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1 | 1 | 1 | 14µs | 30µs | BEGIN@89 | Bio::Range::
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1 | 1 | 1 | 9µs | 12µs | BEGIN@91 | Bio::Range::
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0 | 0 | 0 | 0s | 0s | new | Bio::Range::
0 | 0 | 0 | 0s | 0s | start | Bio::Range::
0 | 0 | 0 | 0s | 0s | strand | Bio::Range::
0 | 0 | 0 | 0s | 0s | toString | Bio::Range::
0 | 0 | 0 | 0s | 0s | unions | Bio::Range::
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1 | # | ||||
2 | # BioPerl module for Bio::Range | ||||
3 | # | ||||
4 | # Please direct questions and support issues to <bioperl-l@bioperl.org> | ||||
5 | # | ||||
6 | # Cared for by Heikki Lehvaslaiho <heikki-at-bioperl-dot-org> | ||||
7 | # | ||||
8 | # Copywright Matthew Pocock | ||||
9 | # | ||||
10 | # You may distribute this module under the same terms as perl itself | ||||
11 | # | ||||
12 | # POD documentation - main docs before the code | ||||
13 | # | ||||
14 | |||||
15 | =head1 NAME | ||||
16 | |||||
17 | Bio::Range - Pure perl RangeI implementation | ||||
18 | |||||
19 | =head1 SYNOPSIS | ||||
20 | |||||
21 | $range = Bio::Range->new(-start=>10, -end=>30, -strand=>+1); | ||||
22 | $r2 = Bio::Range->new(-start=>15, -end=>200, -strand=>+1); | ||||
23 | |||||
24 | print join(', ', $range->union($r2)), "\n"; | ||||
25 | print join(', ', $range->intersection($r2)), "\n"; | ||||
26 | |||||
27 | print $range->overlaps($r2), "\n"; | ||||
28 | print $range->contains($r2), "\n"; | ||||
29 | |||||
30 | =head1 DESCRIPTION | ||||
31 | |||||
32 | This provides a pure perl implementation of the BioPerl range | ||||
33 | interface. | ||||
34 | |||||
35 | Ranges are modeled as having (start, end, length, strand). They use | ||||
36 | Bio-coordinates - all points E<gt>= start and E<lt>= end are within the | ||||
37 | range. End is always greater-than or equal-to start, and length is | ||||
38 | greather than or equal to 1. The behaviour of a range is undefined if | ||||
39 | ranges with negative numbers or zero are used. | ||||
40 | |||||
41 | So, in summary: | ||||
42 | |||||
43 | length = end - start + 1 | ||||
44 | end >= start | ||||
45 | strand = (-1 | 0 | +1) | ||||
46 | |||||
47 | =head1 FEEDBACK | ||||
48 | |||||
49 | =head2 Mailing Lists | ||||
50 | |||||
51 | User feedback is an integral part of the evolution of this and other | ||||
52 | Bioperl modules. Send your comments and suggestions preferably to one | ||||
53 | of the Bioperl mailing lists. Your participation is much appreciated. | ||||
54 | |||||
55 | bioperl-l@bioperl.org - General discussion | ||||
56 | http://bioperl.org/wiki/Mailing_lists - About the mailing lists | ||||
57 | |||||
58 | =head2 Support | ||||
59 | |||||
60 | Please direct usage questions or support issues to the mailing list: | ||||
61 | |||||
62 | I<bioperl-l@bioperl.org> | ||||
63 | |||||
64 | rather than to the module maintainer directly. Many experienced and | ||||
65 | reponsive experts will be able look at the problem and quickly | ||||
66 | address it. Please include a thorough description of the problem | ||||
67 | with code and data examples if at all possible. | ||||
68 | |||||
69 | =head2 Reporting Bugs | ||||
70 | |||||
71 | Report bugs to the Bioperl bug tracking system to help us keep track | ||||
72 | the bugs and their resolution. Bug reports can be submitted via the web: | ||||
73 | |||||
74 | https://github.com/bioperl/bioperl-live/issues | ||||
75 | |||||
