/usr/share/perl5/Bio/Map/PositionI.pm is in libbio-perl-perl 1.6.924-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600 601 602 603 604 605 606 607 608 609 610 611 612 613 614 615 616 617 618 619 620 621 622 623 624 625 626 627 628 629 630 631 632 633 634 635 636 637 638 639 640 641 642 643 644 645 646 647 648 649 650 651 652 653 654 655 656 657 658 659 660 661 662 663 664 665 666 667 668 669 670 671 672 673 674 675 676 677 678 679 680 681 682 683 684 685 686 687 688 689 690 691 692 693 694 695 696 697 698 699 700 701 702 703 704 705 706 707 708 709 710 711 712 713 714 715 716 717 718 719 720 721 722 723 724 725 726 727 728 729 730 731 732 733 734 735 736 737 738 739 740 741 742 743 744 745 746 747 748 749 750 751 752 753 754 755 756 757 758 759 760 761 762 763 764 765 766 767 768 769 770 771 772 773 774 775 776 777 778 779 780 781 782 783 784 785 786 787 788 789 790 791 792 793 794 795 796 797 798 799 800 801 802 803 804 805 806 807 808 809 810 811 812 813 814 815 816 817 818 819 820 821 822 823 824 825 826 827 828 829 830 831 832 833 834 835 836 837 838 839 840 841 842 843 844 845 846 847 848 849 850 851 852 853 854 855 856 857 858 859 860 861 862 863 864 865 866 867 868 869 870 871 872 873 874 875 876 877 878 879 880 881 882 883 884 885 886 887 888 889 890 891 892 893 894 895 896 897 898 899 900 901 902 903 904 905 906 907 908 909 910 911 912 913 914 915 916 917 918 919 920 921 922 923 924 925 926 927 928 929 930 931 932 933 934 935 936 937 938 | #
# BioPerl module for Bio::Map::PositionI
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Sendu Bala <bix@sendu.me.uk>
#
# Copyright Jason Stajich
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::Map::PositionI - Abstracts the notion of a position having a value in the context of a marker and a Map
=head1 SYNOPSIS
# do not use this module directly
# See Bio::Map::Position for an example of
# implementation.
=head1 DESCRIPTION
This object stores one of the postions that a mappable object
(e.g. Marker) may have in a map.
Positions can have non-numeric values or other methods to store the locations,
so they have a method numeric() which does the conversion. numeric()
returns the position in a form that can be compared between other positions of
the same type. It is not necessarily a value suitable for sorting positions (it
may be the distance from the previous position); for that purpose the result of
sortable() should be used.
A 'position', in addition to being a single point, can also be an area and so
can be imagined as a range and compared with other positions on the basis of
overlap, intersection etc.
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<bioperl-l@bioperl.org>
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via the
web:
https://github.com/bioperl/bioperl-live/issues
=head1 AUTHOR - Jason Stajich
Email jason-at-bioperl.org
=head1 CONTRIBUTORS
Lincoln Stein, lstein-at-cshl.org
Heikki Lehvaslaiho, heikki-at-bioperl-dot-org
Sendu Bala, bix@sendu.me.uk
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::Map::PositionI;
use strict;
use Bio::Map::PositionHandler;
use Bio::Map::Mappable;
use Scalar::Util qw(looks_like_number);
use base qw(Bio::Map::EntityI Bio::RangeI);
=head2 EntityI methods
These are fundamental to coordination of Positions and other entities, so are
implemented at the interface level
=cut
=head2 get_position_handler
Title : get_position_handler
Usage : my $position_handler = $entity->get_position_handler();
Function: Gets a PositionHandlerI that $entity is registered with.
Returns : Bio::Map::PositionHandlerI object
Args : none
=cut
sub get_position_handler {
my $self = shift;
unless (defined $self->{_eh}) {
my $ph = Bio::Map::PositionHandler->new(-self => $self);
$self->{_eh} = $ph;
$ph->register;
}
return $self->{_eh};
}
=head2 PositionHandlerI-related methods
These are fundamental to coordination of Positions and other entities, so are
implemented at the interface level
=cut
=head2 map
Title : map
Usage : my $map = $position->map();
$position->map($map);
Function: Get/Set the map the position is in.
