|
0
|
1 # $Id: Chain.pm,v 1.1 2002/10/24 17:35:30 heikki Exp $
|
|
|
2 #
|
|
|
3 # bioperl module for Bio::Coordinate::Chain
|
|
|
4 #
|
|
|
5 # Cared for by Heikki Lehvaslaiho <heikki@ebi.ac.uk>
|
|
|
6 #
|
|
|
7 # Copyright Heikki Lehvaslaiho
|
|
|
8 #
|
|
|
9 # You may distribute this module under the same terms as perl itself
|
|
|
10
|
|
|
11 # POD documentation - main docs before the code
|
|
|
12
|
|
|
13 =head1 NAME
|
|
|
14
|
|
|
15 Bio::Coordinate::Chain - Mapping locations through a chain of coordinate mappers
|
|
|
16
|
|
|
17 =head1 SYNOPSIS
|
|
|
18
|
|
|
19 # create Bio::Coordinate::Pairs, or any MapperIs, somehow
|
|
|
20 $pair1; $pair2;
|
|
|
21
|
|
|
22 # add them into a Chain
|
|
|
23 $collection = Bio::Coordinate::Chain->new;
|
|
|
24 $collection->add_mapper($pair1);
|
|
|
25 $collection->add_mapper($pair2);
|
|
|
26
|
|
|
27 # create a position and map it
|
|
|
28 $pos = Bio::Location::Simple->new (-start => 5, -end => 9 );
|
|
|
29 $match = $collection->map($pos);
|
|
|
30 if ($match) {
|
|
|
31 sprintf "Matches at %d-%d\n", $match->start, $match->end,
|
|
|
32 } else {
|
|
|
33 print "No match\n";
|
|
|
34 }
|
|
|
35
|
|
|
36 =head1 DESCRIPTION
|
|
|
37
|
|
|
38 This class assumes that you have built several mappers and want to
|
|
|
39 link them together so that output from the previous mapper is the next
|
|
|
40 mappers input. This way you can build arbitrarily complex mappers from
|
|
|
41 simpler components.
|
|
|
42
|
|
|
43 Note that Chain does not do any sanity checking on its mappers. You
|
|
|
44 are solely responsible that input and output coordinate systems,
|
|
|
45 direction of mapping and parameters internal to mappers make sense
|
|
|
46 when chained together.
|
|
|
47
|
|
|
48 To put it bluntly, the present class is just a glorified foreach loop
|
|
|
49 over an array of mappers calling the map method.
|
|
|
50
|
|
|
51 It would be neat to an internal function that would generate a new
|
|
|
52 single step mapper from those included in the chain. It should speed
|
|
|
53 things up considerably. Any volunteers?
|
|
|
54
|
|
|
55 =head1 FEEDBACK
|
|
|
56
|
|
|
57 =head2 Mailing Lists
|
|
|
58
|
|
|
59 User feedback is an integral part of the evolution of this and other
|
|
|
60 Bioperl modules. Send your comments and suggestions preferably to the
|
|
|
61 Bioperl mailing lists Your participation is much appreciated.
|
|
|
62
|
|
|
63 bioperl-l@bioperl.org - General discussion
|
|
|
64 http://bio.perl.org/MailList.html - About the mailing lists
|
|
|
65
|
|
|
66 =head2 Reporting Bugs
|
|
|
67
|
|
|
68 report bugs to the Bioperl bug tracking system to help us keep track
|
|
|
69 the bugs and their resolution. Bug reports can be submitted via
|
|
|
70 email or the web:
|
|
|
71
|
|
|
72 bioperl-bugs@bio.perl.org
|
|
|
73 http://bio.perl.org/bioperl-bugs/
|
|
|
74
|
|
|
75 =head1 AUTHOR - Heikki Lehvaslaiho
|
|
|
76
|
|
|
77 Email: heikki@ebi.ac.uk
|
|
|
78 Address:
|
|
|
79
|
|
|
80 EMBL Outstation, European Bioinformatics Institute
|
|
|
81 Wellcome Trust Genome Campus, Hinxton
|
|
|
82 Cambs. CB10 1SD, United Kingdom
|
|
|
83
|
|
|
84 =head1 CONTRIBUTORS
|
|
|
85
|
|
|
86 Ewan Birney, birney@ebi.ac.uk
|
|
|
87
|
|
|
88 =head1 APPENDIX
|
|
|
89
|
|
|
90 The rest of the documentation details each of the object
|
|
|
91 methods. Internal methods are usually preceded with a _
|
|
|
92
|
|
|
93 =cut
|
|
|
94
|
|
|
95
|
|
|
96 # Let the code begin...