76 | =head1 AUTHOR - Heikki Lehvaslaiho | ||||
77 | |||||
78 | Email heikki-at-bioperl-dot-org | ||||
79 | |||||
80 | =head1 APPENDIX | ||||
81 | |||||
82 | The rest of the documentation details each of the object | ||||
83 | methods. Internal methods are usually preceded with a _ | ||||
84 | |||||
85 | =cut | ||||
86 | |||||
87 | package Bio::Range; | ||||
88 | |||||
89 | 2 | 25µs | 2 | 45µs | # spent 30µs (14+16) within Bio::Range::BEGIN@89 which was called:
# once (14µs+16µs) by Bio::SeqUtils::BEGIN@585 at line 89 # spent 30µs making 1 call to Bio::Range::BEGIN@89
# spent 16µs making 1 call to strict::import |
90 | 2 | 26µs | 2 | 92µs | # spent 51µs (10+41) within Bio::Range::BEGIN@90 which was called:
# once (10µs+41µs) by Bio::SeqUtils::BEGIN@585 at line 90 # spent 51µs making 1 call to Bio::Range::BEGIN@90
# spent 41µs making 1 call to Exporter::import |
91 | 2 | 26µs | 2 | 14µs | # spent 12µs (9+2) within Bio::Range::BEGIN@91 which was called:
# once (9µs+2µs) by Bio::SeqUtils::BEGIN@585 at line 91 # spent 12µs making 1 call to Bio::Range::BEGIN@91
# spent 2µs making 1 call to integer::import |
92 | |||||
93 | |||||
94 | 2 | 693µs | 2 | 127µs | # spent 127µs (9+118) within Bio::Range::BEGIN@94 which was called:
# once (9µs+118µs) by Bio::SeqUtils::BEGIN@585 at line 94 # spent 127µs making 1 call to Bio::Range::BEGIN@94
# spent 118µs making 1 call to base::import, recursion: max depth 2, sum of overlapping time 118µs |
95 | |||||
96 | =head1 Constructors | ||||
97 | |||||
98 | =head2 new | ||||
99 | |||||
100 | Title : new | ||||
101 | Usage : $range = Bio::Range->new(-start => 100, -end=> 200, -strand = +1); | ||||
102 | Function: generates a new Bio::Range | ||||
103 | Returns : a new range | ||||
104 | Args : -strand (defaults to 0) and any two of (-start, -end, -length), | ||||
105 | the third will be calculated | ||||
106 | |||||
107 | =cut | ||||
108 | |||||
109 | sub new { | ||||
110 | my ($caller, @args) = @_; | ||||
111 | my $self = $caller->SUPER::new(@args); | ||||
112 | my ($strand, $start, $end, $length) = | ||||
113 | $self->_rearrange([qw(STRAND | ||||
114 | START | ||||
115 | END | ||||
116 | LENGTH | ||||
117 | )],@args); | ||||
118 | $self->strand($strand || 0); | ||||
119 | |||||
120 | if(defined $start ) { | ||||
121 | $self->start($start); | ||||
122 | if(defined $end) { | ||||
123 | $self->end($end); | ||||
124 | } elsif(defined $length) { | ||||
125 | $self->end($self->start()+ $length - 1); | ||||
126 | } | ||||
127 | } elsif(defined $end && defined $length ) { | ||||
128 | $self->end($end); | ||||
129 | $self->start($self->end() - $length + 1); | ||||
130 | } | ||||
131 | return $self; | ||||
132 | } | ||||
133 | |||||
134 | =head2 unions | ||||
135 | |||||
136 | Title : unions | ||||
137 | Usage : @unions = Bio::Range->unions(@ranges); | ||||
138 | Function: generate a list of non-intersecting Bio::Range objects | ||||
139 | from a list of Bio::Range objects which may intersect | ||||
140 | Returns : a list of Bio::Range objects | ||||
141 | Args : a list of Bio::Range objects | ||||
142 | |||||
143 | |||||
144 | =cut | ||||
145 | |||||
146 | sub unions { | ||||
147 | my ($class,@i) = @_; | ||||
148 | |||||
149 | my $i = 0; | ||||
150 | my %i = map { $i++ => $_ } @i; | ||||
151 | |||||
152 | my $lastsize = scalar(keys %i); | ||||
153 | |||||
154 | do { | ||||
155 | |||||
156 | foreach my $j (sort { $i{$a}->start <=> $i{$b}->start } keys %i){ | ||||
157 | foreach my $k (sort { $i{$a}->start <=> $i{$b}->start } keys %i){ | ||||
