| Filename | /Users/ap13/perl5/lib/perl5/Bio/Range.pm |
| Statements | Executed 11 statements in 782µs |
| Calls | P | F | Exclusive Time |
Inclusive Time |
Subroutine |
|---|---|---|---|---|---|
| 1 | 1 | 1 | 14µs | 30µs | Bio::Range::BEGIN@89 |
| 1 | 1 | 1 | 10µs | 51µs | Bio::Range::BEGIN@90 |
| 1 | 1 | 1 | 9µs | 12µs | Bio::Range::BEGIN@91 |
| 1 | 1 | 1 | 9µs | 127µs | Bio::Range::BEGIN@94 |
| 0 | 0 | 0 | 0s | 0s | Bio::Range::end |
| 0 | 0 | 0 | 0s | 0s | Bio::Range::length |
| 0 | 0 | 0 | 0s | 0s | Bio::Range::new |
| 0 | 0 | 0 | 0s | 0s | Bio::Range::start |
| 0 | 0 | 0 | 0s | 0s | Bio::Range::strand |
| 0 | 0 | 0 | 0s | 0s | Bio::Range::toString |
| 0 | 0 | 0 | 0s | 0s | Bio::Range::unions |
| Line | State ments |
Time on line |
Calls | Time in subs |
Code |
|---|---|---|---|---|---|
| 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; |