|
0
|
1 =head1 LICENSE
|
|
|
2
|
|
|
3 Copyright (c) 1999-2012 The European Bioinformatics Institute and
|
|
|
4 Genome Research Limited. All rights reserved.
|
|
|
5
|
|
|
6 This software is distributed under a modified Apache license.
|
|
|
7 For license details, please see
|
|
|
8
|
|
|
9 http://www.ensembl.org/info/about/code_licence.html
|
|
|
10
|
|
|
11 =head1 CONTACT
|
|
|
12
|
|
|
13 Please email comments or questions to the public Ensembl
|
|
|
14 developers list at <dev@ensembl.org>.
|
|
|
15
|
|
|
16 Questions may also be sent to the Ensembl help desk at
|
|
|
17 <helpdesk@ensembl.org>.
|
|
|
18
|
|
|
19 =cut
|
|
|
20
|
|
|
21 =head1 NAME
|
|
|
22
|
|
|
23 Bio::EnsEMBL::Mapper::IndelCoordinate
|
|
|
24
|
|
|
25 =head1 SYNOPSIS
|
|
|
26
|
|
|
27 =head1 DESCRIPTION
|
|
|
28
|
|
|
29 Representation of a indel in a sequence; returned from Mapper.pm when
|
|
|
30 the target region is in a deletion.
|
|
|
31
|
|
|
32 =head1 METHODS
|
|
|
33
|
|
|
34 =cut
|
|
|
35
|
|
|
36 package Bio::EnsEMBL::Mapper::IndelCoordinate;
|
|
|
37
|
|
|
38 use Bio::EnsEMBL::Mapper::Gap;
|
|
|
39 use Bio::EnsEMBL::Mapper::Coordinate;
|
|
|
40
|
|
|
41 use vars qw(@ISA);
|
|
|
42 use strict;
|
|
|
43
|
|
|
44 @ISA = qw(Bio::EnsEMBL::Mapper::Coordinate Bio::EnsEMBL::Mapper::Gap);
|
|
|
45
|
|
|
46
|
|
|
47 =head2 new
|
|
|
48
|
|
|
49 Arg [1] : Bio::EnsEMBL::Mapper::Gap $gap
|
|
|
50 Arg [2] : Bio::EnsEMBL::Mapper::Coordinate $coordinate
|
|
|
51 Example : $indelCoord = Bio::EnsEMBL::Mapper::IndelCoordinate($gap, $coordinate);
|
|
|
52 Description: Creates a new IndelCoordinate object.
|
|
|
53 Returntype : Bio::EnsEMBL::Mapper::IndelCoordinate
|
|
|
54 Exceptions : none
|
|
|
55 Caller : Bio::EnsEMBL::Mapper
|
|
|
56
|
|
|
57 =cut
|
|
|
58
|
|
|
59 sub new {
|
|
|
60 my ( $proto, $gap, $coordinate ) = @_;
|
|
|
61
|
|
|
62 my $class = ref($proto) || $proto;
|
|
|
63
|
|
|
64 return
|
|
|
65 bless( { 'start' => $coordinate->start(),
|
|
|
66 'end' => $coordinate->end(),
|
|
|
67 'strand' => $coordinate->strand(),
|
|
|
68 'id' => $coordinate->id(),
|
|
|
69 'coord_system' => $coordinate->coord_system(),
|
|
|
70 'gap_start' => $gap->start(),
|
|
|
71 'gap_end' => $gap->end()
|
|
|
72 },
|
|
|
73 $class );
|
|
|
74 }
|
|
|
75
|
|
|
76 =head2 gap_start
|
|
|
77
|
|
|
78 Arg[1] : (optional) int $gap_start
|
|
|
79 Example : $gap_start = $ic->gap_start()
|
|
|
80 Description : Getter/Setter for the start of the Gap region
|
|
|
81 ReturnType : int
|
|
|
82 Exceptions : none
|
|
|
83 Caller : general
|
|
|
84
|
|
|
85 =cut
|
|
|
86
|
|
|
87 sub gap_start {
|
|
|
88 my ( $self, $value ) = @_;
|
|
|
89
|
|
|
90 if ( defined($value) ) {
|
|
|
91 $self->{'gap_start'} = $value;
|
|
|
92 }
|
|
|
93
|
|
|
94 return $self->{'gap_start'};
|
|
|
95 }
|
|
|
96
|
|
|
97 =head2 gap_end
|
|
|
98
|
|
|
99 Arg[1] : (optional) int $gap_end
|
|
|
100 Example : $gap_end = $ic->gap_end()
|
|
|
101 Description : Getter/Setter for the end of the Gap region
|
|
|
102 ReturnType : int
|
|
|
103 Exceptions : none
|
|
|
104 Caller : general
|
|
|
105
|
|
|
106 =cut
|
|
|
107
|
|
|
108 sub gap_end {
|
|
|
109 my ( $self, $value ) = @_;
|
|
|
110
|
|
|
111 if ( defined($value) ) {
|
|
|
112 $self->{'gap_end'} = $value;
|
|
|
113 }
|
|
|
114
|
|
|
115 return $self->{'gap_end'};
|
|
|
116 }
|
|
|
117
|
|
|
118 =head2 gap_length
|
|
|
119
|
|
|
120 Args : None
|
|
|
121 Example : $gap_length = $ic->gap_length()
|
|
|
122 Description : Getter for the length of the Gap region
|
|
|
123 ReturnType : int
|
|
|
124 Exceptions : none
|
|
|
125 Caller : general
|
|
|
126
|
|
|
127 =cut
|
|
|
128
|
|
|
129 sub gap_length {
|
|
|
130 my ($self) = @_;
|
|
|
131
|
|
|
132 return $self->{'gap_end'} - $self->{'gap_start'} + 1;
|
|
|
133 }
|
|
|
134
|
|
|
135 1;
|
