > 2 ? $a->[2] <=> $b->[2] : 0) |
|
227
|
|
|
|
|
|
|
} @in); |
|
228
|
|
|
|
|
|
|
} |
|
229
|
0
|
|
|
|
|
0
|
my @out; |
|
230
|
0
|
0
|
|
|
|
0
|
push(@out, shift @in) if @in; |
|
231
|
0
|
|
|
|
|
0
|
while (@in) { |
|
232
|
0
|
|
|
|
|
0
|
my $top = shift @in; |
|
233
|
|
|
|
|
|
|
|
|
234
|
0
|
0
|
0
|
|
|
0
|
if ($out[-1][1] > $top->[0]) { |
|
|
|
0
|
0
|
|
|
|
|
|
|
|
|
0
|
|
|
|
|
|
235
|
0
|
0
|
|
|
|
0
|
$out[-1][1] = $top->[1] if $out[-1][1] < $top->[1]; |
|
236
|
|
|
|
|
|
|
} |
|
237
|
|
|
|
|
|
|
elsif (!$nojoin |
|
238
|
|
|
|
|
|
|
and $out[-1][1] == $top->[0] |
|
239
|
|
|
|
|
|
|
## |
|
240
|
|
|
|
|
|
|
## don't connect regions in different pattern group |
|
241
|
|
|
|
|
|
|
## |
|
242
|
|
|
|
|
|
|
and (@$top < 3 or $out[-1][2] == $top->[2]) |
|
243
|
|
|
|
|
|
|
) { |
|
244
|
0
|
0
|
|
|
|
0
|
$out[-1][1] = $top->[1] if $out[-1][1] < $top->[1]; |
|
245
|
|
|
|
|
|
|
} |
|
246
|
|
|
|
|
|
|
else { |
|
247
|
0
|
|
|
|
|
0
|
push @out, $top; |
|
248
|
|
|
|
|
|
|
} |
|
249
|
|
|
|
|
|
|
} |
|
250
|
0
|
|
|
|
|
0
|
@out; |
|
251
|
|
|
|
|
|
|
} |
|
252
|
|
|
|
|
|
|
|
|
253
|
2
|
|
|
2
|
|
16
|
use List::Util qw(pairmap); |
|
|
2
|
|
|
|
|
4
|
|
|
|
2
|
|
|
|
|
794
|
|
|
254
|
|
|
|
|
|
|
|
|
255
|
|
|
|
|
|
|
sub reverse_regions { |
|
256
|
12
|
50
|
|
12
|
0
|
8960
|
my $option = ref $_[0] eq 'HASH' ? shift : {}; |
|
257
|
12
|
|
|
|
|
25
|
my($from, $max) = @_; |
|
258
|
12
|
|
|
|
|
18
|
my @reverse = do { |
|
259
|
29
|
|
|
29
|
|
79
|
pairmap { [ $a, $b ] } |
|
260
|
12
|
|
|
|
|
70
|
0, map( { $_->[0] => $_->[1] } @$from ), $max |
|
|
17
|
|
|
|
|
63
|
|
|
261
|
|
|
|
|
|
|
}; |
|
262
|
12
|
100
|
|
|
|
57
|
return @reverse if $option->{leave_empty}; |
|
263
|
9
|
|
|
|
|
14
|
grep { $_->[0] != $_->[1] } @reverse |
|
|
20
|
|
|
|
|
64
|
|
|
264
|
|
|
|
|
|
|
} |
|
265
|
|
|
|
|
|
|
|
|
266
|
|
|
|
|
|
|
sub match_borders { |
|
267
|
0
|
|
|
0
|
0
|
|
my $regex = shift; |
|
268
|
0
|
|
|
|
|
|
my @border = (0); |
|
269
|
0
|
|
|
|
|
|
while (/$regex/gp) { |
|
270
|
0
|
|
|
|
|
|
my $pos = pos(); |
|
271
|
0
|
|
|
|
|
|
for my $i ($pos - length(${^MATCH}), $pos) { |
|
272
|
0
|
0
|
|
|
|
|
push @border, $i if $border[-1] != $i; |
|
273
|
|
|
|
|
|
|
} |
|
274
|
|
|
|
|
|
|
} |
|
275
|
0
|
0
|
|
|
|
|
push @border, length if $border[-1] != length; |
|
276
|
0
|
|
|
|
|
|
@border; |
|
277
|
|
|
|
|
|
|
} |
|
278
|
|
|
|
|
|
|
|
|
279
|
|
|
|
|
|
|
sub borders_to_regions { |
|
280
|
0
|
0
|
|
0
|
0
|
|
return () if @_ < 2; |
|
281
|
0
|
|
|
|
|
|
map { [ $_[$_-1], $_[$_] ] } 1..$#_; |
|
|
0
|
|
|
|
|
|
|
|
282
|
|
|
|
|
|
|
} |
|
283
|
|
|
|
|
|
|
|
|
284
|
|
|
|
|
|
|
1; |