|  line  | 
 stmt  | 
 bran  | 
 cond  | 
 sub  | 
 pod  | 
 time  | 
 code  | 
| 
1
 | 
  
 
  
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 package AlignDB::IntSpan;  | 
| 
2
 | 
14
 | 
 
 | 
 
 | 
  
14
  
 | 
 
 | 
282322
 | 
 use strict;  | 
| 
 
 | 
14
 | 
 
 | 
 
 | 
 
 | 
 
 | 
25
 | 
    | 
| 
 
 | 
14
 | 
 
 | 
 
 | 
 
 | 
 
 | 
488
 | 
    | 
| 
3
 | 
14
 | 
 
 | 
 
 | 
  
14
  
 | 
 
 | 
61
 | 
 use warnings;  | 
| 
 
 | 
14
 | 
 
 | 
 
 | 
 
 | 
 
 | 
24
 | 
    | 
| 
 
 | 
14
 | 
 
 | 
 
 | 
 
 | 
 
 | 
436
 | 
    | 
| 
4
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
5
 | 
14
 | 
 
 | 
 
 | 
  
14
  
 | 
 
 | 
56
 | 
 use Carp;  | 
| 
 
 | 
14
 | 
 
 | 
 
 | 
 
 | 
 
 | 
22
 | 
    | 
| 
 
 | 
14
 | 
 
 | 
 
 | 
 
 | 
 
 | 
1188
 | 
    | 
| 
6
 | 
14
 | 
 
 | 
 
 | 
  
14
  
 | 
 
 | 
69
 | 
 use Scalar::Util;  | 
| 
 
 | 
14
 | 
 
 | 
 
 | 
 
 | 
 
 | 
23
 | 
    | 
| 
 
 | 
14
 | 
 
 | 
 
 | 
 
 | 
 
 | 
777
 | 
    | 
| 
7
 | 
14
 | 
 
 | 
 
 | 
  
14
  
 | 
 
 | 
7928
 | 
 use Scalar::Util::Numeric;  | 
| 
 
 | 
14
 | 
 
 | 
 
 | 
 
 | 
 
 | 
10065
 | 
    | 
| 
 
 | 
14
 | 
 
 | 
 
 | 
 
 | 
 
 | 
1418
 | 
    | 
| 
8
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
9
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 use overload (  | 
| 
10
 | 
  
0
  
 | 
 
 | 
 
 | 
  
0
  
 | 
 
 | 
0
 | 
     q{0+}   => sub { Carp::confess "Can't numerify an AlignDB::IntSpan\n" },  | 
| 
11
 | 
14
 | 
 
 | 
 
 | 
 
 | 
 
 | 
175
 | 
     q{bool} => q{is_not_empty},  | 
| 
12
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
     q{""}   => q{as_string},  | 
| 
13
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
14
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
     # use Perl standard behaviours for other operations  | 
| 
15
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
     fallback => 1,  | 
| 
16
 | 
14
 | 
 
 | 
 
 | 
  
14
  
 | 
 
 | 
19454
 | 
 );  | 
| 
 
 | 
14
 | 
 
 | 
 
 | 
 
 | 
 
 | 
15516
 | 
    | 
| 
17
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
18
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 our $VERSION = '1.1.1';  | 
| 
19
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
20
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 my $POS_INF = 2_147_483_647 - 1;             # INT_MAX - 1  | 
| 
21
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 my $NEG_INF = ( -2_147_483_647 - 1 ) + 1;    # INT_MIN + 1  | 
| 
22
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
23
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 sub POS_INF {  | 
| 
24
 | 
40
 | 
 
 | 
 
 | 
  
40
  
 | 
  
1
  
 | 
69
 | 
     return $POS_INF - 1;  | 
| 
25
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 }  | 
| 
26
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
27
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 sub NEG_INF {  | 
| 
28
 | 
40
 | 
 
 | 
 
 | 
  
40
  
 | 
  
1
  
 | 
68
 | 
     return $NEG_INF;  | 
| 
29
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 }  | 
| 
30
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
31
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 sub EMPTY_STRING {  | 
| 
32
 | 
973
 | 
 
 | 
 
 | 
  
973
  
 | 
  
1
  
 | 
4030
 | 
     return '-';  | 
| 
33
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 }  | 
| 
34
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
35
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 sub new {  | 
| 
36
 | 
12257
 | 
 
 | 
 
 | 
  
12257
  
 | 
  
1
  
 | 
2409723
 | 
     my $class = shift;  | 
| 
37
 | 
12257
 | 
 
 | 
 
 | 
 
 | 
 
 | 
15021
 | 
     my $self  = {};  | 
| 
38
 | 
12257
 | 
 
 | 
 
 | 
 
 | 
 
 | 
23012
 | 
     $self->{edges} = [];  | 
| 
39
 | 
12257
 | 
 
 | 
 
 | 
 
 | 
 
 | 
14728
 | 
     bless $self, $class;  | 
| 
40
 | 
12257
 | 
  
100
  
 | 
 
 | 
 
 | 
 
 | 
26135
 | 
     $self->add(@_) if @_ > 0;  | 
| 
41
 | 
12251
 | 
 
 | 
 
 | 
 
 | 
 
 | 
23815
 | 
     return $self;  | 
| 
42
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 }  | 
| 
43
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
44
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 sub valid {  | 
| 
45
 | 
6
 | 
 
 | 
 
 | 
  
6
  
 | 
  
1
  
 | 
3120
 | 
     my $this    = shift;  | 
| 
46
 | 
6
 | 
 
 | 
 
 | 
 
 | 
 
 | 
6
 | 
     my $runlist = shift;  | 
| 
47
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
48
 | 
6
 | 
 
 | 
  
 33
  
 | 
 
 | 
 
 | 
31
 | 
     my $class = ref($this) || $this;  | 
| 
49
 | 
6
 | 
 
 | 
 
 | 
 
 | 
 
 | 
11
 | 
     my $set = new $class;  | 
| 
50
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
51
 | 
6
 | 
 
 | 
 
 | 
 
 | 
 
 | 
9
 | 
     eval { $set->_runlist_to_ranges($runlist) };  | 
| 
 
 | 
6
 | 
 
 | 
 
 | 
 
 | 
 
 | 
10
 | 
    | 
| 
52
 | 
6
 | 
  
 50
  
 | 
 
 | 
 
 | 
 
 | 
492
 | 
     return $@ ? 0 : 1;  | 
| 
53
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 }  | 
| 
54
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
55
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 sub clear {  | 
| 
56
 | 
2
 | 
 
 | 
 
 | 
  
2
  
 | 
  
1
  
 | 
4
 | 
     my $self = shift;  | 
| 
57
 | 
2
 | 
 
 | 
 
 | 
 
 | 
 
 | 
7
 | 
     $self->{edges} = [];  | 
| 
58
 | 
2
 | 
 
 | 
 
 | 
 
 | 
 
 | 
5
 | 
     return $self;  | 
| 
59
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 }  | 
| 
60
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
61
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 sub edges_ref {  | 
| 
62
 | 
231342
 | 
 
 | 
 
 | 
  
231342
  
 | 
  
1
  
 | 
181034
 | 
     my $self = shift;  | 
| 
63
 | 
231342
 | 
 
 | 
 
 | 
 
 | 
 
 | 
326340
 | 
     return $self->{edges};  | 
| 
64
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 }  | 
| 
65
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
66
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 sub edges {  | 
| 
67
 | 
105340
 | 
 
 | 
 
 | 
  
105340
  
 | 
  
1
  
 | 
83748
 | 
     my $self = shift;  | 
| 
68
 | 
105340
 | 
 
 | 
 
 | 
 
 | 
 
 | 
82139
 | 
     return @{ $self->edges_ref };  | 
| 
 
 | 
105340
 | 
 
 | 
 
 | 
 
 | 
 
 | 
117606
 | 
    | 
| 
69
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 }  | 
| 
70
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
71
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 sub edge_size {  | 
| 
72
 | 
87530
 | 
 
 | 
 
 | 
  
87530
  
 | 
  
1
  
 | 
67201
 | 
     my $self = shift;  | 
| 
73
 | 
87530
 | 
 
 | 
 
 | 
 
 | 
 
 | 
98914
 | 
     return scalar $self->edges;  | 
| 
74
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 }  | 
| 
75
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
76
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 sub span_size {  | 
| 
77
 | 
11
 | 
 
 | 
 
 | 
  
11
  
 | 
  
1
  
 | 
10
 | 
     my $self = shift;  | 
| 
78
 | 
11
 | 
 
 | 
 
 | 
 
 | 
 
 | 
14
 | 
     return $self->edge_size / 2;  | 
| 
79
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 }  | 
| 
80
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
81
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 sub as_string {  | 
| 
82
 | 
498
 | 
 
 | 
 
 | 
  
498
  
 | 
  
1
  
 | 
8338
 | 
     my $self = shift;  | 
| 
83
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
84
 | 
498
 | 
  
100
  
 | 
 
 | 
 
 | 
 
 | 
805
 | 
     if ( $self->is_empty ) {  | 
| 
85
 | 
107
 | 
 
 | 
 
 | 
 
 | 
 
 | 
191
 | 
         return $self->EMPTY_STRING;  | 
| 
86
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
     }  | 
| 
87
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
88
 | 
391
 | 
 
 | 
 
 | 
 
 | 
 
 | 
359
 | 
     my @runs;  | 
| 
89
 | 
391
 | 
 
 | 
 
 | 
 
 | 
 
 | 
541
 | 
     my @edges = $self->edges;  | 
| 
90
 | 
391
 | 
 
 | 
 
 | 
 
 | 
 
 | 
856
 | 
     while (@edges) {  | 
| 
91
 | 
597
 | 
 
 | 
 
 | 
 
 | 
 
 | 
665
 | 
         my $lower = shift @edges;  | 
| 
92
 | 
597
 | 
 
 | 
 
 | 
 
 | 
 
 | 
620
 | 
         my $upper = shift(@edges) - 1;  | 
| 
93
 | 
597
 | 
  
100
  
 | 
 
 | 
 
 | 
 
 | 
1890
 | 
         push @runs, $lower == $upper ? $lower : "$lower-$upper";  | 
| 
94
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
     }  | 
| 
95
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
96
 | 
391
 | 
 
 | 
 
 | 
 
 | 
 
 | 
5069
 | 
     return join( ',', @runs );  | 
| 
97
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 }  | 
| 
98
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
99
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 sub as_array {  | 
| 
100
 | 
6015
 | 
 
 | 
 
 | 
  
6015
  
 | 
  
1
  
 | 
389014
 | 
     my $self = shift;  | 
| 
101
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
102
 | 
6015
 | 
 
 | 
 
 | 
 
 | 
 
 | 
5546
 | 
     my @elements;  | 
| 
103
 | 
6015
 | 
 
 | 
 
 | 
 
 | 
 
 | 
8050
 | 
     my @edges = $self->edges;  | 
| 
104
 | 
6015
 | 
 
 | 
 
 | 
 
 | 
 
 | 
14145
 | 
     while (@edges) {  | 
| 
105
 | 
25814
 | 
 
 | 
 
 | 
 
 | 
 
 | 
23268
 | 
         my $lower = shift @edges;  | 
| 
106
 | 
25814
 | 
 
 | 
 
 | 
 
 | 
 
 | 
22889
 | 
         my $upper = shift(@edges) - 1;  | 
| 
107
 | 
25814
 | 
 
 | 
 
 | 
 
 | 
 
 | 
55870
 | 
         push @elements, ( $lower .. $upper );  | 
| 
108
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
     }  | 
| 
109
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
110
 | 
6015
 | 
 
 | 
 
 | 
 
 | 
 
 | 
29574
 | 
     return @elements;  | 
| 
111
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 }  | 
| 
112
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
113
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 sub ranges {  | 
| 
114
 | 
10374
 | 
 
 | 
 
 | 
  
10374
  
 | 
  
1
  
 | 
1950227
 | 
     my $self = shift;  | 
| 
115
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
116
 | 
10374
 | 
 
 | 
 
 | 
 
 | 
 
 | 
9477
 | 
     my @ranges;  | 
| 
117
 | 
10374
 | 
 
 | 
 
 | 
 
 | 
 
 | 
13925
 | 
     my @edges = $self->edges;  | 
| 
118
 | 
10374
 | 
 
 | 
 
 | 
 
 | 
 
 | 
21018
 | 
     while (@edges) {  | 
| 
119
 | 
18917
 | 
 
 | 
 
 | 
 
 | 
 
 | 
17303
 | 
         my $lower = shift @edges;  | 
| 
120
 | 
18917
 | 
 
 | 
 
 | 
 
 | 
 
 | 
17927
 | 
         my $upper = shift(@edges) - 1;  | 
| 
121
 | 
18917
 | 
 
 | 
 
 | 
 
 | 
 
 | 
39170
 | 
         push @ranges, ( $lower, $upper );  | 
| 
122
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
     }  | 
| 
123
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
124
 | 
10374
 | 
 
 | 
 
 | 
 
 | 
 
 | 
23483
 | 
     return @ranges;  | 
| 
125
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 }  | 
| 
126
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
127
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 sub spans {  | 
| 
128
 | 
24
 | 
 
 | 
 
 | 
  
24
  
 | 
  
1
  
 | 
62
 | 
     my $self = shift;  | 
| 
129
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
130
 | 
24
 | 
 
 | 
 
 | 
 
 | 
 
 | 
21
 | 
     my @spans;  | 
| 
131
 | 
24
 | 
 
 | 
 
 | 
 
 | 
 
 | 
39
 | 
     my @edges = $self->edges;  | 
| 
132
 | 
24
 | 
 
 | 
 
 | 
 
 | 
 
 | 
63
 | 
     while (@edges) {  | 
| 
133
 | 
27
 | 
 
 | 
 
 | 
 
 | 
 
 | 
33
 | 
         my $lower = shift @edges;  | 
| 
134
 | 
27
 | 
 
 | 
 
 | 
 
 | 
 
 | 
31
 | 
         my $upper = shift(@edges) - 1;  | 
| 
135
 | 
27
 | 
 
 | 
 
 | 
 
 | 
 
 | 
80
 | 
         push @spans, [ $lower, $upper ];  | 
| 
136
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
     }  | 
| 
137
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
138
 | 
24
 | 
  