158 | |||||
159 | #it may have been replaced by a union under the key of | ||||
160 | #the overlapping range, we are altering the hash in-place | ||||
161 | next unless $i{$j}; | ||||
162 | |||||
163 | next if $i{$k}->end < $i{$j}->start; | ||||
164 | last if $i{$k}->start > $i{$j}->end; | ||||
165 | |||||
166 | if($i{$j}->overlaps($i{$k})){ | ||||
167 | my($start,$end,$strand) = $i{$j}->union($i{$k}); | ||||
168 | delete($i{$k}); | ||||
169 | $i{$j} = Bio::Range->new( -start => $start , -end => $end , -strand => $strand ); | ||||
170 | } | ||||
171 | } | ||||
172 | } | ||||
173 | |||||
174 | goto DONE if scalar(keys %i) == $lastsize; | ||||
175 | $lastsize = scalar(keys %i); | ||||
176 | |||||
177 | #warn $lastsize; | ||||
178 | |||||
179 | } while(1); | ||||
180 | |||||
181 | DONE: | ||||
182 | |||||
183 | return values %i; | ||||
184 | } | ||||
185 | |||||
186 | |||||
187 | =head1 Member variable access | ||||
188 | |||||
189 | These methods let you get at and set the member variables | ||||
190 | |||||
191 | =head2 start | ||||
192 | |||||
193 | Title : start | ||||
194 | Function : return or set the start co-ordinate | ||||
195 | Example : $s = $range->start(); $range->start(7); | ||||
196 | Returns : the value of the start co-ordinate | ||||
197 | Args : optionally, the new start co-ordinate | ||||
198 | Overrides: Bio::RangeI::start | ||||
199 | |||||
200 | =cut | ||||
201 | |||||
202 | sub start { | ||||
203 | my ($self,$value) = @_; | ||||
204 | if( defined $value) { | ||||
205 | $self->throw("'$value' is not an integer.\n") | ||||
206 | unless $value =~ /^[-+]?\d+$/; | ||||
207 | $self->{'start'} = $value; | ||||
208 | } | ||||
209 | return $self->{'start'}; | ||||
210 | } | ||||
211 | |||||
212 | =head2 end | ||||
213 | |||||
214 | Title : end | ||||
215 | Function : return or set the end co-ordinate | ||||
216 | Example : $e = $range->end(); $range->end(2000); | ||||
217 | Returns : the value of the end co-ordinate | ||||
218 | Args : optionally, the new end co-ordinate | ||||
219 | Overrides: Bio::RangeI::end | ||||
220 | |||||
221 | =cut | ||||
222 | |||||
223 | sub end { | ||||
224 | |||||
225 | my ($self,$value) = @_; | ||||
226 | if( defined $value) { | ||||
227 | $self->throw("'$value' is not an integer.\n") | ||||
228 | unless $value =~ /^[-+]?\d+$/; | ||||
229 | $self->{'end'} = $value; | ||||
230 | } | ||||
231 | return $self->{'end'}; | ||||
232 | } | ||||
233 | |||||
234 | =head2 strand | ||||
235 | |||||
236 | Title : strand | ||||
237 | Function : return or set the strandedness | ||||
238 | Example : $st = $range->strand(); $range->strand(-1); | ||||
239 | Returns : the value of the strandedness (-1, 0 or 1) | ||||
240 | Args : optionally, the new strand - (-1, 0, 1) or (-, ., +). | ||||
241 | Overrides: Bio::RangeI::strand | ||||
242 | |||||
243 | =cut | ||||
244 | |||||
245 | { | ||||
246 | |||||
247 | 2 | 5µs | my %VALID_STRAND = ( | ||
248 | -1 => -1, | ||||
249 | 0 => 0, | ||||
250 | 1 => 1, | ||||
251 | '+' => 1, | ||||
252 | '-' => -1, | ||||
253 | '.' => 0 | ||||
254 | ); | ||||
255 | |||||
256 | sub strand { | ||||
257 | my $self = shift; | ||||
258 | if(@_) { | ||||
259 | my $val = shift; | ||||
260 | if (exists $VALID_STRAND{$val}) { | ||||
261 | $self->{'strand'} = $VALID_STRAND{$val}; | ||||
262 | } else { | ||||
263 | $self->throw("Invalid strand: $val"); | ||||
264 | } | ||||
265 | } | ||||
266 | return $self->{'strand'}; | ||||
267 | } | ||||
268 | |||||
269 | } | ||||
270 | |||||
271 | =head2 length | ||||
