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stmt |
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cond |
sub |
pod |
time |
code |
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1
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package AlignDB::IntSpan; |
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2
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14
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14
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282322
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use strict; |
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14
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25
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14
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488
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3
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14
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14
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61
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use warnings; |
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14
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24
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14
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436
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4
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5
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14
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14
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56
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use Carp; |
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14
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22
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14
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1188
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6
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14
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14
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69
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use Scalar::Util; |
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14
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23
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14
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777
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7
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14
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14
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7928
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use Scalar::Util::Numeric; |
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14
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10065
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14
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1418
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8
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9
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use overload ( |
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10
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0
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0
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0
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q{0+} => sub { Carp::confess "Can't numerify an AlignDB::IntSpan\n" }, |
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11
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14
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175
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q{bool} => q{is_not_empty}, |
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12
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q{""} => q{as_string}, |
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13
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14
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# use Perl standard behaviours for other operations |
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15
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fallback => 1, |
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16
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14
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14
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19454
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); |
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14
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15516
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17
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18
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our $VERSION = '1.1.1'; |
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19
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20
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my $POS_INF = 2_147_483_647 - 1; # INT_MAX - 1 |
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21
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my $NEG_INF = ( -2_147_483_647 - 1 ) + 1; # INT_MIN + 1 |
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22
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23
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sub POS_INF { |
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24
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40
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40
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1
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69
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return $POS_INF - 1; |
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25
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} |
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26
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27
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sub NEG_INF { |
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28
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40
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40
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1
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68
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return $NEG_INF; |
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29
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} |
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30
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31
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sub EMPTY_STRING { |
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32
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973
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973
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1
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4030
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return '-'; |
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33
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} |
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34
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35
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sub new { |
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36
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12257
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12257
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1
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2409723
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my $class = shift; |
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37
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12257
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15021
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my $self = {}; |
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38
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12257
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23012
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$self->{edges} = []; |
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39
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12257
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14728
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bless $self, $class; |
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40
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12257
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100
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26135
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$self->add(@_) if @_ > 0; |
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41
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12251
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23815
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return $self; |
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42
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} |
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43
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44
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sub valid { |
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45
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6
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6
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1
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3120
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my $this = shift; |
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46
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6
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6
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my $runlist = shift; |
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47
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48
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6
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33
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31
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my $class = ref($this) || $this; |
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49
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6
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11
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my $set = new $class; |
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50
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51
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6
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9
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eval { $set->_runlist_to_ranges($runlist) }; |
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6
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10
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52
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6
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50
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492