100
  
 | 
 
 | 
 
 | 
 
 | 
46
 | 
     if (@spans) {  | 
| 
139
 | 
21
 | 
 
 | 
 
 | 
 
 | 
 
 | 
58
 | 
         return @spans;  | 
| 
140
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
     }  | 
| 
141
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
     else {  | 
| 
142
 | 
3
 | 
 
 | 
 
 | 
 
 | 
 
 | 
9
 | 
         return;  | 
| 
143
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
     }  | 
| 
144
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 }  | 
| 
145
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
146
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 sub sets {  | 
| 
147
 | 
128
 | 
 
 | 
 
 | 
  
128
  
 | 
  
1
  
 | 
143
 | 
     my $self = shift;  | 
| 
148
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
149
 | 
128
 | 
 
 | 
 
 | 
 
 | 
 
 | 
94
 | 
     my @sets;  | 
| 
150
 | 
128
 | 
 
 | 
 
 | 
 
 | 
 
 | 
158
 | 
     my @edges = $self->edges;  | 
| 
151
 | 
128
 | 
 
 | 
 
 | 
 
 | 
 
 | 
229
 | 
     while (@edges) {  | 
| 
152
 | 
163
 | 
 
 | 
 
 | 
 
 | 
 
 | 
173
 | 
         my $lower = shift @edges;  | 
| 
153
 | 
163
 | 
 
 | 
 
 | 
 
 | 
 
 | 
176
 | 
         my $upper = shift(@edges) - 1;  | 
| 
154
 | 
163
 | 
 
 | 
 
 | 
 
 | 
 
 | 
598
 | 
         push @sets, Scalar::Util::blessed($self)->new("$lower-$upper");  | 
| 
155
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
     }  | 
| 
156
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
157
 | 
128
 | 
  
100
  
 | 
 
 | 
 
 | 
 
 | 
224
 | 
     if (@sets) {  | 
| 
158
 | 
125
 | 
 
 | 
 
 | 
 
 | 
 
 | 
252
 | 
         return @sets;  | 
| 
159
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
     }  | 
| 
160
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
     else {  | 
| 
161
 | 
3
 | 
 
 | 
 
 | 
 
 | 
 
 | 
9
 | 
         return;  | 
| 
162
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
     }  | 
| 
163
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 }  | 
| 
164
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
165
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 sub runlists {  | 
| 
166
 | 
19
 | 
 
 | 
 
 | 
  
19
  
 | 
  
1
  
 | 
72
 | 
     my $self = shift;  | 
| 
167
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
168
 | 
19
 | 
  
100
  
 | 
 
 | 
 
 | 
 
 | 
47
 | 
     if ( $self->is_empty ) {  | 
| 
169
 | 
2
 | 
 
 | 
 
 | 
 
 | 
 
 | 
8
 | 
         return $self->EMPTY_STRING;  | 
| 
170
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
     }  | 
| 
171
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
172
 | 
17
 | 
 
 | 
 
 | 
 
 | 
 
 | 
23
 | 
     my @runlists;  | 
| 
173
 | 
17
 | 
 
 | 
 
 | 
 
 | 
 
 | 
46
 | 
     my @edges = $self->edges;  | 
| 
174
 | 
17
 | 
 
 | 
 
 | 
 
 | 
 
 | 
46
 | 
     while (@edges) {  | 
| 
175
 | 
20
 | 
 
 | 
 
 | 
 
 | 
 
 | 
28
 | 
         my $lower  = shift @edges;  | 
| 
176
 | 
20
 | 
 
 | 
 
 | 
 
 | 
 
 | 
29
 | 
         my $upper  = shift(@edges) - 1;  | 
| 
177
 | 
20
 | 
  
100
  
 | 
 
 | 
 
 | 
 
 | 
94
 | 
         my $string = $lower == $upper ? $lower : $lower . '-' . $upper;  | 
| 
178
 | 
20
 | 
 
 | 
 
 | 
 
 | 
 
 | 
67
 | 
         push @runlists, $string;  | 
| 
179
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
     }  | 
| 
180
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
181
 | 
17
 | 
  
 50
  
 | 
 
 | 
 
 | 
 
 | 
34
 | 
     if (@runlists) {  | 
| 
182
 | 
17
 | 
 
 | 
 
 | 
 
 | 
 
 | 
76
 | 
         return @runlists;  | 
| 
183
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
     }  | 
| 
184
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
     else {  | 
| 
185
 | 
  
0
  
 | 
 
 | 
 
 | 
 
 | 
 
 | 
0
 | 
         return;  | 
| 
186
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
     }  | 
| 
187
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 }  | 
| 
188
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
189
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 sub cardinality {  | 
| 
190
 | 
168
 | 
 
 | 
 
 | 
  
168
  
 | 
  
1
  
 | 
1275
 | 
     my $self = shift;  | 
| 
191
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
192
 | 
168
 | 
 
 | 
 
 | 
 
 | 
 
 | 
140
 | 
     my $cardinality = 0;  | 
| 
193
 | 
168
 | 
 
 | 
 
 | 
 
 | 
 
 | 
196
 | 
     my @edges       = $self->edges;  | 
| 
194
 | 
168
 | 
 
 | 
 
 | 
 
 | 
 
 | 
309
 | 
     while (@edges) {  | 
| 
195
 | 
218
 | 
 
 | 
 
 | 
 
 | 
 
 | 
202
 | 
         my $lower = shift @edges;  | 
| 
196
 | 
218
 | 
 
 | 
 
 | 
 
 | 
 
 | 
191
 | 
         my $upper = shift(@edges) - 1;  | 
| 
197
 | 
218
 | 
 
 | 
 
 | 
 
 | 
 
 | 
369
 | 
         $cardinality += $upper - $lower + 1;  | 
| 
198
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
     }  | 
| 
199
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
200
 | 
168
 | 
 
 | 
 
 | 
 
 | 
 
 | 
423
 | 
     return $cardinality;  | 
| 
201
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 }  | 
| 
202
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
203
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 sub is_empty {  | 
| 
204
 | 
6404
 | 
 
 | 
 
 | 
  
6404
  
 | 
  
1
  
 | 
5856
 | 
     my $self = shift;  | 
| 
205
 | 
6404
 | 
  
100
  
 | 
 
 | 
 
 | 
 
 | 
8746
 | 
     my $result = $self->edge_size == 0 ? 1 : 0;  | 
| 
206
 | 
6404
 | 
 
 | 
 
 | 
 
 | 
 
 | 
10859
 | 
     return $result;  | 
| 
207
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 }  | 
| 
208
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
209
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 sub is_not_empty {  | 
| 
210
 | 
8
 | 
 
 | 
 
 | 
  
8
  
 | 
  
1
  
 | 
21
 | 
     my $self = shift;  | 
| 
211
 | 
8
 | 
 
 | 
 
 | 
 
 | 
 
 | 
20
 | 
     return !$self->is_empty;  | 
| 
212
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 }  | 
| 
213
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
214
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 sub is_neg_inf {  | 
| 
215
 | 
19
 | 
 
 | 
 
 | 
  
19
  
 | 
  
1
  
 | 
19
 | 
     my $self = shift;  | 
| 
216
 | 
19
 | 
 
 | 
 
 | 
 
 | 
 
 | 
26
 | 
     return $self->edges_ref->[0] == $NEG_INF;  | 
| 
217
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 }  | 
| 
218
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
219
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 sub is_pos_inf {  | 
| 
220
 | 
14
 | 
 
 | 
 
 | 
  
14
  
 | 
  
1
  
 | 
15
 | 
     my $self = shift;  | 
| 
221
 | 
14
 | 
 
 | 
 
 | 
 
 | 
 
 | 
17
 | 
     return $self->edges_ref->[-1] == $POS_INF;  | 
| 
222
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 }  | 
| 
223
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
224
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 sub is_infinite {  | 
| 
225
 | 
2
 | 
 
 | 
 
 | 
  
2
  
 | 
  
1
  
 | 
3
 | 
     my $self = shift;  | 
| 
226
 | 
2
 | 
 
 | 
  
 33
  
 | 
 
 | 
 
 | 
8
 | 
     return $self->is_neg_inf || $self->is_pos_inf;  | 
| 
227
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 }  | 
| 
228
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
229
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 sub is_finite {  | 
| 
230
 | 
1
 | 
 
 | 
 
 | 
  
1
  
 | 
  
1
  
 | 
9
 | 
     my $self = shift;  | 
| 
231
 | 
1
 | 
 
 | 
 
 | 
 
 | 
 
 | 
3
 | 
     return !$self->is_infinite;  | 
| 
232
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 }  | 
| 
233
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
234
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 sub is_universal {  | 
| 
235
 | 
13
 | 
 
 | 
 
 | 
  
13
  
 | 
  
1
  
 | 
12
 | 
     my $self = shift;  | 
| 
236
 | 
13
 | 
 
 | 
  
 33
  
 | 
 
 | 
 
 | 
17
 | 
     return $self->edge_size == 2 && $self->is_neg_inf && $self->is_pos_inf;  | 
| 
237
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 }  | 
| 
238
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
239
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 sub contains_all {  | 
| 
240
 | 
184
 | 
 
 | 
 
 | 
  
184
  
 | 
  
1
  
 | 
141
 | 
     my $self = shift;  | 
| 
241
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
242
 | 
184
 | 
 
 | 
 
 | 
 
 | 
 
 | 
182
 | 
     for my $i (@_) {  | 
| 
243
 | 
184
 | 
 
 | 
 
 | 
 
 | 
 
 | 
218
 | 
         my $pos = $self->_find_pos( $i + 1, 0 );  | 
| 
244
 | 
184
 | 
  
100
  
 | 
 
 | 
 
 | 
 
 | 
383
 | 
         return 0 unless $pos & 1;  | 
| 
245
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
     }  | 
| 
246
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
247
 | 
100
 | 
 
 | 
 
 | 
 
 | 
 
 | 
114
 | 
     return 1;  | 
| 
248
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 }  | 
| 
249
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
250
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 sub contains_any {  | 
| 
251
 | 
3
 | 
 
 | 
 
 | 
  
3
  
 | 
  
1
  
 | 
7
 | 
     my $self = shift;  | 
| 
252
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
253
 | 
3
 | 
 
 | 
 
 | 
 
 | 
 
 | 
6
 | 
     for my $i (@_) {  | 
| 
254
 | 
7
 | 
 
 | 
 
 | 
 
 | 
 
 | 
13
 | 
         my $pos = $self->_find_pos( $i + 1, 0 );  | 
| 
255
 | 
7
 | 
  
100
  
 | 
 
 | 
 
 | 
 
 | 
17
 | 
         return 1 if $pos & 1;  | 
| 
256
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
     }  | 
| 
257
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
258
 | 
2
 | 
 
 | 
 
 | 
 
 | 
 
 | 
7
 | 
     return 0;  | 
| 
259
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 }  | 
| 
260
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
261
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 #@returns AlignDB::IntSpan  | 
| 
262
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 sub add_pair {  | 
| 
263
 | 
40155
 | 
 
 | 
 
 | 
  
40155
  
 | 
  
1
  
 | 
32921
 | 
     my $self   = shift;  | 
| 
264
 | 
40155
 | 
 
 | 
 
 | 
 
 | 
 
 | 
52145
 | 
     my @ranges = @_;  | 
| 
265
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
266
 | 
40155
 | 
  
 50
  
 | 
 
 | 
 
 | 
 
 | 
64680
 | 
     if ( scalar(@ranges) != 2 ) {  | 
| 
267
 | 
  
0
  
 | 
 
 | 
 
 | 
 
 | 
 
 | 
0
 | 
         Carp::confess "Number of ranges must be two: @ranges\n";  | 
| 
268
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
     }  | 
| 
269
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
270
 | 
40155
 | 
 
 | 
 
 | 
 
 | 
 
 | 
53171
 | 
     my $edges_ref = $self->edges_ref;  | 
| 
271
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
272
 | 
40155
 | 
 
 | 
 
 | 
 
 | 
 
 | 
37914
 | 
     my $from = shift @ranges;  | 
| 
273
 | 
40155
 | 
 
 | 
 
 | 
 
 | 
 
 | 
40330
 | 
     my $to   = shift(@ranges) + 1;  | 
| 
274
 | 
40155
 | 
  
 50
  
 | 
 
 | 
 
 | 
 
 | 
63279
 | 
     if ( $from > $to ) {  | 
| 
275
 | 
  
0
  
 | 
 
 | 
 
 | 
 
 | 
 
 | 
0
 | 
         Carp::confess "Bad order: $from-$to\n";  | 
| 
276
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
     }  | 
| 
277
 | 
40155
 | 
 
 | 
 
 | 
 
 | 
 
 | 
53112
 | 
     my $from_pos = $self->_find_pos( $from,   0 );  | 
| 
278
 | 
40155
 | 
 
 | 
 
 | 
 
 | 
 
 | 
59450
 | 
     my $to_pos   = $self->_find_pos( $to + 1, $from_pos );  | 
| 
279
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
280
 | 
40155
 | 
  
