NAME
AlignDB::IntSpan - Handling of sets containing integer spans.
SYNOPSIS
use AlignDB::IntSpan;
my $set = AlignDB::IntSpan->new;
$set->add(1, 2, 3, 5, 7, 9);
$set->add_range(100, 1_000_000);
print $set->as_string, "\n"; # 1-3,5,7,9,100-1000000
Operator overloads
if ($set) { ... } # true if $set is not empty
print "$set\n"; # stringizes to the run list
DESCRIPTION
The AlignDB::IntSpan module represents sets of integers as a number of
inclusive ranges, for example '1-10,19-23,45-48'. Because many of its
operations involve linear searches of the list of ranges its overall
performance tends to be proportional to the number of distinct ranges.
This is fine for small sets but suffers compared to other possible set
representations (bit vectors, hash keys) when the number of ranges
grows large.
This module also represents sets as ranges of values but stores those
ranges in order and uses a binary search for many internal operations
so that overall performance tends towards O log N where N is the number
of ranges.
The internal representation used by this module is extremely simple: a
set is represented as a list of integers. Integers in even numbered
positions (0, 2, 4 etc) represent the start of a run of numbers while
those in odd numbered positions represent the ends of runs. As an
example the set (1, 3-7, 9, 11, 12) would be represented internally as
(1, 2, 3, 8, 11, 13).
Sets may be infinite - assuming you're prepared to accept that infinity
is actually no more than a fairly large integer. Specifically the
constants $NEG_INF and $POS_INF are defined to be -(2^31-1) and
(2^31-2) respectively. To create an infinite set invert an empty one:
my $inf = AlignDB::IntSpan->new->complement;
Sets need only be bounded in one direction - for example this is the
set of all positive integers (assuming you accept the slightly feeble
definition of infinity we're using):
my $pos_int = AlignDB::IntSpan->new;
$pos_int->add_range(1, $pos_int->POS_INF);
Many codes come from Set::IntSpan, Set::IntSpan::Fast and
Set::IntSpan::Island.
METHODS
CONSTANTS
POS_INF
Normally used in construction of infinite sets
NEG_INF
Normally used in construction of infinite sets
EMPTY_STRING
INTERFACE: Set creation
new
my $set = AlignDB::Intspan->new; # empty set
my $set = AlignDB::Intspan->new($set_spec); # the content of $set_spec
my $set = AlignDB::Intspan->new(@set_specs); # the union of @set_specs
Creates and returns an AlignDB::IntSpan object.
valid
my $ok = AlignDB::IntSpan->valid($run_list);
Returns true if $run_list is a valid run list.
clear
$set->clear;
Clear all contents of $set
INTERFACE: Set contents
edges_ref
Return the internal used ArrayRef representing the set.
I don't think you should use this method.
edges
Return the internal used Array representing the set.
I don't think you should use this method.
edge_size
Return the number of edges
span_size
Return the number of spans
as_string
Return a string representation of the set.
as_array
Return an array containing all the members of the set in ascending
order.
INTERFACE: Span contents
ranges
Returns the runs in $set, as a list of ($lower, $upper)
spans
Returns the runs in $set, as a list of [$lower, $upper]
sets
Returns the runs in $set, as a list of AlignDB::IntSpan objects. The
sets in the list are in order.
runlists
Returns the runs in $set, as a list of "$lower-$upper"
INTERFACE: Set cardinality
cardinality
Returns the number of elements in $set.
is_empty
Return true if the set is empty.
is_not_empty
Return true if the set is not empty.
is_neg_inf
Return true if the set is negtive infinite.
is_pos_inf
Return true if the set is positive infinite.
is_infinite
Return true if the set is infinite.
is_finite
Return true if the set is finite.
is_universal
Return true if the set contains all integers.
INTERFACE: Membership test
contains_all
Return true if the set contains all of the specified numbers.
contains_any
Return true if the set contains any of the specified numbers.
INTERFACE: Member operations
add_pair
$set->add_pair($lower, $upper);
Add a pair of inclusive integers to the set.
A pair of arguments constitute a range
add_range
$set->add_range($lower, $upper);
Add the inclusive range of integers to the set.
Multiple ranges may be specified. Each pair of arguments constitute a
range
add_runlist
$set->add_runlist($runlist);
Add the specified runlist to the set.
add
$set->add($number1, $number2, $number3 ...)
$set->add($runlist);
Add the specified integers or a runlist to the set.
invert
$set = $set->invert;
Complement the set.
Because our notion of infinity is actually disappointingly finite
inverting a finite set results in another finite set. For example
inverting the empty set makes it contain all the integers between
$NEG_INF and $POS_INF inclusive.
As noted above $NEG_INF and $POS_INF are actually just big integers.
remove_range
$set->remove_range($lower, $upper);
Remove the inclusive range of integers to the set.
Multiple ranges may be specified. Each pair of arguments constitute a
range.
remove
$set->remove($number1, $number2, $number3 ...);
$set->remove($runlist);
Remove the specified integers or a runlist to the set.
merge
$set->merge($another_set);
$set->merge($set_spec);
Merge the members of the supplied sets or set_specs into this set. Any
number of sets may be supplied as arguments.
subtract
$set->subtract($another_set);
$set->subtract($set_spec);
Subtract the members of the supplied sets or set_specs out of this set.