|
|
|
97
|
|
|
98 package Bio::Coordinate::Chain;
|
|
|
99 use vars qw(@ISA );
|
|
|
100 use strict;
|
|
|
101
|
|
|
102 # Object preamble - inherits from Bio::Root::Root
|
|
|
103 use Bio::Root::Root;
|
|
|
104 use Bio::Coordinate::MapperI;
|
|
|
105 use Bio::Coordinate::Result;
|
|
|
106 use Bio::Coordinate::Collection;
|
|
|
107
|
|
|
108 @ISA = qw(Bio::Coordinate::Collection Bio::Coordinate::MapperI);
|
|
|
109
|
|
|
110
|
|
|
111 =head2 map
|
|
|
112
|
|
|
113 Title : map
|
|
|
114 Usage : $newpos = $obj->map($pos);
|
|
|
115 Function: Map the location through all the mappers in the chain.
|
|
|
116 Example :
|
|
|
117 Returns : new Location in the output coordiante system
|
|
|
118 Args : a Bio::Location::Simple object
|
|
|
119
|
|
|
120 =cut
|
|
|
121
|
|
|
122 sub map {
|
|
|
123 my ($self,$value) = @_;
|
|
|
124
|
|
|
125 $self->throw("Need to pass me a value.")
|
|
|
126 unless defined $value;
|
|
|
127 $self->throw("I need a Bio::Location, not [$value]")
|
|
|
128 unless $value->isa('Bio::LocationI');
|
|
|
129 $self->throw("No coordinate mappers!")
|
|
|
130 unless $self->each_mapper;
|
|
|
131
|
|
|
132 my $res = new Bio::Coordinate::Result;
|
|
|
133
|
|
|
134 foreach my $mapper ($self->each_mapper) {
|
|
|
135
|
|
|
136 my $res = $mapper->map($value);
|
|
|
137 return undef unless $res->each_match;
|
|
|
138 $value = $res->match;
|
|
|
139 }
|
|
|
140
|
|
|
141 return $value;
|
|
|
142 }
|
|
|
143
|
|
|
144
|
|
|
145 =head2 Inherited methods
|
|
|
146
|
|
|
147 =cut
|
|
|
148
|
|
|
149 =head2 add_mapper
|
|
|
150
|
|
|
151 Title : add_mapper
|
|
|
152 Usage : $obj->add_mapper($mapper)
|
|
|
153 Function: Pushes one Bio::Coodinate::MapperI into the list of mappers.
|
|
|
154 Sets _is_sorted() to false.
|
|
|
155 Example :
|
|
|
156 Returns : 1 when succeeds, 0 for failure.
|
|
|
157 Args : mapper object
|
|
|
158
|
|
|
159 =cut
|
|
|
160
|
|
|
161 =head2 mappers
|
|
|
162
|
|
|
163 Title : mappers
|
|
|
164 Usage : $obj->mappers();
|
|
|
165 Function: Returns or sets a list of mappers.
|
|
|
166 Example :
|
|
|
167 Returns : array of mappers
|
|
|
168 Args : array of mappers
|
|
|
169
|
|
|
170 =cut
|
|
|
171
|
|
|
172 =head2 each_mapper
|
|
|
173
|
|
|
174 Title : each_mapper
|
|
|
175 Usage : $obj->each_mapper();
|
|
|
176 Function: Returns a list of mappers.
|
|
|
177 Example :
|
|
|
178 Returns : array of mappers
|
|
|
179 Args : none
|
|
|
180
|
|
|
181 =cut
|
|
|
182
|
|
|
183 =head2 swap
|
|
|
184
|
|
|
185 Title : swap
|
|
|
186 Usage : $obj->swap;
|
|
|
187 Function: Swap the direction of mapping;input <-> output
|
|
|
188 Example :
|
|
|
189 Returns : 1
|
|
|
190 Args :
|
|
|
191
|
|
|
192 =cut
|
|
|
193
|
|
|
194 =head2 test
|
|
|
195
|
|
|
196 Title : test
|
|
|
197 Usage : $obj->test;
|
|
|
198 Function: test that both components of all pairs are of the same length.
|
|
|
199 Ran automatically.
|
|
|
200 Example :
|
|
|
201 Returns : boolean
|
|
|
202 Args :
|
|
|
203
|
|
|
204 =cut
|
|
|
205
|
|
|
206
|
|
|
207
|
|
|
208 sub sort{
|
|
|
209 my ($self) = @_;
|
|
|
210 $self->warn("You do not really want to sort your chain, do you!\nDoing nothing.");
|
|
|
211 }
|
|
|
212
|
|
|
213 1;
|
|
|
214
|