100
  
 | 
 
 | 
 
 | 
 
 | 
66468
 | 
     if ( $from_pos & 1 ) {  | 
| 
281
 | 
9936
 | 
 
 | 
 
 | 
 
 | 
 
 | 
11996
 | 
         $from = $edges_ref->[ --$from_pos ];  | 
| 
282
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
     }  | 
| 
283
 | 
40155
 | 
  
100
  
 | 
 
 | 
 
 | 
 
 | 
55684
 | 
     if ( $to_pos & 1 ) {  | 
| 
284
 | 
7291
 | 
 
 | 
 
 | 
 
 | 
 
 | 
7819
 | 
         $to = $edges_ref->[ $to_pos++ ];  | 
| 
285
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
     }  | 
| 
286
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
287
 | 
40155
 | 
 
 | 
 
 | 
 
 | 
 
 | 
30759
 | 
     splice @{$edges_ref}, $from_pos, $to_pos - $from_pos, ( $from, $to );  | 
| 
 
 | 
40155
 | 
 
 | 
 
 | 
 
 | 
 
 | 
81978
 | 
    | 
| 
288
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
289
 | 
40155
 | 
 
 | 
 
 | 
 
 | 
 
 | 
88430
 | 
     return $self;  | 
| 
290
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 }  | 
| 
291
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
292
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 #@returns AlignDB::IntSpan  | 
| 
293
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 sub add_range {  | 
| 
294
 | 
31307
 | 
 
 | 
 
 | 
  
31307
  
 | 
  
1
  
 | 
832207
 | 
     my $self   = shift;  | 
| 
295
 | 
31307
 | 
 
 | 
 
 | 
 
 | 
 
 | 
46116
 | 
     my @ranges = @_;  | 
| 
296
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
297
 | 
31307
 | 
  
 50
  
 | 
 
 | 
 
 | 
 
 | 
60331
 | 
     if ( scalar(@ranges) % 2 == 1 ) {  | 
| 
298
 | 
  
0
  
 | 
 
 | 
 
 | 
 
 | 
 
 | 
0
 | 
         Carp::confess "Number of ranges must be even: @ranges\n";  | 
| 
299
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
     }  | 
| 
300
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
301
 | 
31307
 | 
 
 | 
 
 | 
 
 | 
 
 | 
51854
 | 
     while (@ranges) {  | 
| 
302
 | 
39277
 | 
 
 | 
 
 | 
 
 | 
 
 | 
39537
 | 
         my $from = shift @ranges;  | 
| 
303
 | 
39277
 | 
 
 | 
 
 | 
 
 | 
 
 | 
32485
 | 
         my $to   = shift @ranges;  | 
| 
304
 | 
39277
 | 
 
 | 
 
 | 
 
 | 
 
 | 
55461
 | 
         $self->add_pair( $from, $to );  | 
| 
305
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
     }  | 
| 
306
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
307
 | 
31307
 | 
 
 | 
 
 | 
 
 | 
 
 | 
38663
 | 
     return $self;  | 
| 
308
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 }  | 
| 
309
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
310
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 #@returns AlignDB::IntSpan  | 
| 
311
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 sub add_runlist {  | 
| 
312
 | 
  
0
  
 | 
 
 | 
 
 | 
  
0
  
 | 
  
1
  
 | 
0
 | 
     my $self  = shift;  | 
| 
313
 | 
  
0
  
 | 
 
 | 
 
 | 
 
 | 
 
 | 
0
 | 
     my $first = shift;  | 
| 
314
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
315
 | 
  
0
  
 | 
 
 | 
 
 | 
 
 | 
 
 | 
0
 | 
     $self->add_range( $self->_runlist_to_ranges($first) );  | 
| 
316
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
317
 | 
  
0
  
 | 
 
 | 
 
 | 
 
 | 
 
 | 
0
 | 
     return $self;  | 
| 
318
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 }  | 
| 
319
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
320
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 #@returns AlignDB::IntSpan  | 
| 
321
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 sub add {  | 
| 
322
 | 
8120
 | 
 
 | 
 
 | 
  
8120
  
 | 
  
1
  
 | 
15882
 | 
     my $self  = shift;  | 
| 
323
 | 
8120
 | 
 
 | 
 
 | 
 
 | 
 
 | 
6589
 | 
     my $first = shift;  | 
| 
324
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
325
 | 
8120
 | 
  
100
  
 | 
 
 | 
 
 | 
 
 | 
16698
 | 
     if ( ref $first eq __PACKAGE__ ) {  | 
| 
 
 | 
 
 | 
  
100
  
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
326
 | 
6447
 | 
 
 | 
 
 | 
 
 | 
 
 | 
8267
 | 
         $self->add_range( $first->ranges );  | 
| 
327
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
     }  | 
| 
328
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
     elsif ( Scalar::Util::Numeric::isint($first) ) {  | 
| 
329
 | 
815
 | 
  
100
  
 | 
 
 | 
 
 | 
 
 | 
1372
 | 
         if ( scalar @_ > 0 ) {  | 
| 
330
 | 
41
 | 
 
 | 
 
 | 
 
 | 
 
 | 
90
 | 
             $self->add_range( $self->_list_to_ranges( $first, @_ ) );  | 
| 
331
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
         }  | 
| 
332
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
         else {  | 
| 
333
 | 
774
 | 
 
 | 
 
 | 
 
 | 
 
 | 
1146
 | 
             $self->add_pair( $first, $first );  | 
| 
334
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
         }  | 
| 
335
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
     }  | 
| 
336
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
     else {  | 
| 
337
 | 
858
 | 
 
 | 
 
 | 
 
 | 
 
 | 
1536
 | 
         $self->add_range( $self->_runlist_to_ranges($first) );  | 
| 
338
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
     }  | 
| 
339
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
340
 | 
8114
 | 
 
 | 
 
 | 
 
 | 
 
 | 
10539
 | 
     return $self;  | 
| 
341
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 }  | 
| 
342
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
343
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 #@returns AlignDB::IntSpan  | 
| 
344
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 sub invert {  | 
| 
345
 | 
5180
 | 
 
 | 
 
 | 
  
5180
  
 | 
  
1
  
 | 
5033
 | 
     my $self = shift;  | 
| 
346
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
347
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
     # $edges_ref is an ArrayRef, which points to the same array as the  | 
| 
348
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
     #   'edges' attribute. So manipulate $edges_ref affects the attribute  | 
| 
349
 | 
5180
 | 
 
 | 
 
 | 
 
 | 
 
 | 
7029
 | 
     my $edges_ref = $self->edges_ref;  | 
| 
350
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
351
 | 
5180
 | 
  
100
  
 | 
 
 | 
 
 | 
 
 | 
8496
 | 
     if ( $self->is_empty ) {  | 
| 
352
 | 
41
 | 
 
 | 
 
 | 
 
 | 
 
 | 
128
 | 
         $self->{edges} = [ $NEG_INF, $POS_INF ];    # Universal set  | 
| 
353
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
     }  | 
| 
354
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
     else {  | 
| 
355
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
356
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
         # Either add or remove infinity from each end. The net  | 
| 
357
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
         # effect is always an even number of additions and deletions  | 
| 
358
 | 
5139
 | 
  
100
  
 | 
 
 | 
 
 | 
 
 | 
8186
 | 
         if ( $edges_ref->[0] == $NEG_INF ) {  | 
| 
359
 | 
2536
 | 
 
 | 
 
 | 
 
 | 
 
 | 
2171
 | 
             shift @{$edges_ref};  | 
| 
 
 | 
2536
 | 
 
 | 
 
 | 
 
 | 
 
 | 
3193
 | 
    | 
| 
360
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
         }  | 
| 
361
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
         else {  | 
| 
362
 | 
2603
 | 
 
 | 
 
 | 
 
 | 
 
 | 
2176
 | 
             unshift @{$edges_ref}, $NEG_INF;  | 
| 
 
 | 
2603
 | 
 
 | 
 
 | 
 
 | 
 
 | 
6468
 | 
    | 
| 
363
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
         }  | 
| 
364
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
365
 | 
5139
 | 
  
100
  
 | 
 
 | 
 
 | 
 
 | 
7843
 | 
         if ( $edges_ref->[-1] == $POS_INF ) {  | 
| 
366
 | 
2536
 | 
 
 | 
 
 | 
 
 | 
 
 | 
1966
 | 
             pop @{$edges_ref};  | 
| 
 
 | 
2536
 | 
 
 | 
 
 | 
 
 | 
 
 | 
2794
 | 
    | 
| 
367
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
         }  | 
| 
368
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
         else {  | 
| 
369
 | 
2603
 | 
 
 | 
 
 | 
 
 | 
 
 | 
2177
 | 
             push @{$edges_ref}, $POS_INF;  | 
| 
 
 | 
2603
 | 
 
 | 
 
 | 
 
 | 
 
 | 
3655
 | 
    | 
| 
370
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
         }  | 
| 
371
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
     }  | 
| 
372
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
373
 | 
5180
 | 
 
 | 
 
 | 
 
 | 
 
 | 
5688
 | 
     return $self;  | 
| 
374
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 }  | 
| 
375
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
376
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 #@returns AlignDB::IntSpan  | 
| 
377
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 sub remove_range {  | 
| 
378
 | 
2429
 | 
 
 | 
 
 | 
  
2429
  
 | 
  
1
  
 | 
735560
 | 
     my $self = shift;  | 
| 
379
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
380
 | 
2429
 | 
 
 | 
 
 | 
 
 | 
 
 | 
4310
 | 
     $self->invert;  | 
| 
381
 | 
2429
 | 
 
 | 
 
 | 
 
 | 
 
 | 
4235
 | 
     $self->add_range(@_);  | 
| 
382
 | 
2429
 | 
 
 | 
 
 | 
 
 | 
 
 | 
3702
 | 
     $self->invert;  | 
| 
383
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
384
 | 
2429
 | 
 
 | 
 
 | 
 
 | 
 
 | 
3374
 | 
     return $self;  | 
| 
385
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 }  | 
| 
386
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
387
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 #@returns AlignDB::IntSpan  | 
| 
388
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 sub remove {  | 
| 
389
 | 
861
 | 
 
 | 
 
 | 
  
861
  
 | 
  
1
  
 | 
2509
 | 
     my $self  = shift;  | 
| 
390
 | 
861
 | 
 
 | 
 
 | 
 
 | 
 
 | 
704
 | 
     my $first = shift;  | 
| 
391
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
392
 | 
861
 | 
  
 50
  
 | 
 
 | 
 
 | 
 
 | 
1754
 | 
     if ( ref $first eq __PACKAGE__ ) {  | 
| 
 
 | 
 
 | 
  
  0
  
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
393
 | 
861
 | 
 
 | 
 
 | 
 
 | 
 
 | 
1306
 | 
         $self->remove_range( $first->ranges );  | 
| 
394
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
     }  | 
| 
395
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
     elsif ( Scalar::Util::Numeric::isint($first) ) {  | 
| 
396
 | 
  
0
  
 | 
  
  0
  
 | 
 
 | 
 
 | 
 
 | 
0
 | 
         if ( scalar @_ > 0 ) {  | 
| 
397
 | 
  
0
  
 | 
 
 | 
 
 | 
 
 | 
 
 | 
0
 | 
             $self->remove_range( $self->_list_to_ranges( $first, @_ ) );  | 
| 
398
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
         }  | 
| 
399
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
         else {  | 
| 
400
 | 
  
0
  
 | 
 
 | 
 
 | 
 
 | 
 
 | 
0
 | 
             $self->remove_range( $first, $first );  | 
| 
401
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
         }  | 
| 
402
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
     }  | 
| 
403
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
     else {  | 
| 
404
 | 
  