Any number of sets may be supplied as arguments.
INTERFACE: Set operations
copy
my $new_set = $set->copy;
Return an identical copy of the set.
union
Be called either as a method
my $new_set = $set->union( $other_set );
or as a function:
my $new_set = AlignDB::IntSpan::union( $set1, $set2, $set3 );
Return a new set that is the union of this set and all of the supplied
sets.
complement
my $new_set = $set->complement;
Returns a new set that is the complement of this set.
diff
my $new_set = $set->diff( $other_set );
Return a set containing all the elements that are in this set but not
the supplied set.
intersect
Be called either as a method
my $new_set = $set->intersect( $other_set );
or as a function:
my $new_set = AlignDB::IntSpan::intersect( $set1, $set2, $set3 );
Return a new set that is the intersection of this set and all the
supplied sets.
xor
Be called either as a method
my $new_set = $set->xor( $other_set );
or as a function:
my $new_set = AlignDB::IntSpan::xor( $set1, $set2, $set3 );
Return a new set that contains all of the members that are in this set
or the supplied set but not both.
Can actually handle more than two setsin which case it returns a set
that contains all the members that are in some of the sets but not all
of the sets.
INTERFACE: Set comparison
equal
Returns true if $set and $set_spec contain the same elements.
subset
Returns true if $set is a subset of $set_spec.
superset
Returns true if $set is a superset of $set_spec.
smaller_than
Returns true if $set is smaller than $set_spec.
larger_than
Returns true if $set is larger than $set_spec.
INTERFACE: Indexing
at
Returns the indexth element of set, index start from "1". Negtive
indices count backwards from the end of the set.
index
Returns the index fo a element in the set, index start from "1"
slice
Give two indexes, return a subset. These indexes must be positive.
INTERFACE: Extrema
min
Returns the smallest element of $set, or undef if there is none.
max
Returns the largest element of $set, or undef if there is none.
INTERFACE: Utils
grep_set
Evaluates the $code_ref for each integer in $set (locally setting $_ to
each integer) and returns an AlignDB::IntSpan object containing those
integers for which the $code_ref returns TRUE.
map_set
Evaluates the $code_ref for each integer in $set (locally setting $_ to
each integer) and returns an AlignDB::IntSpan object containing all the
integers returned as results of all those evaluations.
Evaluates the $code_ref in list context, so each element of $set may
produce zero, one, or more elements in the returned set. The elements
may be returned in any order, and need not be disjoint.
substr_span
my $substring = $set->substr_span($string);
INTERFACE: Spans operations
banish_span
cover
Returns a set consisting of a single span from $set->min to $set->max.
holes
Returns a set containing all the holes in $set, that is, all the
integers that are in-between spans of $set.
inset
inset returns a set constructed by removing $n integers from each end
of each span of $set. If $n is negative, then -$n integers are added to
each end of each span.
In the first case, spans may vanish from the set; in the second case,
holes may vanish.
trim
trim is provided as a synonym for inset.
pad
pad $set $n is the same as $set->inset( -$n )
excise
my $new_set = $set->excise( $minlength )
Removes all spans within $set smaller than $minlength
fill
my $new_set = $set->fill( $maxlength )
Fills in all holes in $set smaller than $maxlength
INTERFACE: Inter-set operations
overlap
my $overlap_amount = $set->overlap( $another_set );
Returns the size of intersection of two sets. Equivalent to
$set->intersect( $another_set )->size;
distance
my $distance = $set->distance( $another_set );
Returns the distance between sets, measured as follows.
If the sets overlap, then the distance is negative and given by
$d = - $set->overlap( $another_set )
If the sets do not overlap, $d is positive and given by the distance on
the integer line between the two closest islands of the sets.
INTERFACE: Islands
find_islands
my $island = $set->find_islands( $integer );
my $new_set = $set->find_islands( $another_set );
Returns a set containing the island in $set containing $integer. If
$integer is not in $set, an empty set is returned. Returns a set
containing all islands in $set intersecting $another_set. If $set and
$another_set have an empty intersection, an empty set is returned.
nearest_island
my $island = $set->nearest_island( $integer );
my $island = $set->nearest_island( $another_set );
Returns the nearest island(s) in $set that contains, but does not
overlap with, $integer. If $integer lies exactly between two islands,
then the returned set contains these two islands.
Returns the nearest island(s) in $set that intersects, but does not
overlap with, $another_set. If $another_set lies exactly between two
islands, then the returned set contains these two islands.
at_island
my $island = $set->at_island( $island_index );
Returns the island indexed by $island_index. Islands are 1-indexed. For
a set with N islands, the first island (ordered left-to-right) has
index 1 and the last island has index N. If $island_index is negative,
counting is done back from the last island (c.f. negative indexes of
Perl arrays).
INTERFACE: Aliases
runlist, run_list => as_string
elements => as_array
size, count => cardinality
empty => is_empty
contains, contain, member => contains_all
duplicate => copy
intersection => intersect
equals => equal
AUTHOR
Qiang Wang
COPYRIGHT AND LICENSE
This software is copyright (c) 2008 by Qiang Wang.
This is free software; you can redistribute it and/or modify it under
the same terms as the Perl 5 programming language system itself.