Returns : L<Bio::Map::MapI>
Args : none to get
new L<Bio::Map::MapI> to set
=cut
sub map {
my ($self, $map) = @_;
return $self->get_position_handler->map($map);
}
=head2 element
Title : element
Usage : my $element = $position->element();
$position->element($element);
Function: Get/Set the element the position is for.
Returns : L<Bio::Map::MappableI>
Args : none to get
new L<Bio::Map::MappableI> to set
=cut
sub element {
my ($self, $element) = @_;
return $self->get_position_handler->element($element);
}
=head2 marker
Title : marker
Function: This is a synonym of the element() method
Status : deprecated, will be removed in the next version
=cut
*marker = \&element;
=head2 PositionI-specific methods
=cut
=head2 value
Title : value
Usage : my $pos = $position->value();
Function: Get/Set the value for this position
Returns : scalar, value
Args : [optional] new value to set
=cut
sub value {
my $self = shift;
$self->throw_not_implemented();
}
=head2 numeric
Title : numeric
Usage : my $num = $position->numeric;
Function: Read-only method that is guaranteed to return a numeric
representation of the start of this position.
Returns : scalar numeric
Args : none to get the co-ordinate normally (see absolute() method), OR
Bio::Map::RelativeI to get the co-ordinate converted to be
relative to what this Relative describes.
=cut
sub numeric {
my $self = shift;
$self->throw_not_implemented();
}
=head2 sortable
Title : sortable
Usage : my $num = $position->sortable();
Function: Read-only method that is guaranteed to return a value suitable
for correctly sorting this kind of position amongst other positions
of the same kind on the same map. Note that sorting different kinds
of position together is unlikely to give sane results.
Returns : numeric
Args : none
=cut
sub sortable {
my $self = shift;
$self->throw_not_implemented();
}
=head2 relative
Title : relative
Usage : my $relative = $position->relative();
$position->relative($relative);
Function: Get/set the thing this Position's coordinates (numerical(), start(),
end()) are relative to, as described by a Relative object.
Returns : Bio::Map::RelativeI (default is one describing "relative to the
start of the Position's map")
Args : none to get, OR
Bio::Map::RelativeI to set
=cut
sub relative {
my $self = shift;
$self->throw_not_implemented();
}
=head2 absolute
Title : absolute
Usage : my $absolute = $position->absolute();
$position->absolute($absolute);
Function: Get/set how this Position's co-ordinates (numerical(), start(),
end()) are reported. When absolute is off, co-ordinates are
relative to the thing described by relative(). Ie. the value
returned by start() will be the same as the value you set start()
to. When absolute is on, co-ordinates are converted to be relative
to the start of the map.
So if relative() currently points to a Relative object describing
"relative to another position which is 100 bp from the start of
the map", this Position's start() had been set to 50 and absolute()
returns 1, $position->start() will return 150. If absolute() returns
0 in the same situation, $position->start() would return 50.
Returns : boolean (default 0)
Args : none to get, OR
boolean to set
=cut
sub absolute {
my $self = shift;
$self->throw_not_implemented();
}
=head2 RangeI-based methods
=cut
=head2 start
Title : start
Usage : my $start = $position->start();
$position->start($start);
Function: Get/set the start co-ordinate of this position.
Returns : the start of this position
Args : scalar numeric to set, OR
none to get the co-ordinate normally (see absolute() method), OR
Bio::Map::RelativeI to get the co-ordinate converted to be
relative to what this Relative describes.
=cut
=head2 end
Title : end
Usage : my $end = $position->end();
$position->end($end);
Function: Get/set the end co-ordinate of this position.