0
  
 | 
 
 | 
 
 | 
 
 | 
 
 | 
0
 | 
         $self->remove_range( $self->_runlist_to_ranges($first) );  | 
| 
405
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
     }  | 
| 
406
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
407
 | 
861
 | 
 
 | 
 
 | 
 
 | 
 
 | 
2275
 | 
     return $self;  | 
| 
408
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 }  | 
| 
409
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
410
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 #@returns AlignDB::IntSpan  | 
| 
411
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 sub merge {  | 
| 
412
 | 
167
 | 
 
 | 
 
 | 
  
167
  
 | 
  
1
  
 | 
1144
 | 
     my $self = shift;  | 
| 
413
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
414
 | 
167
 | 
 
 | 
 
 | 
 
 | 
 
 | 
256
 | 
     for my $supplied (@_) {  | 
| 
415
 | 
173
 | 
 
 | 
 
 | 
 
 | 
 
 | 
277
 | 
         my @ranges = $self->_real_set($supplied)->ranges;  | 
| 
416
 | 
173
 | 
 
 | 
 
 | 
 
 | 
 
 | 
353
 | 
         $self->add_range(@ranges);  | 
| 
417
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
     }  | 
| 
418
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
419
 | 
167
 | 
 
 | 
 
 | 
 
 | 
 
 | 
366
 | 
     return $self;  | 
| 
420
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 }  | 
| 
421
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
422
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 #@returns AlignDB::IntSpan  | 
| 
423
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 sub subtract {  | 
| 
424
 | 
141
 | 
 
 | 
 
 | 
  
141
  
 | 
  
1
  
 | 
135
 | 
     my $self = shift;  | 
| 
425
 | 
141
 | 
  
 50
  
 | 
 
 | 
 
 | 
 
 | 
197
 | 
     return $self if $self->is_empty;  | 
| 
426
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
427
 | 
141
 | 
 
 | 
 
 | 
 
 | 
 
 | 
211
 | 
     for my $supplied (@_) {  | 
| 
428
 | 
141
 | 
 
 | 
 
 | 
 
 | 
 
 | 
199
 | 
         my @ranges = $self->_real_set($supplied)->ranges;  | 
| 
429
 | 
141
 | 
 
 | 
 
 | 
 
 | 
 
 | 
253
 | 
         $self->remove_range(@ranges);  | 
| 
430
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
     }  | 
| 
431
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
432
 | 
141
 | 
 
 | 
 
 | 
 
 | 
 
 | 
131
 | 
     return $self;  | 
| 
433
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 }  | 
| 
434
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
435
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 #@returns AlignDB::IntSpan  | 
| 
436
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 sub copy {  | 
| 
437
 | 
419
 | 
 
 | 
 
 | 
  
419
  
 | 
  
1
  
 | 
401
 | 
     my $self = shift;  | 
| 
438
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
439
 | 
419
 | 
 
 | 
 
 | 
 
 | 
 
 | 
1491
 | 
     my $copy = Scalar::Util::blessed($self)->new;  | 
| 
440
 | 
419
 | 
 
 | 
 
 | 
 
 | 
 
 | 
724
 | 
     $copy->{edges} = [ $self->edges ];  | 
| 
441
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
442
 | 
419
 | 
 
 | 
 
 | 
 
 | 
 
 | 
688
 | 
     return $copy;  | 
| 
443
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 }  | 
| 
444
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
445
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 #@returns AlignDB::IntSpan  | 
| 
446
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 sub union {  | 
| 
447
 | 
33
 | 
 
 | 
 
 | 
  
33
  
 | 
  
1
  
 | 
1059
 | 
     my $self = shift;  | 
| 
448
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
449
 | 
33
 | 
 
 | 
 
 | 
 
 | 
 
 | 
81
 | 
     my $new = $self->copy;  | 
| 
450
 | 
33
 | 
 
 | 
 
 | 
 
 | 
 
 | 
96
 | 
     $new->merge(@_);  | 
| 
451
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
452
 | 
33
 | 
 
 | 
 
 | 
 
 | 
 
 | 
81
 | 
     return $new;  | 
| 
453
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 }  | 
| 
454
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
455
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 #@returns AlignDB::IntSpan  | 
| 
456
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 sub complement {  | 
| 
457
 | 
224
 | 
 
 | 
 
 | 
  
224
  
 | 
  
1
  
 | 
202
 | 
     my $self = shift;  | 
| 
458
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
459
 | 
224
 | 
 
 | 
 
 | 
 
 | 
 
 | 
319
 | 
     my $new = $self->copy;  | 
| 
460
 | 
224
 | 
 
 | 
 
 | 
 
 | 
 
 | 
368
 | 
     $new->invert;  | 
| 
461
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
462
 | 
224
 | 
 
 | 
 
 | 
 
 | 
 
 | 
281
 | 
     return $new;  | 
| 
463
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 }  | 
| 
464
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
465
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 #@returns AlignDB::IntSpan  | 
| 
466
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 sub diff {  | 
| 
467
 | 
167
 | 
 
 | 
 
 | 
  
167
  
 | 
  
1
  
 | 
204
 | 
     my $self = shift;  | 
| 
468
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
469
 | 
167
 | 
  
100
  
 | 
 
 | 
 
 | 
 
 | 
273
 | 
     return $self if $self->is_empty;  | 
| 
470
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
471
 | 
141
 | 
 
 | 
 
 | 
 
 | 
 
 | 
240
 | 
     my $new = $self->copy;  | 
| 
472
 | 
141
 | 
 
 | 
 
 | 
 
 | 
 
 | 
253
 | 
     $new->subtract(@_);  | 
| 
473
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
474
 | 
141
 | 
 
 | 
 
 | 
 
 | 
 
 | 
234
 | 
     return $new;  | 
| 
475
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 }  | 
| 
476
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
477
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 #@returns AlignDB::IntSpan  | 
| 
478
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 sub intersect {  | 
| 
479
 | 
102
 | 
 
 | 
 
 | 
  
102
  
 | 
  
1
  
 | 
159
 | 
     my $self = shift;  | 
| 
480
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
481
 | 
102
 | 
  
100
  
 | 
 
 | 
 
 | 
 
 | 
168
 | 
     return $self if $self->is_empty;  | 
| 
482
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
483
 | 
98
 | 
 
 | 
 
 | 
 
 | 
 
 | 
157
 | 
     my $new = $self->complement;  | 
| 
484
 | 
98
 | 
 
 | 
 
 | 
 
 | 
 
 | 
149
 | 
     for my $supplied (@_) {  | 
| 
485
 | 
102
 | 
 
 | 
 
 | 
 
 | 
 
 | 
160
 | 
         my $temp_set = $self->_real_set($supplied)->complement;  | 
| 
486
 | 
102
 | 
 
 | 
 
 | 
 
 | 
 
 | 
194
 | 
         $new->merge($temp_set);  | 
| 
487
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
     }  | 
| 
488
 | 
98
 | 
 
 | 
 
 | 
 
 | 
 
 | 
151
 | 
     $new->invert;  | 
| 
489
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
490
 | 
98
 | 
 
 | 
 
 | 
 
 | 
 
 | 
171
 | 
     return $new;  | 
| 
491
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 }  | 
| 
492
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
493
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 #@method  | 
| 
494
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 #@returns AlignDB::IntSpan  | 
| 
495
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 sub xor {  | 
| 
496
 | 
10
 | 
 
 | 
 
 | 
  
10
  
 | 
  
1
  
 | 
64
 | 
     return intersect( union(@_), intersect(@_)->complement );  | 
| 
497
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 }  | 
| 
498
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
499
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 sub equal {  | 
| 
500
 | 
115
 | 
 
 | 
 
 | 
  
115
  
 | 
  
1
  
 | 
395
 | 
     my $self = shift;  | 
| 
501
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
502
 | 
115
 | 
 
 | 
 
 | 
 
 | 
 
 | 
220
 | 
     for (@_) {  | 
| 
503
 | 
128
 | 
 
 | 
 
 | 
 
 | 
 
 | 
188
 | 
         my $supplied = $self->_real_set($_);  | 
| 
504
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
505
 | 
128
 | 
  
100
  
 | 
 
 | 
 
 | 
 
 | 
179
 | 
         if ( $self->edge_size != $supplied->edge_size ) {  | 
| 
506
 | 
40
 | 
 
 | 
 
 | 
 
 | 
 
 | 
93
 | 
             return 0;  | 
| 
507
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
         }  | 
| 
508
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
509
 | 
88
 | 
 
 | 
 
 | 
 
 | 
 
 | 
147
 | 
         my @edges_a = $self->edges;  | 
| 
510
 | 
88
 | 
 
 | 
 
 | 
 
 | 
 
 | 
137
 | 
         my @edges_b = $supplied->edges;  | 
| 
511
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
512
 | 
88
 | 
 
 | 
 
 | 
 
 | 
 
 | 
198
 | 
         for ( my $i = 0; $i < $self->edge_size; $i++ ) {  | 
| 
513
 | 
268
 | 
  
100
  
 | 
 
 | 
 
 | 
 
 | 
542
 | 
             if ( $edges_a[$i] != $edges_b[$i] ) {  | 
| 
514
 | 
18
 | 
 
 | 
 
 | 
 
 | 
 
 | 
95
 | 
                 return 0;  | 
| 
515
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
             }  | 
| 
516
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
         }  | 
| 
517
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
     }  | 
| 
518
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
519
 | 
57
 | 
 
 | 
 
 | 
 
 | 
 
 | 
151
 | 
     return 1;  | 
| 
520
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 }  | 
| 
521
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
522
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 sub subset {  | 
| 
523
 | 
74
 | 
 
 | 
 
 | 
  
74
  
 | 
  
1
  
 | 
116
 | 
     my $self     = shift;  | 
| 
524
 | 
74
 | 
 
 | 
 
 | 
 
 | 
 
 | 
107
 | 
     my $supplied = $self->_real_set(shift);  | 
| 
525
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
526
 | 
74
 | 
 
 | 
 
 | 
 
 | 
 
 | 
126
 | 
     return $self->diff($supplied)->is_empty;  | 
| 
527
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 }  | 
| 
528
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
529
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 sub superset {  | 
| 
530
 | 
74
 | 
 
 | 
 
 | 
  
74
  
 | 
  
1
  
 | 
320
 | 
     my $self     = shift;  | 
| 
531
 | 
74
 | 
 
 | 
 
 | 
 
 | 
 
 | 
97
 | 
     my $supplied = $self->_real_set(shift);  | 
| 
532
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
533
 | 
74
 | 
 
 | 
 
 | 
 
 | 
 
 | 
130
 | 
     return $supplied->diff($self)->is_empty;  | 
| 
534
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 }  | 
| 
535
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
536
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 sub smaller_than {  | 
| 
537
 | 
36
 | 
 
 | 
 
 | 
  
36
  
 | 
  
1
  
 | 
80
 | 
     my $self     = shift;  | 
| 
538
 | 
36
 | 
 
 | 
 
 | 
 
 | 
 
 | 
26
 | 
     my $supplied = shift;  | 
| 
539
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
540
 | 
36
 | 
 
 | 
  
100
  
 | 
 
 | 
 
 | 
58
 | 
     my $result = $self->subset($supplied) && !$self->equal($supplied);  | 
| 
541
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
542
 | 
36
 | 
  
100
  
 | 
 
 | 
 
 | 
 
 | 
92
 | 
     return $result ? 1 : 0;  | 
| 
543
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 }  | 
| 
544
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
545
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 sub larger_than {  | 
| 
546
 | 
36
 | 
 
 | 
 
 | 
  
36
  
 | 
  
1
  
 | 
84
 | 
     my $self     = shift;  | 
| 
547
 | 
36
 | 
 
 | 
 
 | 
 
 | 
 
 | 
29
 | 
     my $supplied = shift;  | 
| 
548
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
549
 | 
36
 | 
 
 | 
  
100
  
 | 
 
 | 
 
 | 
58
 | 
     my $result = $self->superset($supplied) && !$self->equal($supplied);  | 
| 
550
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
551
 | 
36
 | 
  
100
  
 | 
 
 | 
 
 | 
 
 | 
110
 | 
     return $result ? 1 : 0;  | 
| 
552
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 }  | 
| 
553
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
554
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 sub at {  | 
| 
555
 | 
21
 | 
 
 | 
 
 | 
  
21
  
 | 
  
1
  
 | 
71
 | 
     my $self  = shift;  | 
| 
556
 | 
21
 | 
 
 | 
 
 | 
 
 | 
 
 | 
14
 | 
     my $index = shift;  | 
| 
557
 | 
21
 | 
  
100
  
 | 
  
 66
  
 | 
 
 | 
 
 | 
78
 | 
     if ( $index == 0 || abs($index) > $self->cardinality ) {  | 
| 
558
 | 
8
 | 
 
 | 
 
 | 
 
 | 
 
 | 
44
 | 
         return;  | 
| 
559
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
     }  | 
| 
560
 | 
13
 | 
  
100
  
 | 
 
 | 
 
 | 
 
 | 
42
 | 
     my $member = $index < 0 ? $self->_at_neg( -$index ) : $self->_at_pos($index);  | 
| 
561
 | 
13
 | 
 
 | 
 
 | 
 
 | 
 
 | 
46
 | 
     return $member;  | 
| 
562
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 }  | 
| 
563
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
564
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 sub _at_pos {  | 
| 
565
 | 
6
 | 
 
 | 
 
 | 
  
6
  
 | 
 
 | 
7
 | 
     my $self  = shift;  | 
| 
566
 | 
6
 | 
 
 | 
 
 | 
 
 | 
 
 | 
6
 | 
     my $index = shift;  | 
| 
567
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
568
 | 
6
 | 
 
 | 
 
 | 
 
 | 
 
 | 
6
 | 
     my $member;  | 
| 
569
 | 
6
 | 
 
 | 
 
 | 
 
 | 
 
 | 
6
 | 
     my $element_before = 0;  | 
| 
570
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
571
 | 
6
 | 
 
 | 
 
 | 
 
 | 
 
 | 
9
 | 
     my @edges = $self->edges;  | 
| 
572
 | 
6
 | 
 
 | 
 
 | 
 
 | 
 
 | 
16
 | 
     while (@edges) {  | 
| 
573
 | 
9
 | 
 
 | 
 
 | 
 
 | 
 
 | 
12
 | 
         my $lower     = shift @edges;  | 
| 
574
 | 
9
 | 
 
 | 
 
 | 
 
 | 
 
 | 
13
 | 
         my $upper     = shift(@edges) - 1;  | 
| 
575
 | 
9
 | 
 
 | 
 
 | 
 
 | 
 
 | 
15
 | 
         my $span_size = $upper - $lower + 1;  | 
| 
576
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
577
 | 
9
 | 
  
