ensembl-hive  2.7.0
Node.pm
Go to the documentation of this file.
1 =head1 LICENSE
2 
3 See the NOTICE file distributed with this work for additional information
4 regarding copyright ownership.
5 
6 Licensed under the Apache License, Version 2.0 (the "License");
7 you may not use this file except in compliance with the License.
8 You may obtain a copy of the License at
9 
10  http://www.apache.org/licenses/LICENSE-2.0
11 
12 Unless required by applicable law or agreed to in writing, software
13 distributed under the License is distributed on an "AS IS" BASIS,
14 WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
15 See the License for the specific language governing permissions and
16 limitations under the License.
17 
18 =cut
19 
20 
21 =head1 CONTACT
22 
23  Please email comments or questions to the public Ensembl
24  developers list at <http://lists.ensembl.org/mailman/listinfo/dev>.
25 
26  Questions may also be sent to the Ensembl help desk at
27  <http://www.ensembl.org/Help/Contact>.
28 
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