Returns : the end of this position
Args : scalar numeric to set, OR
none to get the co-ordinate normally (see absolute() method), OR
Bio::Map::RelativeI to get the co-ordinate converted to be
relative to what this Relative describes.
=cut
=head2 length
Title : length
Usage : $length = $position->length();
Function: Get the length of this position.
Returns : the length of this position
Args : none
=cut
=head2 strand
Title : strand
Usage : $strand = $position->strand();
Function: Get the strand of this position; it is always 1 since maps to not
have strands.
Returns : 1
Args : none
=cut
sub strand {
return 1;
}
=head2 toString
Title : toString
Usage : print $position->toString(), "\n";
Function: stringifies this range
Returns : a string representation of the range of this Position
Args : optional Bio::Map::RelativeI to have the co-ordinates reported
relative to the thing described by that Relative
=cut
sub toString {
my $self = shift;
$self->throw_not_implemented();
}
=head1 RangeI-related methods
These methods work by considering only the values of start() and end(), as
modified by considering every such co-ordinate relative to the start of the map
(ie. absolute(1) is set temporarily during the calculation), or any supplied
Relative. For the boolean methods, when the comparison Position is on the same
map as the calling Position, there is no point supplying a Relative since the
answer will be the same as without. Relative is most useful when comparing
Positions on different maps and you have a Relative that describes some special
place on each map like 'the start of the gene', where the actual start of the
gene relative to the start of the map is different for each map.
The methods do not consider maps during their calculations - things on different
maps can overlap/contain/intersect/etc. each other.
The geometrical methods (intersect, union etc.) do things to the geometry of
ranges, and return Bio::Map::PositionI compliant objects or triplets (start,
stop, strand) from which new positions could be built. When a PositionI is made
it will have a map transferred to it if all the arguments shared the same map.
If a Relative was supplied the result will have that same Relative.
Note that the strand-testing args are there for compatibility with the RangeI
interface. They have no meaning when only using PositionI objects since maps do
not have strands. Typically you will just set the argument to undef if you want
to supply the argument after it.
=head2 equals
Title : equals
Usage : if ($p1->equals($p2)) {...}
Function: Test whether $p1 has the same start, end, length as $p2.
Returns : true if they are describing the same position (regardless of map)
Args : arg #1 = a Bio::RangeI (eg. a Bio::Map::Position) to compare this
one to (mandatory)
arg #2 = optional strand-testing arg ('strong', 'weak', 'ignore')
arg #3 = optional Bio::Map::RelativeI to ask if the Positions
equal in terms of their relative position to the thing
described by that Relative
=cut
sub equals {
# overriding the RangeI implementation so we can handle Relative
my ($self, $other, $so, $rel) = @_;
my ($own_start, $own_end) = $self->_pre_rangei($self, $rel);
my ($other_start, $other_end) = $self->_pre_rangei($other, $rel);
return ($self->_testStrand($other, $so) and
$own_start == $other_start and $own_end == $other_end);
}
=head2 less_than
Title : less_than
Usage : if ($position->less_than($other_position)) {...}
Function: Ask if this Position ends before another starts.
Returns : boolean
Args : arg #1 = a Bio::RangeI (eg. a Bio::Map::Position) to compare this
one to (mandatory)
arg #2 = optional Bio::Map::RelativeI to ask if the Position is less
in terms of their relative position to the thing described
by that Relative
=cut
sub less_than {
my ($self, $other, $rel) = @_;
my ($own_start, $own_end) = $self->_pre_rangei($self, $rel);
my ($other_start, $other_end) = $self->_pre_rangei($other, $rel);
return $own_end < $other_start;
}
=head2 greater_than
Title : greater_than
Usage : if ($position->greater_than($other_position)) {...}
Function: Ask if this Position starts after another ends.