100
  
 | 
 
 | 
 
 | 
 
 | 
14
 | 
         if ( $index > $element_before + $span_size ) {  | 
| 
578
 | 
3
 | 
 
 | 
 
 | 
 
 | 
 
 | 
7
 | 
             $element_before += $span_size;  | 
| 
579
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
         }  | 
| 
580
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
         else {  | 
| 
581
 | 
6
 | 
 
 | 
 
 | 
 
 | 
 
 | 
9
 | 
             $member = $index - $element_before - 1 + $lower;  | 
| 
582
 | 
6
 | 
 
 | 
 
 | 
 
 | 
 
 | 
12
 | 
             last;  | 
| 
583
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
         }  | 
| 
584
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
     }  | 
| 
585
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
586
 | 
6
 | 
 
 | 
 
 | 
 
 | 
 
 | 
10
 | 
     return $member;  | 
| 
587
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 }  | 
| 
588
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
589
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 sub _at_neg {  | 
| 
590
 | 
7
 | 
 
 | 
 
 | 
  
7
  
 | 
 
 | 
5
 | 
     my $self  = shift;  | 
| 
591
 | 
7
 | 
 
 | 
 
 | 
 
 | 
 
 | 
8
 | 
     my $index = shift;  | 
| 
592
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
593
 | 
7
 | 
 
 | 
 
 | 
 
 | 
 
 | 
5
 | 
     my $member;  | 
| 
594
 | 
7
 | 
 
 | 
 
 | 
 
 | 
 
 | 
8
 | 
     my $element_after = 0;  | 
| 
595
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
596
 | 
7
 | 
 
 | 
 
 | 
 
 | 
 
 | 
9
 | 
     my @r_edges = reverse $self->edges;  | 
| 
597
 | 
7
 | 
 
 | 
 
 | 
 
 | 
 
 | 
16
 | 
     while (@r_edges) {  | 
| 
598
 | 
12
 | 
 
 | 
 
 | 
 
 | 
 
 | 
13
 | 
         my $upper     = shift(@r_edges) - 1;  | 
| 
599
 | 
12
 | 
 
 | 
 
 | 
 
 | 
 
 | 
13
 | 
         my $lower     = shift @r_edges;  | 
| 
600
 | 
12
 | 
 
 | 
 
 | 
 
 | 
 
 | 
13
 | 
         my $span_size = $upper - $lower + 1;  | 
| 
601
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
602
 | 
12
 | 
  
100
  
 | 
 
 | 
 
 | 
 
 | 
19
 | 
         if ( $index > $element_after + $span_size ) {  | 
| 
603
 | 
5
 | 
 
 | 
 
 | 
 
 | 
 
 | 
7
 | 
             $element_after += $span_size;  | 
| 
604
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
         }  | 
| 
605
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
         else {  | 
| 
606
 | 
7
 | 
 
 | 
 
 | 
 
 | 
 
 | 
10
 | 
             $member = $upper - ( $index - $element_after ) + 1;  | 
| 
607
 | 
7
 | 
 
 | 
 
 | 
 
 | 
 
 | 
11
 | 
             last;  | 
| 
608
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
         }  | 
| 
609
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
     }  | 
| 
610
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
611
 | 
7
 | 
 
 | 
 
 | 
 
 | 
 
 | 
11
 | 
     return $member;  | 
| 
612
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 }  | 
| 
613
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
614
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 sub index {  | 
| 
615
 | 
11
 | 
 
 | 
 
 | 
  
11
  
 | 
  
1
  
 | 
72
 | 
     my $self   = shift;  | 
| 
616
 | 
11
 | 
 
 | 
 
 | 
 
 | 
 
 | 
8
 | 
     my $member = shift;  | 
| 
617
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
618
 | 
11
 | 
 
 | 
 
 | 
 
 | 
 
 | 
11
 | 
     my $index;  | 
| 
619
 | 
11
 | 
 
 | 
 
 | 
 
 | 
 
 | 
9
 | 
     my $element_before = 0;  | 
| 
620
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
621
 | 
11
 | 
 
 | 
 
 | 
 
 | 
 
 | 
17
 | 
     my @edges = $self->edges;  | 
| 
622
 | 
11
 | 
 
 | 
 
 | 
 
 | 
 
 | 
27
 | 
     while (@edges) {  | 
| 
623
 | 
16
 | 
 
 | 
 
 | 
 
 | 
 
 | 
18
 | 
         my $lower     = shift @edges;  | 
| 
624
 | 
16
 | 
 
 | 
 
 | 
 
 | 
 
 | 
19
 | 
         my $upper     = shift(@edges) - 1;  | 
| 
625
 | 
16
 | 
 
 | 
 
 | 
 
 | 
 
 | 
14
 | 
         my $span_size = $upper - $lower + 1;  | 
| 
626
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
627
 | 
16
 | 
  
100
  
 | 
  
100
  
 | 
 
 | 
 
 | 
69
 | 
         if ( $member >= $lower and $member <= $upper ) {  | 
| 
628
 | 
8
 | 
 
 | 
 
 | 
 
 | 
 
 | 
11
 | 
             $index = $member - $lower + 1 + $element_before;  | 
| 
629
 | 
8
 | 
 
 | 
 
 | 
 
 | 
 
 | 
10
 | 
             last;  | 
| 
630
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
         }  | 
| 
631
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
         else {  | 
| 
632
 | 
8
 | 
 
 | 
 
 | 
 
 | 
 
 | 
24
 | 
             $element_before += $span_size;  | 
| 
633
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
         }  | 
| 
634
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
     }  | 
| 
635
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
636
 | 
11
 | 
 
 | 
 
 | 
 
 | 
 
 | 
55
 | 
     return $index;  | 
| 
637
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 }  | 
| 
638
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
639
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 #@returns AlignDB::IntSpan  | 
| 
640
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 sub slice {  | 
| 
641
 | 
11
 | 
 
 | 
 
 | 
  
11
  
 | 
  
1
  
 | 
36
 | 
     my $self = shift;  | 
| 
642
 | 
11
 | 
 
 | 
 
 | 
 
 | 
 
 | 
8
 | 
     my $from = shift;  | 
| 
643
 | 
11
 | 
 
 | 
 
 | 
 
 | 
 
 | 
9
 | 
     my $to   = shift;  | 
| 
644
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
645
 | 
11
 | 
  
100
  
 | 
 
 | 
 
 | 
 
 | 
22
 | 
     if ( $from < 1 ) {  | 
| 
646
 | 
2
 | 
 
 | 
 
 | 
 
 | 
 
 | 
277
 | 
         carp "Start index less than 1\n";  | 
| 
647
 | 
2
 | 
 
 | 
 
 | 
 
 | 
 
 | 
127
 | 
         $from = 1;  | 
| 
648
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
     }  | 
| 
649
 | 
11
 | 
 
 | 
 
 | 
 
 | 
 
 | 
22
 | 
     my $slice = $self->_splice( $from, $to - $from + 1 );  | 
| 
650
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
651
 | 
11
 | 
 
 | 
 
 | 
 
 | 
 
 | 
25
 | 
     return $slice;  | 
| 
652
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 }  | 
| 
653
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
654
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 sub _splice {  | 
| 
655
 | 
56
 | 
 
 | 
 
 | 
  
56
  
 | 
 
 | 
146
 | 
     my $self   = shift;  | 
| 
656
 | 
56
 | 
 
 | 
 
 | 
 
 | 
 
 | 
46
 | 
     my $offset = shift;  | 
| 
657
 | 
56
 | 
 
 | 
 
 | 
 
 | 
 
 | 
51
 | 
     my $length = shift;  | 
| 
658
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
659
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
     #@type AlignDB::IntSpan  | 
| 
660
 | 
56
 | 
 
 | 
 
 | 
 
 | 
 
 | 
229
 | 
     my $slice = Scalar::Util::blessed($self)->new;  | 
| 
661
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
662
 | 
56
 | 
 
 | 
 
 | 
 
 | 
 
 | 
94
 | 
     my @edges = $self->edges;  | 
| 
663
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
664
 | 
56
 | 
 
 | 
 
 | 
 
 | 
 
 | 
118
 | 
     while ( @edges > 1 ) {  | 
| 
665
 | 
75
 | 
 
 | 
 
 | 
 
 | 
 
 | 
101
 | 
         my ( $lower, $upper ) = @edges[ 0, 1 ];  | 
| 
666
 | 
75
 | 
 
 | 
 
 | 
 
 | 
 
 | 
69
 | 
         my $span_size = $upper - $lower;  | 
| 
667
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
668
 | 
75
 | 
  
100
  
 | 
 
 | 
 
 | 
 
 | 
95
 | 
         if ( $offset <= $span_size ) {  | 
| 
669
 | 
45
 | 
 
 | 
 
 | 
 
 | 
 
 | 
64
 | 
             last;  | 
| 
670
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
         }  | 
| 
671
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
         else {  | 
| 
672
 | 
30
 | 
 
 | 
 
 | 
 
 | 
 
 | 
40
 | 
             splice( @edges, 0, 2 );  | 
| 
673
 | 
30
 | 
 
 | 
 
 | 
 
 | 
 
 | 
53
 | 
             $offset -= $span_size;  | 
| 
674
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
         }  | 
| 
675
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
     }  | 
| 
676
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
677
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
     @edges  | 
| 
678
 | 
56
 | 
  
100
  
 | 
 
 | 
 
 | 
 
 | 
115
 | 
         or return $slice;    # empty set  | 
| 
679
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
680
 | 
45
 | 
 
 | 
 
 | 
 
 | 
 
 | 
56
 | 
     $edges[0] += $offset - 1;  | 
| 
681
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
682
 | 
45
 | 
 
 | 
 
 | 
 
 | 
 
 | 
93
 | 
     my @slices = $self->_splice_length( \@edges, $length );  | 
| 
683
 | 
45
 | 
 
 | 
 
 | 
 
 | 
 
 | 
97
 | 
     while (@slices) {  | 
| 
684
 | 
67
 | 
 
 | 
 
 | 
 
 | 
 
 | 
67
 | 
         my $lower = shift @slices;  | 
| 
685
 | 
67
 | 
 
 | 
 
 | 
 
 | 
 
 | 
71
 | 
         my $upper = shift(@slices) - 1;  | 
| 
686
 | 
67
 | 
 
 | 
 
 | 
 
 | 
 
 | 
96
 | 
         $slice->add_pair( $lower, $upper );  | 
| 
687
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
     }  | 
| 
688
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
689
 | 
45
 | 
 
 | 
 
 | 
 
 | 
 
 | 
97
 | 
     return $slice;  | 
| 
690
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 }  | 
| 
691
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
692
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 sub _splice_length {  | 
| 
693
 | 
45
 | 
 
 | 
 
 | 
  
45
  
 | 
 
 | 
42
 | 
     my $self      = shift;  | 
| 
694
 | 
45
 | 
 
 | 
 
 | 
 
 | 
 
 | 
39
 | 
     my $edges_ref = shift;  | 
| 
695
 | 
45
 | 
 
 | 
 
 | 
 
 | 
 
 | 
32
 | 
     my $length    = shift;  | 
| 
696
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
697
 | 
45
 | 
  
100
  
 | 
 
 | 
 
 | 
 
 | 
87
 | 
     if ( !defined $length ) {  | 
| 
698
 | 
8
 | 
 
 | 
 
 | 
 
 | 
 
 | 
7
 | 
         return @{$edges_ref};    # everything  | 
| 
 
 | 
8
 | 
 
 | 
 
 | 
 
 | 
 
 | 
24
 | 
    | 
| 
699
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
     }  | 
| 
700
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
701
 | 
37
 | 
  
100
  
 | 
 
 | 
 
 | 
 
 | 
56
 | 
     if ( $length <= 0 ) {  | 
| 
702
 | 
2
 | 
 
 | 
 
 | 
 
 | 
 
 | 
5
 | 
         return ();               # empty  | 
| 
703
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
     }  | 
| 
704
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
705
 | 
35
 | 
 
 | 
 
 | 
 
 | 
 
 | 
24
 | 
     my @slices;  | 
| 
706
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
707
 | 
35
 | 
 
 | 
 
 | 
 
 | 
 
 | 
68
 | 
     while ( @$edges_ref > 1 ) {  | 
| 
708
 | 
54
 | 
 
 | 
 
 | 
 
 | 
 
 | 
63
 | 
         my ( $lower, $upper ) = @$edges_ref[ 0, 1 ];  | 
| 
709
 | 
54
 | 
 
 | 
 
 | 
 
 | 
 
 | 
53
 | 
         my $span_size = $upper - $lower;  | 
| 
710
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
711
 | 
54
 | 
  
100
  
 | 
 
 | 
 
 | 
 
 | 
62
 | 
         if ( $length <= $span_size ) {  | 
| 
712
 | 
28
 | 
 
 | 
 
 | 
 
 | 
 
 | 
28
 | 
             last;  | 
| 
713
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
         }  | 
| 
714
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
         else {  | 
| 
715
 | 
26
 | 
 
 | 
 
 | 
 
 | 
 
 | 
40
 | 
             push @slices, splice( @$edges_ref, 0, 2 );  | 
| 
716
 | 
26
 | 
 
 | 
 
 | 
 
 | 
 
 | 
53
 | 
             $length -= $span_size;  | 
| 
717
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
         }  | 
| 
718
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
     }  | 
| 
719
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
720
 | 
35
 | 
  