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return $@ ? 0 : 1; |
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53
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} |
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54
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55
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sub clear { |
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56
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2
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2
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1
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4
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my $self = shift; |
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57
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2
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7
|
$self->{edges} = []; |
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58
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2
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5
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return $self; |
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59
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} |
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60
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61
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sub edges_ref { |
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62
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231342
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231342
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1
|
181034
|
my $self = shift; |
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63
|
231342
|
|
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|
326340
|
return $self->{edges}; |
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64
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} |
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65
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66
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sub edges { |
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67
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105340
|
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|
105340
|
1
|
83748
|
my $self = shift; |
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68
|
105340
|
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|
82139
|
return @{ $self->edges_ref }; |
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|
105340
|
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|
117606
|
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69
|
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} |
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70
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71
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sub edge_size { |
|
72
|
87530
|
|
|
87530
|
1
|
67201
|
my $self = shift; |
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73
|
87530
|
|
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|
|
98914
|
return scalar $self->edges; |
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74
|
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} |
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75
|
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76
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sub span_size { |
|
77
|
11
|
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11
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1
|
10
|
my $self = shift; |
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78
|
11
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|
14
|
return $self->edge_size / 2; |
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79
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} |
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80
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|
81
|
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sub as_string { |
|
82
|
498
|
|
|
498
|
1
|
8338
|
my $self = shift; |
|
83
|
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84
|
498
|
100
|
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|
805
|
if ( $self->is_empty ) { |
|
85
|
107
|
|
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|
191
|
return $self->EMPTY_STRING; |
|
86
|
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} |
|
87
|
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88
|
391
|
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|
359
|
my @runs; |
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89
|
391
|
|
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|
|
541
|
my @edges = $self->edges; |
|
90
|
391
|
|
|
|
|
856
|
while (@edges) { |
|
91
|
597
|
|
|
|
|
665
|
my $lower = shift @edges; |
|
92
|
597
|
|
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|
|
620
|
my $upper = shift(@edges) - 1; |
|
93
|
597
|
100
|
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|
|
1890
|
push @runs, $lower == $upper ? $lower : "$lower-$upper"; |
|
94
|
|
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|
|
} |
|
95
|
|
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|
96
|
391
|
|
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|
|
5069
|
return join( ',', @runs ); |
|
97
|
|
|
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|
|
} |
|
98
|
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|
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|
|
99
|
|
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|
|
|
|
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
|
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} |
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199
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200
|
168
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|
423
|
return $cardinality; |
|
201
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} |
|
202
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203
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sub is_empty { |
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204
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6404
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6404
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1
|
5856
|
my $self = shift; |
|
205
|
6404
|
100
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|
8746
|
my $result = $self->edge_size == 0 ? 1 : 0; |
|
206
|
6404
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|
10859
|
return $result; |
|
207
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} |
|
208
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209
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|
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sub is_not_empty { |
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210
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8
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8
|
1
|
21
|
my $self = shift; |
|
211
|
8
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|
20
|
return !$self->is_empty; |
|
212
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} |
|
213
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214
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|
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sub is_neg_inf { |
|
215
|
19
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|
19
|
1
|
19
|
my $self = shift; |
|
216
|
19
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|
26
|
return $self->edges_ref->[0] == $NEG_INF; |
|
217
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|
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} |
|
218
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219
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|
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sub is_pos_inf { |
|
220
|
14
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|
14
|
1
|
15
|
my $self = shift; |
|
221
|
14
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|
17
|
return $self->edges_ref->[-1] == $POS_INF; |
|
222
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} |
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223
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224
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|
|
sub is_infinite { |
|
225
|
2
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2
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1
|
3
|
my $self = shift; |
|
226
|
2
|
|
33
|
|
|
8
|
return $self->is_neg_inf || $self->is_pos_inf; |
|
227
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} |
|
228
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|
229
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|
|
sub is_finite { |
|
230
|
1
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|
|
1
|
1
|
9
|
my $self = shift; |
|
231
|
1
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|
|
3
|
return !$self->is_infinite; |
|
232
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|
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} |
|
233
|
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|
234
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|
|
sub is_universal { |
|
235
|
13
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|
13
|
1
|
12
|
my $self = shift; |
|
236
|
13
|
|
33
|
|
|
17
|
return $self->edge_size == 2 && $self->is_neg_inf && $self->is_pos_inf; |
|
237
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|
|
} |
|
238
|
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|
239
|
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|
|
sub contains_all { |
|
240
|
184
|
|
|
184
|
1
|
141
|
my $self = shift; |
|
241
|
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|
242
|
184
|
|
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|
|
182
|
for my $i (@_) { |
|
243
|
184
|
|
|
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|
218
|
my $pos = $self->_find_pos( $i + 1, 0 ); |
|
244
|
184
|
100
|
|
|
|
383
|
return 0 unless $pos & 1; |
|
245
|
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|
|
} |
|
246
|
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|
247
|
100
|
|
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|
114
|
return 1; |
|
248
|
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|
|
} |
|
249
|
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|
250
|
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|
|
sub contains_any { |
|
251
|
3
|
|
|
3
|
1
|
7
|
my $self = shift; |
|
252
|
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|
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
|
|
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|
|
} |
|
257
|
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|
258
|
2
|
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|
7
|
return 0; |
|
259
|
|
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|
|
} |
|
260
|
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|
261
|
|
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|
|
|
|
#@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__ |