Returns : boolean
Args : arg #1 = a Bio::RangeI (eg. a Bio::Map::Position) to compare this
one to (mandatory)
arg #2 = optional Bio::Map::RelativeI to ask if the Position is
greater in terms of their relative position to the thing
described by that Relative
=cut
sub greater_than {
my ($self, $other, $rel) = @_;
my ($own_start, $own_end) = $self->_pre_rangei($self, $rel);
my ($other_start, $other_end) = $self->_pre_rangei($other, $rel);
return $own_start > $other_end;
}
=head2 overlaps
Title : overlaps
Usage : if ($p1->overlaps($p2)) {...}
Function: Tests if $p1 overlaps $p2.
Returns : True if the positions overlap (regardless of map), false otherwise
Args : arg #1 = a Bio::RangeI (eg. a Bio::Map::Position) to compare this
one to (mandatory)
arg #2 = optional strand-testing arg ('strong', 'weak', 'ignore')
arg #3 = optional Bio::Map::RelativeI to ask if the Positions
overlap in terms of their relative position to the thing
described by that Relative
arg #4 = optional minimum percentage length of the overlap before
reporting an overlap exists (default 0)
=cut
sub overlaps {
# overriding the RangeI implementation so we can handle Relative
my ($self, $other, $so, $rel, $min_percent) = @_;
$min_percent ||= 0;
my ($own_min, $other_min) = (0, 0);
if ($min_percent > 0) {
$own_min = (($self->length / 100) * $min_percent) - 1;
$other_min = (($other->length / 100) * $min_percent) - 1;
}
my ($own_start, $own_end) = $self->_pre_rangei($self, $rel);
my ($other_start, $other_end) = $self->_pre_rangei($other, $rel);
return ($self->_testStrand($other, $so) and not
(($own_start + $own_min > $other_end or $own_end - $own_min < $other_start) ||
($own_start > $other_end - $other_min or $own_end < $other_start + $other_min)));
}
=head2 contains
Title : contains
Usage : if ($p1->contains($p2)) {...}
Function: Tests whether $p1 totally contains $p2.
Returns : true if the argument is totally contained within this position
(regardless of map), false otherwise
Args : arg #1 = a Bio::RangeI (eg. a Bio::Map::Position) to compare this
one to, or scalar number (mandatory)
arg #2 = optional strand-testing arg ('strong', 'weak', 'ignore')
arg #3 = optional Bio::Map::RelativeI to ask if the Position
is contained in terms of their relative position to the
thing described by that Relative
=cut
sub contains {
# overriding the RangeI implementation so we can handle Relative
my ($self, $other, $so, $rel) = @_;
my ($own_start, $own_end) = $self->_pre_rangei($self, $rel);
my ($other_start, $other_end) = $self->_pre_rangei($other, $rel);
return ($self->_testStrand($other, $so) and
$other_start >= $own_start and $other_end <= $own_end);
}
=head2 intersection
Title : intersection
Usage : ($start, $stop, $strand) = $p1->intersection($p2)
($start, $stop, $strand) = Bio::Map::Position->intersection(\@positions);
$mappable = $p1->intersection($p2, undef, $relative);
$mappable = Bio::Map::Position->intersection(\@positions);
Function: gives the range that is contained by all ranges
Returns : undef if they do not overlap, OR
Bio::Map::Mappable object who's positions are the
cross-map-calculated intersection of the input positions on all the
maps that the input positions belong to, OR, in list context, a three
element array (start, end, strand)
Args : arg #1 = [REQUIRED] a Bio::RangeI (eg. a Bio::Map::Position) to
compare this one to, or an array ref of Bio::RangeI
arg #2 = optional strand-testing arg ('strong', 'weak', 'ignore')
arg #3 = optional Bio::Map::RelativeI to ask how the Positions
intersect in terms of their relative position to the thing
described by that Relative
=cut
sub intersection {
# overriding the RangeI implementation so we can transfer map and handle
# Relative
my ($self, $given, $so, $rel) = @_;
$self->throw("missing arg: you need to pass in another argument") unless $given;
my @positions;