100
  
 | 
 
 | 
 
 | 
 
 | 
71
 | 
     if (@$edges_ref) {  | 
| 
721
 | 
28
 | 
 
 | 
 
 | 
 
 | 
 
 | 
31
 | 
         my $lower = shift @$edges_ref;  | 
| 
722
 | 
28
 | 
 
 | 
 
 | 
 
 | 
 
 | 
55
 | 
         push @slices, $lower, $lower + $length;  | 
| 
723
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
     }  | 
| 
724
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
725
 | 
35
 | 
 
 | 
 
 | 
 
 | 
 
 | 
76
 | 
     return @slices;  | 
| 
726
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 }  | 
| 
727
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
728
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 sub min {  | 
| 
729
 | 
63
 | 
 
 | 
 
 | 
  
63
  
 | 
  
1
  
 | 
52
 | 
     my $self = shift;  | 
| 
730
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
731
 | 
63
 | 
  
 50
  
 | 
 
 | 
 
 | 
 
 | 
79
 | 
     if ( $self->is_empty ) {  | 
| 
732
 | 
  
0
  
 | 
 
 | 
 
 | 
 
 | 
 
 | 
0
 | 
         return;  | 
| 
733
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
     }  | 
| 
734
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
     else {  | 
| 
735
 | 
63
 | 
 
 | 
 
 | 
 
 | 
 
 | 
75
 | 
         return $self->edges_ref->[0];  | 
| 
736
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
     }  | 
| 
737
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 }  | 
| 
738
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
739
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 sub max {  | 
| 
740
 | 
63
 | 
 
 | 
 
 | 
  
63
  
 | 
  
1
  
 | 
53
 | 
     my $self = shift;  | 
| 
741
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
742
 | 
63
 | 
  
 50
  
 | 
 
 | 
 
 | 
 
 | 
75
 | 
     if ( $self->is_empty ) {  | 
| 
743
 | 
  
0
  
 | 
 
 | 
 
 | 
 
 | 
 
 | 
0
 | 
         return;  | 
| 
744
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
     }  | 
| 
745
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
     else {  | 
| 
746
 | 
63
 | 
 
 | 
 
 | 
 
 | 
 
 | 
75
 | 
         return $self->edges_ref->[-1] - 1;  | 
| 
747
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
     }  | 
| 
748
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 }  | 
| 
749
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
750
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 sub grep_set {  | 
| 
751
 | 
30
 | 
 
 | 
 
 | 
  
30
  
 | 
  
1
  
 | 
198
 | 
     my $self     = shift;  | 
| 
752
 | 
30
 | 
 
 | 
 
 | 
 
 | 
 
 | 
32
 | 
     my $code_ref = shift;  | 
| 
753
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
754
 | 
30
 | 
 
 | 
 
 | 
 
 | 
 
 | 
34
 | 
     my @sub_elements;  | 
| 
755
 | 
30
 | 
 
 | 
 
 | 
 
 | 
 
 | 
64
 | 
     for ( $self->elements ) {  | 
| 
756
 | 
150
 | 
  
100
  
 | 
 
 | 
 
 | 
 
 | 
2787
 | 
         if ( $code_ref->() ) {  | 
| 
757
 | 
60
 | 
 
 | 
 
 | 
 
 | 
 
 | 
2541
 | 
             push @sub_elements, $_;  | 
| 
758
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
         }  | 
| 
759
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
760
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
     }  | 
| 
761
 | 
30
 | 
 
 | 
 
 | 
 
 | 
 
 | 
776
 | 
     my $sub_set = Scalar::Util::blessed($self)->new(@sub_elements);  | 
| 
762
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
763
 | 
30
 | 
 
 | 
 
 | 
 
 | 
 
 | 
96
 | 
     return $sub_set;  | 
| 
764
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 }  | 
| 
765
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
766
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 sub map_set {  | 
| 
767
 | 
48
 | 
 
 | 
 
 | 
  
48
  
 | 
  
1
  
 | 
271
 | 
     my $self     = shift;  | 
| 
768
 | 
48
 | 
 
 | 
 
 | 
 
 | 
 
 | 
47
 | 
     my $code_ref = shift;  | 
| 
769
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
770
 | 
48
 | 
 
 | 
 
 | 
 
 | 
 
 | 
49
 | 
     my @map_elements;  | 
| 
771
 | 
48
 | 
 
 | 
 
 | 
 
 | 
 
 | 
104
 | 
     for ( $self->elements ) {  | 
| 
772
 | 
227
 | 
 
 | 
 
 | 
 
 | 
 
 | 
769
 | 
         for my $element ( $code_ref->() ) {  | 
| 
773
 | 
224
 | 
  
 50
  
 | 
 
 | 
 
 | 
 
 | 
7998
 | 
             if ( defined $element ) {  | 
| 
774
 | 
224
 | 
 
 | 
 
 | 
 
 | 
 
 | 
645
 | 
                 push @map_elements, $element;  | 
| 
775
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
             }  | 
| 
776
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
         }  | 
| 
777
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
778
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
     }  | 
| 
779
 | 
48
 | 
 
 | 
 
 | 
 
 | 
 
 | 
332
 | 
     my $map_set = Scalar::Util::blessed($self)->new(@map_elements);  | 
| 
780
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
781
 | 
48
 | 
 
 | 
 
 | 
 
 | 
 
 | 
118
 | 
     return $map_set;  | 
| 
782
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 }  | 
| 
783
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
784
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 sub substr_span {  | 
| 
785
 | 
5
 | 
 
 | 
 
 | 
  
5
  
 | 
  
1
  
 | 
29
 | 
     my $self   = shift;  | 
| 
786
 | 
5
 | 
 
 | 
 
 | 
 
 | 
 
 | 
7
 | 
     my $string = shift;  | 
| 
787
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
788
 | 
5
 | 
 
 | 
 
 | 
 
 | 
 
 | 
6
 | 
     my $sub_string = "";  | 
| 
789
 | 
5
 | 
 
 | 
 
 | 
 
 | 
 
 | 
14
 | 
     my @spans      = $self->spans;  | 
| 
790
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
791
 | 
5
 | 
 
 | 
 
 | 
 
 | 
 
 | 
13
 | 
     for (@spans) {  | 
| 
792
 | 
7
 | 
 
 | 
 
 | 
 
 | 
 
 | 
17
 | 
         my ( $lower, $upper ) = @$_;  | 
| 
793
 | 
7
 | 
 
 | 
 
 | 
 
 | 
 
 | 
13
 | 
         my $length = $upper - $lower + 1;  | 
| 
794
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
795
 | 
7
 | 
 
 | 
 
 | 
 
 | 
 
 | 
21
 | 
         $sub_string .= substr( $string, $lower - 1, $length );  | 
| 
796
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
     }  | 
| 
797
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
798
 | 
5
 | 
 
 | 
 
 | 
 
 | 
 
 | 
20
 | 
     return $sub_string;  | 
| 
799
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 }  | 
| 
800
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
801
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 #@returns AlignDB::IntSpan  | 
| 
802
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 sub banish_span {  | 
| 
803
 | 
6
 | 
 
 | 
 
 | 
  
6
  
 | 
  
1
  
 | 
37
 | 
     my $self  = shift;  | 
| 
804
 | 
6
 | 
 
 | 
 
 | 
 
 | 
 
 | 
8
 | 
     my $start = shift;  | 
| 
805
 | 
6
 | 
 
 | 
 
 | 
 
 | 
 
 | 
8
 | 
     my $end   = shift;  | 
| 
806
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
807
 | 
6
 | 
 
 | 
 
 | 
 
 | 
 
 | 
14
 | 
     my $remove_length = $end - $start + 1;  | 
| 
808
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
809
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
     my $new = $self->map_set(  | 
| 
810
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
         sub {  | 
| 
811
 | 
17
 | 
  
100
  
 | 
 
 | 
  
17
  
 | 
 
 | 
56
 | 
                   $_ < $start ? $_  | 
| 
 
 | 
 
 | 
  
100
  
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
812
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
                 : $_ > $end   ? $_ - $remove_length  | 
| 
813
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
                 :               ();  | 
| 
814
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
         }  | 
| 
815
 | 
6
 | 
 
 | 
 
 | 
 
 | 
 
 | 
39
 | 
     );  | 
| 
816
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
817
 | 
6
 | 
 
 | 
 
 | 
 
 | 
 
 | 
36
 | 
     return $new;  | 
| 
818
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 }  | 
| 
819
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
820
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 #@returns AlignDB::IntSpan  | 
| 
821
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 sub cover {  | 
| 
822
 | 
6
 | 
 
 | 
 
 | 
  
6
  
 | 
  
1
  
 | 
26
 | 
     my $self = shift;  | 
| 
823
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
824
 | 
6
 | 
 
 | 
 
 | 
 
 | 
 
 | 
49
 | 
     my $cover = Scalar::Util::blessed($self)->new;  | 
| 
825
 | 
6
 | 
  
100
  
 | 
 
 | 
 
 | 
 
 | 
14
 | 
     if ( $self->is_not_empty ) {  | 
| 
826
 | 
5
 | 
 
 | 
 
 | 
 
 | 
 
 | 
12
 | 
         $cover->add_pair( $self->min, $self->max );  | 
| 
827
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
     }  | 
| 
828
 | 
6
 | 
 
 | 
 
 | 
 
 | 
 
 | 
16
 | 
     return $cover;  | 
| 
829
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 }  | 
| 
830
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
831
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 #@returns AlignDB::IntSpan  | 
| 
832
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 sub holes {  | 
| 
833
 | 
14
 | 
 
 | 
 
 | 
  
14
  
 | 
  
1
  
 | 
32
 | 
     my $self = shift;  | 
| 
834
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
835
 | 
14
 | 
 
 | 
 
 | 
 
 | 
 
 | 
42
 | 
     my $holes = Scalar::Util::blessed($self)->new;  | 
| 
836
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
837
 | 
14
 | 
  
100
  
 | 
  
 66
  
 | 
 
 | 
 
 | 
30
 | 
     if ( $self->is_empty or $self->is_universal ) {  | 
| 
838
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
839
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
         # empty set and universal set have no holes  | 
| 
840
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
     }  | 
| 
841
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
     else {  | 
| 
842
 | 
13
 | 
 
 | 
 
 | 
 
 | 
 
 | 
22
 | 
         my $c_set  = $self->complement;  | 
| 
843
 | 
13
 | 
 
 | 
 
 | 
 
 | 
 
 | 
21
 | 
         my @ranges = $c_set->ranges;  | 
| 
844
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
845
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
         # Remove infinite arms of complement set  | 
| 
846
 | 
13
 | 
  
 50
  
 | 
 
 | 
 
 | 
 
 | 
21
 | 
         if ( $c_set->is_neg_inf ) {  | 
| 
847
 | 
13
 | 
 
 | 
 
 | 
 
 | 
 
 | 
11
 | 
             shift @ranges;  | 
| 
848
 | 
13
 | 
 
 | 
 
 | 
 
 | 
 
 | 
14
 | 
             shift @ranges;  | 
| 
849
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
         }  | 
| 
850
 | 
13
 | 
  
 50
  
 | 
 
 | 
 
 | 
 
 | 
21
 | 
         if ( $c_set->is_pos_inf ) {  | 
| 
851
 | 
13
 | 
 
 | 
 
 | 
 
 | 
 
 | 
14
 | 
             pop @ranges;  | 
| 
852
 | 
13
 | 
 
 | 
 
 | 
 
 | 
 
 | 
11
 | 
             pop @ranges;  | 
| 
853
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
         }  | 
| 
854
 | 
13
 | 
 
 | 
 
 | 
 
 | 
 
 | 
22
 | 
         $holes->add_range(@ranges);  | 
| 
855
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
     }  | 
| 
856
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
857
 | 
14
 | 
 
 | 
 
 | 
 
 | 
 
 | 
32
 | 
     return $holes;  | 
| 
858
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 }  | 
| 
859
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
860
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 #@returns AlignDB::IntSpan  | 
| 
861
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 sub inset {  | 
| 
862
 | 
18
 | 
 
 | 
 
 | 
  
18
  
 | 
  
1
  
 | 
45
 | 
     my $self = shift;  | 
| 
863
 | 
18
 | 
 
 | 
 
 | 
 
 | 
 
 | 
17
 | 
     my $n    = shift;  | 
| 
864
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
865
 | 
18
 | 
 
 | 
 
 | 
 
 | 
 
 | 
68
 | 
     my $inset = Scalar::Util::blessed($self)->new;  | 
| 
866
 | 
18
 | 
 
 | 
 
 | 
 
 | 
 
 | 
30
 | 
     my @edges = $self->edges;  | 
| 
867
 | 
18
 | 
 
 | 
 
 | 
 
 | 
 
 | 
36
 | 
     while (@edges) {  | 
| 
868
 | 
38
 | 
 
 | 
 
 | 
 
 | 
 
 | 
43
 | 
         my $lower = shift @edges;  | 
| 
869
 | 
38
 | 
 
 | 
 
 | 
 
 | 
 
 | 
36
 | 
         my $upper = shift(@edges) - 1;  | 
| 
870
 | 
38
 | 
  
100
  
 | 
 
 | 
 
 | 
 
 | 
57
 | 
         if ( $lower != $self->NEG_INF ) {  | 
| 
871
 | 
34
 | 
 
 | 
 
 | 
 
 | 
 
 | 
35
 | 
             $lower += $n;  | 
| 
872
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
         }  | 
| 
873
 | 
38
 | 
  
100
  
 | 
 
 | 
 
 | 
 
 | 
50
 | 
         if ( $upper != $self->POS_INF ) {  | 
| 
874
 | 
34
 | 
 
 | 
 
 | 
 
 | 
 
 | 
78
 | 
             $upper -= $n;  | 
| 
875
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
         }  | 
| 
876
 | 
38
 | 
  