272 | |||||
273 | Title : length | ||||
274 | Function : returns the length of this range | ||||
275 | Example : $length = $range->length(); | ||||
276 | Returns : the length of this range, equal to end - start + 1 | ||||
277 | Args : if you attempt to set the length an exception will be thrown | ||||
278 | Overrides: Bio::RangeI::Length | ||||
279 | |||||
280 | =cut | ||||
281 | |||||
282 | sub length { | ||||
283 | my $self = shift; | ||||
284 | if(@_) { | ||||
285 | confess ref($self), "->length() is read-only"; | ||||
286 | } | ||||
287 | return $self->end() - $self->start() + 1; | ||||
288 | } | ||||
289 | |||||
290 | =head2 toString | ||||
291 | |||||
292 | Title : toString | ||||
293 | Function: stringifies this range | ||||
294 | Example : print $range->toString(), "\n"; | ||||
295 | Returns : a string representation of this range | ||||
296 | |||||
297 | =cut | ||||
298 | |||||
299 | sub toString { | ||||
300 | my $self = shift; | ||||
301 | return "(${\$self->start}, ${\$self->end}) strand=${\$self->strand}"; | ||||
302 | } | ||||
303 | |||||
304 | =head1 Boolean Methods | ||||
305 | |||||
306 | These methods return true or false. | ||||
307 | |||||
308 | $range->overlaps($otherRange) && print "Ranges overlap\n"; | ||||
309 | |||||
310 | =head2 overlaps | ||||
311 | |||||
312 | Title : overlaps | ||||
313 | Usage : if($r1->overlaps($r2)) { do stuff } | ||||
314 | Function : tests if $r2 overlaps $r1 | ||||
315 | Args : a range to test for overlap with | ||||
316 | Returns : true if the ranges overlap, false otherwise | ||||
317 | Inherited: Bio::RangeI | ||||
318 | |||||
319 | =head2 contains | ||||
320 | |||||
321 | Title : contains | ||||
322 | Usage : if($r1->contains($r2) { do stuff } | ||||
323 | Function : tests whether $r1 totally contains $r2 | ||||
324 | Args : a range to test for being contained | ||||
325 | Returns : true if the argument is totally contained within this range | ||||
326 | Inherited: Bio::RangeI | ||||
327 | |||||
328 | =head2 equals | ||||
329 | |||||
330 | Title : equals | ||||
331 | Usage : if($r1->equals($r2)) | ||||
332 | Function : test whether $r1 has the same start, end, length as $r2 | ||||
333 | Args : a range to test for equality | ||||
334 | Returns : true if they are describing the same range | ||||
335 | Inherited: Bio::RangeI | ||||
336 | |||||
337 | =head1 Geometrical methods | ||||
338 | |||||
339 | These methods do things to the geometry of ranges, and return | ||||
340 | triplets (start, end, strand) from which new ranges could be built. | ||||
341 | |||||
342 | =head2 intersection | ||||
343 | |||||
344 | Title : intersection | ||||
345 | Usage : ($start, $stop, $strand) = $r1->intersection($r2) | ||||
346 | Function : gives the range that is contained by both ranges | ||||
347 | Args : a range to compare this one to | ||||
348 | Returns : nothing if they do not overlap, or the range that they do overlap | ||||
349 | Inherited: Bio::RangeI::intersection | ||||
350 | |||||
351 | =cut | ||||
352 | |||||
353 | =head2 union | ||||
354 | |||||
355 | Title : union | ||||
356 | Usage : ($start, $stop, $strand) = $r1->union($r2); | ||||
357 | : ($start, $stop, $strand) = Bio::Range->union(@ranges); | ||||
358 | Function : finds the minimal range that contains all of the ranges | ||||
359 | Args : a range or list of ranges | ||||
360 | Returns : the range containing all of the ranges | ||||
361 | Inherited: Bio::RangeI::union | ||||
362 | |||||
363 | =cut | ||||
364 | |||||
365 | 1 | 6µs | 1; |