if ($self eq "Bio::Map::PositionI") {
$self = "Bio::Map::Position";
$self->warn("calling static methods of an interface is deprecated; use $self instead");
}
if (ref $self) {
push(@positions, $self);
}
ref($given) eq 'ARRAY' ? push(@positions, @{$given}) : push(@positions, $given);
$self->throw("Need at least 2 Positions") unless @positions >= 2;
my ($intersect, $i_start, $i_end, $c_start, $c_end, %known_maps);
while (@positions > 0) {
unless ($intersect) {
$intersect = shift(@positions);
($i_start, $i_end) = $self->_pre_rangei($intersect, $rel);
my $map = $intersect->map;
$known_maps{$map->unique_id} = $map;
}
my $compare = shift(@positions);
($c_start, $c_end) = $self->_pre_rangei($compare, $rel);
return unless $compare->_testStrand($intersect, $so);
if ($compare->isa('Bio::Map::PositionI')) {
my $this_map = $compare->map;
if ($this_map) {
$known_maps{$this_map->unique_id} = $this_map;
}
}
else {
$self->throw("Only Bio::Map::PositionI objects are supported, not [$compare]");
}
my @starts = sort {$a <=> $b} ($i_start, $c_start);
my @ends = sort {$a <=> $b} ($i_end, $c_end);
my $start = pop @starts; # larger of the 2 starts
my $end = shift @ends; # smaller of the 2 ends
my $intersect_strand; # strand for the intersection
if (defined($intersect->strand) && defined($compare->strand) && $intersect->strand == $compare->strand) {
$intersect_strand = $compare->strand;
}
else {
$intersect_strand = 0;
}
if ($start > $end) {
return;
}
else {
$intersect = $self->new(-start => $start,
-end => $end,
-strand => $intersect_strand);
}
}
$intersect || return;
my ($start, $end, $strand) = ($intersect->start, $intersect->end, $intersect->strand);
my @intersects;
foreach my $known_map (values %known_maps) {
my $new_intersect = $intersect->new(-start => $start,
-end => $end,
-strand => $strand,
-map => $known_map);
$new_intersect->relative($rel) if $rel;
push(@intersects, $new_intersect);
}
unless (@intersects) {
$intersect->relative($rel) if $rel;
@intersects = ($intersect);
}
my $result = Bio::Map::Mappable->new();
$result->add_position(@intersects); # sneaky, add_position can take a list of positions
return $result;
}
=head2 union
Title : union
Usage : ($start, $stop, $strand) = $p1->union($p2);
($start, $stop, $strand) = Bio::Map::Position->union(@positions);
my $mappable = $p1->union($p2);
my $mappable = Bio::Map::Position->union(@positions);
Function: finds the minimal position/range that contains all of the positions
Returns : Bio::Map::Mappable object who's positions are the
cross-map-calculated union of the input positions on all the maps
that the input positions belong to, OR, in list context, a three
element array (start, end, strand)
Args : a Bio::Map::PositionI to compare this one to, or a list of such
OR
a single Bio::Map::PositionI or array ref of such AND a
Bio::Map::RelativeI to ask for the Position's union in terms of their
relative position to the thing described by that Relative
=cut
sub union {
# overriding the RangeI implementation so we can transfer map and handle
# Relative
my ($self, @args) = @_;
$self->throw("Not enough arguments") unless @args >= 1;
my @positions;
my $rel;
if ($self eq "Bio::Map::PositionI") {
$self = "Bio::Map::Position";
$self->warn("calling static methods of an interface is deprecated; use $self instead");
}
if (ref $self) {
push(@positions, $self);
}
if (ref $args[0] eq 'ARRAY') {
push(@positions, @{shift(@args)});
}
else {
push(@positions, shift(@args));
}
if ($args[0] && $args[0]->isa('Bio::Map::RelativeI')) {
$rel = shift(@args);
}
foreach my $arg (@args) {
# avoid pushing undefined values into @positions
push(@positions, $arg) if $arg;
}
$self->throw("Need at least 2 Positions") unless @positions >= 2;
my (@starts, @ends, %known_maps, $union_strand);
foreach my $compare (@positions) {