100
  
 | 
 
 | 
 
 | 
 
 | 
85
 | 
         $inset->add_pair( $lower, $upper )  | 
| 
877
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
             if $lower <= $upper;  | 
| 
878
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
     }  | 
| 
879
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
880
 | 
18
 | 
 
 | 
 
 | 
 
 | 
 
 | 
35
 | 
     return $inset;  | 
| 
881
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 }  | 
| 
882
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
883
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 #@returns AlignDB::IntSpan  | 
| 
884
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 sub trim {  | 
| 
885
 | 
1
 | 
 
 | 
 
 | 
  
1
  
 | 
  
1
  
 | 
2
 | 
     my $self = shift;  | 
| 
886
 | 
1
 | 
 
 | 
 
 | 
 
 | 
 
 | 
2
 | 
     my $n    = shift;  | 
| 
887
 | 
1
 | 
 
 | 
 
 | 
 
 | 
 
 | 
4
 | 
     return $self->inset($n);  | 
| 
888
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 }  | 
| 
889
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
890
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 #@returns AlignDB::IntSpan  | 
| 
891
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 sub pad {  | 
| 
892
 | 
1
 | 
 
 | 
 
 | 
  
1
  
 | 
  
1
  
 | 
2
 | 
     my $self = shift;  | 
| 
893
 | 
1
 | 
 
 | 
 
 | 
 
 | 
 
 | 
3
 | 
     my $n    = shift;  | 
| 
894
 | 
1
 | 
 
 | 
 
 | 
 
 | 
 
 | 
4
 | 
     return $self->inset( -$n );  | 
| 
895
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 }  | 
| 
896
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
897
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 #@returns AlignDB::IntSpan  | 
| 
898
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 sub excise {  | 
| 
899
 | 
7
 | 
 
 | 
 
 | 
  
7
  
 | 
  
1
  
 | 
19
 | 
     my $self      = shift;  | 
| 
900
 | 
7
 | 
 
 | 
 
 | 
 
 | 
 
 | 
8
 | 
     my $minlength = shift;  | 
| 
901
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
902
 | 
7
 | 
 
 | 
 
 | 
 
 | 
 
 | 
24
 | 
     my $set = Scalar::Util::blessed($self)->new;  | 
| 
903
 | 
7
 | 
 
 | 
 
 | 
 
 | 
 
 | 
14
 | 
     map { $set->merge($_) } grep { $_->size >= $minlength } $self->sets;  | 
| 
 
 | 
10
 | 
 
 | 
 
 | 
 
 | 
 
 | 
17
 | 
    | 
| 
 
 | 
14
 | 
 
 | 
 
 | 
 
 | 
 
 | 
20
 | 
    | 
| 
904
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
905
 | 
7
 | 
 
 | 
 
 | 
 
 | 
 
 | 
19
 | 
     return $set;  | 
| 
906
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 }  | 
| 
907
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
908
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 #@returns AlignDB::IntSpan  | 
| 
909
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 sub fill {  | 
| 
910
 | 
8
 | 
 
 | 
 
 | 
  
8
  
 | 
  
1
  
 | 
21
 | 
     my $self      = shift;  | 
| 
911
 | 
8
 | 
 
 | 
 
 | 
 
 | 
 
 | 
9
 | 
     my $maxlength = shift;  | 
| 
912
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
913
 | 
8
 | 
 
 | 
 
 | 
 
 | 
 
 | 
15
 | 
     my $set = $self->copy;  | 
| 
914
 | 
8
 | 
  
 50
  
 | 
 
 | 
 
 | 
 
 | 
17
 | 
     if ( $maxlength > 0 ) {  | 
| 
915
 | 
8
 | 
 
 | 
 
 | 
 
 | 
 
 | 
13
 | 
         for my $hole ( $set->holes->sets ) {  | 
| 
916
 | 
11
 | 
  
100
  
 | 
 
 | 
 
 | 
 
 | 
21
 | 
             if ( $hole->size <= $maxlength ) {  | 
| 
917
 | 
9
 | 
 
 | 
 
 | 
 
 | 
 
 | 
14
 | 
                 $set->merge($hole);  | 
| 
918
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
             }  | 
| 
919
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
         }  | 
| 
920
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
     }  | 
| 
921
 | 
8
 | 
 
 | 
 
 | 
 
 | 
 
 | 
33
 | 
     return $set;  | 
| 
922
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 }  | 
| 
923
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
924
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 sub overlap {  | 
| 
925
 | 
63
 | 
 
 | 
 
 | 
  
63
  
 | 
  
1
  
 | 
65
 | 
     my $self     = shift;  | 
| 
926
 | 
63
 | 
 
 | 
 
 | 
 
 | 
 
 | 
51
 | 
     my $supplied = shift;  | 
| 
927
 | 
63
 | 
 
 | 
 
 | 
 
 | 
 
 | 
92
 | 
     return $self->intersect($supplied)->size;  | 
| 
928
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 }  | 
| 
929
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
930
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 sub distance {  | 
| 
931
 | 
28
 | 
 
 | 
 
 | 
  
28
  
 | 
  
1
  
 | 
42
 | 
     my $self     = shift;  | 
| 
932
 | 
28
 | 
 
 | 
 
 | 
 
 | 
 
 | 
25
 | 
     my $supplied = shift;  | 
| 
933
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
934
 | 
28
 | 
  
 50
  
 | 
  
 33
  
 | 
 
 | 
 
 | 
35
 | 
     return unless $self->size and $supplied->size;  | 
| 
935
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
936
 | 
28
 | 
 
 | 
 
 | 
 
 | 
 
 | 
42
 | 
     my $overlap = $self->overlap($supplied);  | 
| 
937
 | 
28
 | 
  
100
  
 | 
 
 | 
 
 | 
 
 | 
70
 | 
     return -$overlap if $overlap;  | 
| 
938
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
939
 | 
24
 | 
 
 | 
 
 | 
 
 | 
 
 | 
25
 | 
     my $min_d;  | 
| 
940
 | 
24
 | 
 
 | 
 
 | 
 
 | 
 
 | 
35
 | 
     for my $span1 ( $self->sets ) {  | 
| 
941
 | 
29
 | 
 
 | 
 
 | 
 
 | 
 
 | 
46
 | 
         for my $span2 ( $supplied->sets ) {  | 
| 
942
 | 
29
 | 
 
 | 
 
 | 
 
 | 
 
 | 
71
 | 
             my $d1 = abs( $span1->min - $span2->max );  | 
| 
943
 | 
29
 | 
 
 | 
 
 | 
 
 | 
 
 | 
53
 | 
             my $d2 = abs( $span1->max - $span2->min );  | 
| 
944
 | 
29
 | 
  
100
  
 | 
 
 | 
 
 | 
 
 | 
58
 | 
             my $d  = $d1 < $d2 ? $d1 : $d2;  | 
| 
945
 | 
29
 | 
  
100
  
 | 
  
100
  
 | 
 
 | 
 
 | 
86
 | 
             if ( !defined $min_d or $d < $min_d ) {  | 
| 
946
 | 
27
 | 
 
 | 
 
 | 
 
 | 
 
 | 
64
 | 
                 $min_d = $d;  | 
| 
947
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
             }  | 
| 
948
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
         }  | 
| 
949
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
     }  | 
| 
950
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
951
 | 
24
 | 
 
 | 
 
 | 
 
 | 
 
 | 
45
 | 
     return $min_d;  | 
| 
952
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 }  | 
| 
953
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
954
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 #@returns AlignDB::IntSpan  | 
| 
955
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 sub find_islands {  | 
| 
956
 | 
11
 | 
 
 | 
 
 | 
  
11
  
 | 
  
1
  
 | 
63
 | 
     my $self     = shift;  | 
| 
957
 | 
11
 | 
 
 | 
 
 | 
 
 | 
 
 | 
10
 | 
     my $supplied = shift;  | 
| 
958
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
959
 | 
11
 | 
 
 | 
 
 | 
 
 | 
 
 | 
13
 | 
     my $island;  | 
| 
960
 | 
11
 | 
  
100
  
 | 
 
 | 
 
 | 
 
 | 
31
 | 
     if ( ref $supplied eq __PACKAGE__ ) {  | 
| 
 
 | 
 
 | 
  
 50
  
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
961
 | 
4
 | 
 
 | 
 
 | 
 
 | 
 
 | 
12
 | 
         $island = $self->_find_islands_set($supplied);  | 
| 
962
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
     }  | 
| 
963
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
     elsif ( Scalar::Util::Numeric::isint($supplied) ) {  | 
| 
964
 | 
7
 | 
 
 | 
 
 | 
 
 | 
 
 | 
10
 | 
         $island = $self->_find_islands_int($supplied);  | 
| 
965
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
     }  | 
| 
966
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
     else {  | 
| 
967
 | 
  
0
  
 | 
 
 | 
 
 | 
 
 | 
 
 | 
0
 | 
         Carp::confess "Don't know how to deal with input to find_island\n";  | 
| 
968
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
     }  | 
| 
969
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
970
 | 
11
 | 
 
 | 
 
 | 
 
 | 
 
 | 
18
 | 
     return $island;  | 
| 
971
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 }  | 
| 
972
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
973
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 sub _find_islands_int {  | 
| 
974
 | 
7
 | 
 
 | 
 
 | 
  
7
  
 | 
 
 | 
7
 | 
     my $self   = shift;  | 
| 
975
 | 
7
 | 
 
 | 
 
 | 
 
 | 
 
 | 
6
 | 
     my $number = shift;  | 
| 
976
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
977
 | 
7
 | 
 
 | 
 
 | 
 
 | 
 
 | 
30
 | 
     my $island = Scalar::Util::blessed($self)->new;  | 
| 
978
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
979
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
     # if $pos & 1, i.e. $pos is odd number, $val is in the set  | 
| 
980
 | 
7
 | 
 
 | 
 
 | 
 
 | 
 
 | 
14
 | 
     my $pos = $self->_find_pos( $number + 1, 0 );  | 
| 
981
 | 
7
 | 
  
100
  
 | 
 
 | 
 
 | 
 
 | 
16
 | 
     if ( $pos & 1 ) {  | 
| 
982
 | 
5
 | 
 
 | 
 
 | 
 
 | 
 
 | 
9
 | 
         my @ranges = $self->ranges;  | 
| 
983
 | 
5
 | 
 
 | 
 
 | 
 
 | 
 
 | 
12
 | 
         $island->add_range( $ranges[ $pos - 1 ], $ranges[$pos] );  | 
| 
984
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
     }  | 
| 
985
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
986
 | 
7
 | 
 
 | 
 
 | 
 
 | 
 
 | 
10
 | 
     return $island;  | 
| 
987
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 }  | 
| 
988
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
989
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 sub _find_islands_set {  | 
| 
990
 | 
4
 | 
 
 | 
 
 | 
  
4
  
 | 
 
 | 
5
 | 
     my $self     = shift;  | 
| 
991
 | 
4
 | 
 
 | 
 
 | 
 
 | 
 
 | 
2
 | 
     my $supplied = shift;  | 
| 
992
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
993
 | 
4
 | 
 
 | 
 
 | 
 
 | 
 
 | 
13
 | 
     my $islands = Scalar::Util::blessed($self)->new;  | 
| 
994
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
995
 | 
4
 | 
  
 50
  
 | 
 
 | 
 
 | 
 
 | 
11
 | 
     if ( $self->overlap($supplied) ) {  | 
| 
996
 | 
4
 | 
 
 | 
 
 | 
 
 | 
 
 | 
8
 | 
         for my $subset ( $self->sets ) {  | 
| 
997
 | 
8
 | 
  
100
  
 | 
 
 | 
 
 | 
 
 | 
11
 | 
             $islands->merge($subset) if $subset->overlap($supplied);  | 
| 
998
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
         }  | 
| 
999
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
     }  | 
| 
1000
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
1001
 | 
4
 | 
 
 | 
 
 | 
 
 | 
 
 | 
11
 | 
     return $islands;  | 
| 
1002
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 }  | 
| 
1003
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
1004
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 #@returns AlignDB::IntSpan  | 
| 
1005
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 sub nearest_island {  | 
| 
1006
 | 
10
 | 
 
 | 
 
 | 
  
10
  
 | 
  
1
  
 | 
54
 | 
     my $self     = shift;  | 
| 
1007
 | 
10
 | 
 
 | 
 
 | 
 
 | 
 
 | 
10
 | 
     my $supplied = shift;  | 
| 
1008
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
1009
 | 
10
 | 
  
100
  
 | 
 
 | 
 
 | 
 
 | 
31
 | 
     if ( ref $supplied eq __PACKAGE__ ) {    # just OK  | 
| 
 
 | 
 
 | 
  
 50
  
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
1010
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
     }  | 
| 
1011
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
     elsif ( Scalar::Util::Numeric::isint($supplied) ) {  | 
| 
1012
 | 
7
 | 
 
 | 
 
 | 
 
 | 
 
 | 
23
 | 
         $supplied = Scalar::Util::blessed($self)->new($supplied);  | 
| 
1013
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
     }  | 
| 
1014
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
     else {  | 
| 
1015
 | 
  
