ensembl-hive  2.8.1
Node.pm
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1 =head1 LICENSE
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6 Licensed under the Apache License, Version 2.0 (the "License");
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18 =cut
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20 
21 =head1 CONTACT
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29 =cut
30 
31 =head1 NAME
32 
33 Bio::EnsEMBL::Utils::Tree::Interval::Immutable::Node
34 
35 =head1 DESCRIPTION
36 
37 Instances of this class represent nodes in a centered immutable interval tree.
38 
39 =head1 METHODS
40 
41 =cut
42 
43 package Bio::EnsEMBL::Utils::Tree::Interval::Immutable::Node;
44 
45 use strict;
46 
47 use Scalar::Util qw(looks_like_number);
48 use Bio::EnsEMBL::Utils::Exception qw(throw);
49 
50 =head2 new
51 
52  Arg [1] : scalar, $x_center
53  The mid point of the intervals represented by the node
54  Arg [2] : Arrayref of Bio::EnsEMBL::Utils::Interval instances
55  Represents the set of intervals overlapping $x_center
56  Arg [3] : Bio::EnsEMBL::Utils::Tree::Interval::Immutable::Node
57  The left subtree
58  Arg [4] : Bio::EnsEMBL::Utils::Tree::Interval::Immutable::Node
59  The right subtree
60  Description : Constructor. Creates a new centered immutable interval tree node instance
61  Returntype : Bio::EnsEMBL::Utils::Tree::Interval::Immutable::Node
62  Exceptions : if $x_center is not a number or the remaining args are not of the
63  correct type
64  Caller : general
65 
66 =cut
67 
68 sub new {
69  my $caller = shift;
70  my $class = ref($caller) || $caller;
71 
72  my ($x_center, $s_center, $left, $right) = @_;
73  throw 'Node takes arguments (x_center, s_center, left_child, right_child)'
74  unless $x_center and $s_center; # and $left and $right;
75 
76  throw 'x_center must be a number' unless looks_like_number($x_center);
77 
78  # Bio::EnsEMBL::Utils::Scalar::assert_ref is high-overhead, and was
79  # the source of a significant performance penalty in pipelines where
80  # millions of new nodes are being instantiated. Replaced with simpler
81  # low-overhead type validation.
82  throw 's_center must be an array' unless (ref($s_center) eq 'ARRAY');
83 
84  if(defined($left)) {
85  unless (ref($left) eq 'Bio::EnsEMBL::Utils::Tree::Interval::Immutable::Node') {
86  throw 'left must be a Bio::EnsEMBL::Utils::Tree::Interval::Immutable::Node';
87  }
88  }
89 
90  if(defined($right)) {
91  unless (ref($right) eq 'Bio::EnsEMBL::Utils::Tree::Interval::Immutable::Node') {
92  throw 'right must be a Bio::EnsEMBL::Utils::Tree::Interval::Immutable::Node';
93  }
94  }
95 
96  my $self = bless({ 'x_center' => $x_center,
97  's_center_beg' => [ map { $_->[1] } sort { $a->[0] <=> $b->[0] } map { [ $_->start, $_ ] } @{$s_center} ],
98  's_center_end' => [ map { $_->[1] } sort { $b->[0] <=> $a->[0] } map { [ $_->end, $_ ] } @{$s_center} ],
99  'lchild' => $left,
100  'rchild' => $right }, $class);
101  return $self;
102 }
103 
104 =head2 x_center
105 
106  Arg [] : none
107  Description : Return the center point of the intervals represented by the node
108  Returntype : scalar
109  Exceptions : none
110  Caller : general
111 
112 =cut
113 
114 sub x_center {
115  return shift->{x_center};
116 }
117 
118 =head2 s_center_beg
119 
120  Arg [] : none
121  Description : Returns the set of intervals containing the center point sorted by their start point
122  Returntype : Arrayref of Bio::EnsEMBL::Utils::Interval
123  Exceptions : none
124  Caller : general
125 
126 =cut
127 
128 sub s_center_beg {
129  return shift->{s_center_beg};
130 }
131 
132 =head2 s_center_end
133 
134  Arg [] : none
135  Description : Returns the set of intervals containing the center point sorted by their end point
136  Returntype : Arrayref of Bio::EnsEMBL::Utils::Interval
137  Exceptions : none
138  Caller : general
139 
140 =cut
141 
142 sub s_center_end {
143  return shift->{s_center_end};
144 }
145 
146 =head2 left
147 
148  Arg [] : none
149  Description : Returns the node's left child
150  Returntype : Bio::EnsEMBL::Utils::Tree::Interval::Immutable::Node
151  Exceptions : none
152  Caller : general
153 
154 =cut
155 
156 sub left {
157  return shift->{lchild};
158 }
159 
160 =head2 right
161 
162  Arg [] : none
163  Description : Returns the node's right child
164  Returntype : Bio::EnsEMBL::Utils::Tree::Interval::Immutable::Node
165  Exceptions : none
166  Caller : general
167 
168 =cut
169 
170 sub right {
171  return shift->{rchild};
172 }
173 
174 1;
175 
Bio::EnsEMBL::Utils::Interval
Definition: Interval.pm:41
map
public map()
Bio::EnsEMBL::Utils::Tree::Interval::Immutable::Node
Definition: Node.pm:14
Bio::EnsEMBL::Utils::Exception
Definition: Exception.pm:68