# RangeI union allows start or end to be undefined; however _pre_rangei
# will throw
my ($start, $end) = $self->_pre_rangei($compare, $rel);
if ($compare->isa('Bio::Map::PositionI')) {
my $this_map = $compare->map;
if ($this_map) {
$known_maps{$this_map->unique_id} = $this_map;
}
}
else {
$self->throw("Only Bio::Map::PositionI objects are supported, not [$compare]");
}
if (! defined $union_strand) {
$union_strand = $compare->strand;
}
else {
if (! defined $compare->strand or $union_strand ne $compare->strand) {
$union_strand = 0;
}
}
push(@starts, $start);
push(@ends, $end);
}
@starts = sort { $a <=> $b } @starts;
@ends = sort { $a <=> $b } @ends;
my $start = shift @starts;
my $end = pop @ends;
my @unions;
foreach my $known_map (values %known_maps) {
my $new_union = $self->new(-start => $start,
-end => $end,
-strand => $union_strand,
-map => $known_map);
$new_union->relative($rel) if $rel;
push(@unions, $new_union);
}
unless (@unions) {
@unions = ($self->new(-start => $start,
-end => $end,
-strand => $union_strand));
$unions[0]->relative($rel) if $rel;
}
my $result = Bio::Map::Mappable->new();
$result->add_position(@unions); # sneaky, add_position can take a list of positions
return $result;
}
=head2 overlap_extent
Title : overlap_extent
Usage : ($a_unique,$common,$b_unique) = $a->overlap_extent($b)
Function: Provides actual amount of overlap between two different
positions
Example :
Returns : array of values containing the length unique to the calling
position, the length common to both, and the length unique to
the argument position
Args : a position
=cut
#*** should this be overridden from RangeI?
=head2 disconnected_ranges
Title : disconnected_ranges
Usage : my @disc_ranges = Bio::Map::Position->disconnected_ranges(@ranges);
Function: Creates the minimal set of positions such that each input position is
fully contained by at least one output position, and none of the
output positions overlap.
Returns : Bio::Map::Mappable with the calculated disconnected ranges
Args : a Bio::Map::PositionI to compare this one to, or a list of such,
OR
a single Bio::Map::PositionI or array ref of such AND a
Bio::Map::RelativeI to consider all Position's co-ordinates in terms
of their relative position to the thing described by that Relative,
AND, optionally, an int for the minimum percentage of overlap that
must be present before considering two ranges to be overlapping
(default 0)
=cut
sub disconnected_ranges {
# overriding the RangeI implementation so we can transfer map and handle
# Relative
my ($self, @args) = @_;
$self->throw("Not enough arguments") unless @args >= 1;
my @positions;
my $rel;
my $overlap = 0;
if ($self eq "Bio::Map::PositionI") {
$self = "Bio::Map::Position";
$self->warn("calling static methods of an interface is deprecated; use $self instead");
}
if (ref $self) {
push(@positions, $self);
}
if (ref $args[0] eq 'ARRAY') {
push(@positions, @{shift(@args)});
}
else {
push(@positions, shift(@args));
}
if ($args[0] && $args[0]->isa('Bio::Map::RelativeI')) {
$rel = shift(@args);
$overlap = shift(@args);
}
foreach my $arg (@args) {
push(@positions, $arg) if $arg;
}
$self->throw("Need at least 2 Positions") unless @positions >= 2;
my %known_maps;
foreach my $pos (@positions) {
$pos->isa('Bio::Map::PositionI') || $self->throw("Must supply only Bio::Map::PositionI objects, not [$pos]");
my $map = $pos->map || next;
$known_maps{$map->unique_id} = $map;
}
my %prior_positions;
foreach my $map (values %known_maps) {
foreach my $pos ($map->get_positions) {
$prior_positions{$pos} = 1;
}
}
my @outranges = ();
foreach my $inrange (@positions) {
my @outranges_new = ();
my %overlapping_ranges = ();
for (my $i=0; $i<@outranges; $i++) {
my $outrange = $outranges[$i];
if ($inrange->overlaps($outrange, undef, $rel, $overlap)) {
my $union_able = $inrange->union($outrange, $rel); # using $inrange->union($outrange, $rel); gives >6x speedup,