0
  
 | 
 
 | 
 
 | 
 
 | 
 
 | 
0
 | 
         Carp::confess "Don't know how to deal with input to nearest_island\n";  | 
| 
1016
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
     }  | 
| 
1017
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
1018
 | 
10
 | 
 
 | 
 
 | 
 
 | 
 
 | 
31
 | 
     my $island = Scalar::Util::blessed($self)->new;  | 
| 
1019
 | 
10
 | 
 
 | 
 
 | 
 
 | 
 
 | 
11
 | 
     my $min_d;  | 
| 
1020
 | 
10
 | 
 
 | 
 
 | 
 
 | 
 
 | 
17
 | 
     for my $s ( $self->sets ) {  | 
| 
1021
 | 
19
 | 
 
 | 
 
 | 
 
 | 
 
 | 
32
 | 
         for my $ss ( $supplied->sets ) {  | 
| 
1022
 | 
19
 | 
  
100
  
 | 
 
 | 
 
 | 
 
 | 
28
 | 
             next if $s->overlap($ss);  | 
| 
1023
 | 
17
 | 
 
 | 
 
 | 
 
 | 
 
 | 
36
 | 
             my $d = $s->distance($ss);  | 
| 
1024
 | 
17
 | 
  
100
  
 | 
  
100
  
 | 
 
 | 
 
 | 
51
 | 
             if ( !defined $min_d or $d <= $min_d ) {  | 
| 
1025
 | 
14
 | 
  
100
  
 | 
  
100
  
 | 
 
 | 
 
 | 
38
 | 
                 if ( defined $min_d and $d == $min_d ) {  | 
| 
1026
 | 
2
 | 
 
 | 
 
 | 
 
 | 
 
 | 
5
 | 
                     $island->merge($s);  | 
| 
1027
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
                 }  | 
| 
1028
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
                 else {  | 
| 
1029
 | 
12
 | 
 
 | 
 
 | 
 
 | 
 
 | 
17
 | 
                     $min_d  = $d;  | 
| 
1030
 | 
12
 | 
 
 | 
 
 | 
 
 | 
 
 | 
24
 | 
                     $island = $s->copy;  | 
| 
1031
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
                 }  | 
| 
1032
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
             }  | 
| 
1033
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
         }  | 
| 
1034
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
     }  | 
| 
1035
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
1036
 | 
10
 | 
 
 | 
 
 | 
 
 | 
 
 | 
34
 | 
     return $island;  | 
| 
1037
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 }  | 
| 
1038
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
1039
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 sub at_island {  | 
| 
1040
 | 
13
 | 
 
 | 
 
 | 
  
13
  
 | 
  
1
  
 | 
49
 | 
     my $self  = shift;  | 
| 
1041
 | 
13
 | 
 
 | 
 
 | 
 
 | 
 
 | 
11
 | 
     my $index = shift;  | 
| 
1042
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
1043
 | 
13
 | 
  
100
  
 | 
  
100
  
 | 
 
 | 
 
 | 
48
 | 
     return if $index == 0 or abs($index) > $self->span_size;  | 
| 
1044
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
1045
 | 
8
 | 
 
 | 
 
 | 
 
 | 
 
 | 
17
 | 
     my @islands = $self->sets;  | 
| 
1046
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
1047
 | 
8
 | 
  
100
  
 | 
 
 | 
 
 | 
 
 | 
28
 | 
     return $index < 0 ? $islands[$index] : $islands[ $index - 1 ];  | 
| 
1048
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 }  | 
| 
1049
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
1050
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 #----------------------------------------------------------#  | 
| 
1051
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 # Internal methods  | 
| 
1052
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 #----------------------------------------------------------#  | 
| 
1053
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 # Converts a list of integers into pairs of ranges  | 
| 
1054
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 sub _list_to_ranges {  | 
| 
1055
 | 
41
 | 
 
 | 
 
 | 
  
41
  
 | 
 
 | 
46
 | 
     my $self = shift;  | 
| 
1056
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
1057
 | 
41
 | 
 
 | 
 
 | 
 
 | 
 
 | 
122
 | 
     my @list = sort { $a <=> $b } @_;  | 
| 
 
 | 
617
 | 
 
 | 
 
 | 
 
 | 
 
 | 
664
 | 
    | 
| 
1058
 | 
41
 | 
 
 | 
 
 | 
 
 | 
 
 | 
38
 | 
     my @ranges;  | 
| 
1059
 | 
41
 | 
 
 | 
 
 | 
 
 | 
 
 | 
47
 | 
     my $count = scalar @list;  | 
| 
1060
 | 
41
 | 
 
 | 
 
 | 
 
 | 
 
 | 
47
 | 
     my $pos   = 0;  | 
| 
1061
 | 
41
 | 
 
 | 
 
 | 
 
 | 
 
 | 
85
 | 
     while ( $pos < $count ) {  | 
| 
1062
 | 
164
 | 
 
 | 
 
 | 
 
 | 
 
 | 
144
 | 
         my $end = $pos + 1;  | 
| 
1063
 | 
164
 | 
 
 | 
  
100
  
 | 
 
 | 
 
 | 
1181
 | 
         $end++ while $end < $count && $list[$end] <= $list[ $end - 1 ] + 1;  | 
| 
1064
 | 
164
 | 
 
 | 
 
 | 
 
 | 
 
 | 
247
 | 
         push @ranges, ( $list[$pos], $list[ $end - 1 ] );  | 
| 
1065
 | 
164
 | 
 
 | 
 
 | 
 
 | 
 
 | 
281
 | 
         $pos = $end;  | 
| 
1066
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
     }  | 
| 
1067
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
1068
 | 
41
 | 
 
 | 
 
 | 
 
 | 
 
 | 
184
 | 
     return @ranges;  | 
| 
1069
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 }  | 
| 
1070
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
1071
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 # Converts a runlist into pairs of ranges  | 
| 
1072
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 sub _runlist_to_ranges {  | 
| 
1073
 | 
864
 | 
 
 | 
 
 | 
  
864
  
 | 
 
 | 
823
 | 
     my $self = shift;  | 
| 
1074
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
1075
 | 
864
 | 
 
 | 
 
 | 
 
 | 
 
 | 
824
 | 
     my $runlist = shift;  | 
| 
1076
 | 
864
 | 
 
 | 
 
 | 
 
 | 
 
 | 
2711
 | 
     $runlist =~ s/\s|_//g;  | 
| 
1077
 | 
864
 | 
  
100
  
 | 
 
 | 
 
 | 
 
 | 
1393
 | 
     return if $runlist eq $self->EMPTY_STRING;  | 
| 
1078
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
1079
 | 
747
 | 
 
 | 
 
 | 
 
 | 
 
 | 
769
 | 
     my @ranges;  | 
| 
1080
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
1081
 | 
747
 | 
 
 | 
 
 | 
 
 | 
 
 | 
2036
 | 
     for my $run ( split ",", $runlist ) {  | 
| 
1082
 | 
1165
 | 
  
100
  
 | 
 
 | 
 
 | 
 
 | 
5296
 | 
         if ( $run =~ /^ (-?\d+) $/x ) {  | 
| 
 
 | 
 
 | 
  
100
  
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
1083
 | 
199
 | 
 
 | 
 
 | 
 
 | 
 
 | 
492
 | 
             push @ranges, ( $1, $1 );  | 
| 
1084
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
         }  | 
| 
1085
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
         elsif ( $run =~ /^ (-?\d+) - (-?\d+) $/x ) {  | 
| 
1086
 | 
956
 | 
  
100
  
 | 
 
 | 
 
 | 
 
 | 
2993
 | 
             Carp::confess "Bad order: $runlist\n" if $1 > $2;  | 
| 
1087
 | 
954
 | 
 
 | 
 
 | 
 
 | 
 
 | 
2380
 | 
             push @ranges, ( $1, $2 );  | 
| 
1088
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
         }  | 
| 
1089
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
         else {  | 
| 
1090
 | 
10
 | 
 
 | 
 
 | 
 
 | 
 
 | 
1117
 | 
             Carp::confess "Bad syntax: $runlist\n";  | 
| 
1091
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
         }  | 
| 
1092
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
     }  | 
| 
1093
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
1094
 | 
735
 | 
 
 | 
 
 | 
 
 | 
 
 | 
2454
 | 
     return @ranges;  | 
| 
1095
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 }  | 
| 
1096
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
1097
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 # Converts a set specification into a set  | 
| 
1098
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 sub _real_set {  | 
| 
1099
 | 
692
 | 
 
 | 
 
 | 
  
692
  
 | 
 
 | 
640
 | 
     my $self     = shift;  | 
| 
1100
 | 
692
 | 
 
 | 
 
 | 
 
 | 
 
 | 
592
 | 
     my $supplied = shift;  | 
| 
1101
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
1102
 | 
692
 | 
  
100
  
 | 
  
 66
  
 | 
 
 | 
 
 | 
2856
 | 
     if ( defined $supplied and ref $supplied eq __PACKAGE__ ) {  | 
| 
1103
 | 
688
 | 
 
 | 
 
 | 
 
 | 
 
 | 
1272
 | 
         return $supplied;  | 
| 
1104
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
     }  | 
| 
1105
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
     else {  | 
| 
1106
 | 
4
 | 
 
 | 
 
 | 
 
 | 
 
 | 
21
 | 
         return Scalar::Util::blessed($self)->new($supplied);  | 
| 
1107
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
     }  | 
| 
1108
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 }  | 
| 
1109
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
1110
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 # Return the index of the first element >= the supplied value.  | 
| 
1111
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 #  | 
| 
1112
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 # If the supplied value is larger than any element in the list the returned  | 
| 
1113
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 # value will be equal to the size of the list.  | 
| 
1114
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 #  | 
| 
1115
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 # If $pos & 1, i.e. $pos is odd number, $val is in the set  | 
| 
1116
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 sub _find_pos {  | 
| 
1117
 | 
80508
 | 
 
 | 
 
 | 
  
80508
  
 | 
 
 | 
63994
 | 
     my $self = shift;  | 
| 
1118
 | 
80508
 | 
 
 | 
 
 | 
 
 | 
 
 | 
61527
 | 
     my $val  = shift;  | 
| 
1119
 | 
80508
 | 
 
 | 
 
 | 
 
 | 
 
 | 
60926
 | 
     my $low  = shift;  | 
| 
1120
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
1121
 | 
80508
 | 
 
 | 
 
 | 
 
 | 
 
 | 
88028
 | 
     my $edges_ref = $self->edges_ref;  | 
| 
1122
 | 
80508
 | 
 
 | 
 
 | 
 
 | 
 
 | 
96720
 | 
     my $high      = $self->edge_size;  | 
| 
1123
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
1124
 | 
80508
 | 
 
 | 
 
 | 
 
 | 
 
 | 
135467
 | 
     while ( $low < $high ) {  | 
| 
1125
 | 
90913
 | 
 
 | 
 
 | 
 
 | 
 
 | 
99838
 | 
         my $mid = int( ( $low + $high ) / 2 );  | 
| 
1126
 | 
90913
 | 
  
100
  
 | 
 
 | 
 
 | 
 
 | 
137843
 | 
         if ( $val < $edges_ref->[$mid] ) {  | 
| 
 
 | 
 
 | 
  
100
  
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
1127
 | 
33276
 | 
 
 | 
 
 | 
 
 | 
 
 | 
52333
 | 
             $high = $mid;  | 
| 
1128
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
         }  | 
| 
1129
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
         elsif ( $val > $edges_ref->[$mid] ) {  | 
| 
1130
 | 
49079
 | 
 
 | 
 
 | 
 
 | 
 
 | 
81754
 | 
             $low = $mid + 1;  | 
| 
1131
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
         }  | 
| 
1132
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
         else {  | 
| 
1133
 | 
8558
 | 
 
 | 
 
 | 
 
 | 
 
 | 
13062
 | 
             return $mid;  | 
| 
1134
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
         }  | 
| 
1135
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
     }  | 
| 
1136
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
1137
 | 
71950
 | 
 
 | 
 
 | 
 
 | 
 
 | 
74344
 | 
     return $low;  | 
| 
1138
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 }  | 
| 
1139
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
1140
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 #----------------------------------------------------------#  | 
| 
1141
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 # Aliases  | 
| 
1142
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 #----------------------------------------------------------#  | 
| 
1143
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
1144
 | 
298
 | 
 
 | 
 
 | 
  
298
  
 | 
  
0
  
 | 
1073
 | 
 sub runlist      { shift->as_string(@_); }  | 
| 
1145
 | 
78
 | 
 
 | 
 
 | 
  
78
  
 | 
  
0
  
 | 
173
 | 
 sub elements     { shift->as_array(@_); }  | 
| 
1146
 | 
146
 | 
 
 | 
 
 | 
  
146
  
 | 
  
0
  
 | 
211
 | 
 sub size         { shift->cardinality(@_); }  | 
| 
1147
 | 
0
 | 
 
 | 
 
 | 
  
0
  
 | 
  
0
  
 | 
0
 | 
 sub count        { shift->cardinality(@_); }  | 
| 
1148
 | 
184
 | 
 
 | 
 
 | 
  
184
  
 | 
  
0
  
 | 
529
 | 
 sub contains     { shift->contains_all(@_); }  | 
| 
1149
 | 
1
 | 
 
 | 
 
 | 
  
1
  
 | 
  
0
  
 | 
7
 | 
 sub intersection { shift->intersect(@_); }  | 
| 
1150
 | 
17
 | 
 
 | 
 
 | 
  
17
  
 | 
  
0
  
 | 
42
 | 
 sub equals       { shift->equal(@_); }  | 
| 
1151
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
1152
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 1;    # Magic true value required at end of module  | 
| 
1153
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
    | 
| 
1154
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 
 | 
 __END__  |