# but different answer, not necessarily incorrect...
foreach my $pos ($union_able->get_positions) {
$overlapping_ranges{$pos->toString} = $pos; # we flatten down to a result on a single map
# to avoid creating 10s of thousands of positions during this process;
# we then apply the final answer to all maps at the very end
last;
}
}
else {
push(@outranges_new, $outrange);
}
}
@outranges = @outranges_new;
my @overlappers = values %overlapping_ranges;
if (@overlappers) {
if (@overlappers > 1) {
my $merged_range_able = shift(@overlappers)->union(\@overlappers, $rel);
push(@outranges, $merged_range_able->get_positions);
}
else {
push(@outranges, @overlappers);
}
}
else {
push(@outranges, $self->new(-start => $inrange->start($rel), -end => $inrange->end($rel), -strand => $inrange->strand, -map => $inrange->map, -relative => $rel));
}
}
# purge positions that were created whilst calculating the answer, but
# aren't the final answer and weren't there previously
my %answers = map { $_ => 1 } @outranges;
foreach my $map (values %known_maps) {
foreach my $pos ($map->get_positions) {
if (! exists $prior_positions{$pos} && ! exists $answers{$pos}) {
$map->purge_positions($pos);
}
}
}
my %post_positions;
foreach my $map (values %known_maps) {
foreach my $pos ($map->get_positions) {
$post_positions{$pos} = 1;
}
}
@outranges || return;
# make an outrange on all known maps
my @final_positions;
foreach my $map (values %known_maps) {
foreach my $pos (@outranges) {
if ($pos->map eq $map) {
push(@final_positions, $pos);
}
else {
push(@final_positions, $pos->new(-start => $pos->start,
-end => $pos->end,
-relative => $pos->relative,
-map => $map));
}
}
}
# assign the positions to a result mappable
my $result = Bio::Map::Mappable->new();
$result->add_position(@final_positions); # sneaky, add_position can take a list of positions
return $result;
}
# get start & end suitable for rangeI methods, taking relative into account
sub _pre_rangei {
my ($self, $other, $rel) = @_;
$self->throw("Must supply an object") unless $other;
if ($rel) {
$self->throw("Must supply an object for the Relative argument") unless ref($rel);
$self->throw("This is [$rel], not a Bio::Map::RelativeI") unless $rel->isa('Bio::Map::RelativeI');
}
my ($other_start, $other_end);
if (ref($other)) {
if (ref($other) eq 'ARRAY') {
$self->throw("_pre_rangei got an array");
}
$self->throw("This is [$other], not a Bio::RangeI object") unless defined $other && $other->isa('Bio::RangeI');
if ($other->isa('Bio::Map::PositionI')) {
# to get the desired start/end we need the position to be on a map;
# if it isn't on one temporarily place it on self's map
# - this lets us have 'generic' positions that aren't on any map
# but have a relative defined and can thus be usefully compared to
# positions that /are/ on maps
my $other_map = $other->map;
unless ($other_map) {
my $self_map = $self->map || $self->throw("Trying to compare two positions but neither had been placed on a map");
$other->map($self_map);
}
# want start and end positions relative to the supplied rel or map start
$rel ||= $other->absolute_relative;
$other_start = $other->start($rel);
$other_end = $other->end($rel);
unless ($other_map) {
$self->map->purge_positions($other);
}
}
else {
$other_start = $other->start;
$other_end = $other->end;
}
}
else {
$self->throw("not a number") unless looks_like_number($other);
$other_start = $other_end = $other;
}
$other->throw("start is undefined") unless defined $other_start;
$other->throw("end is undefined") unless defined $other_end;
return ($other_start, $other_end);
}
1;
|