Bio::Map Mappable
SummaryIncluded librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
Toolbar
WebCvs
Summary
Bio::Map::Mappable - An object representing a generic map element
that can have multiple locations in several maps.
Package variables
No package variables defined.
Included modules
Bio::Map::Position
Bio::Map::Relative
Inherit
Bio::Map::MappableI Bio::Root::Root
Synopsis
  # a map element in two different positions on the same map
$map1 = Bio::Map::SimpleMap->new();
$position1 = Bio::Map::Position->new(-map => $map1, -value => 100);
$position2 = Bio::Map::Position->new(-map => $map1, -value => 200);
$mappable = Bio::Map::Mappable->new(-positions => [$position1, $position2] );
# add another position on a different map $map2 = Bio::Map::SimpleMap->new(); $position3 = Bio::Map::Position->new(-map => $map2, $value => 50); $mappable->add_position($position3); # get all the places our map element is found, on a particular map of interest foreach $pos ($mappable->get_positions($map1)) { print $pos->value, "\n"; }
Description
This object handles the notion of a generic map element. Mappables are
entities with one or more positions on one or more maps.
This object is a pure perl implementation of Bio::Map::MappableI. That
interface implements some of its own methods so check the docs there for
those.
Methods
newDescriptionCode
nameDescriptionCode
idDescriptionCode
in_mapDescriptionCode
equalsDescriptionCode
less_thanDescriptionCode
greater_thanDescriptionCode
overlapsDescriptionCode
containsDescriptionCode
overlapping_groupsDescriptionCode
disconnected_intersectionsDescriptionCode
disconnected_unionsDescriptionCode
_compare
No description
Code
tupleDescriptionCode
annotationDescriptionCode
Methods description
newcode    nextTop
 Title   : new
Usage : my $mappable = Bio::Map::Mappable->new();
Function: Builds a new Bio::Map::Mappable object
Returns : Bio::Map::Mappable
Args : -name => string : name of the mappable element
-id => string : id of the mappable element
namecodeprevnextTop
 Title   : name
Usage : $mappable->name($new_name);
my $name = $mappable->name();
Function: Get/Set the name for this Mappable
Returns : A scalar representing the current name of this Mappable
Args : none to get
string to set
idcodeprevnextTop
 Title   : id
Usage : my $id = $mappable->id();
$mappable->id($new_id);
Function: Get/Set the id for this Mappable.
Returns : A scalar representing the current id of this Mappable
Args : none to get
string to set
in_mapcodeprevnextTop
 Title   : in_map
Usage : if ($mappable->in_map($map)) {...}
Function: Tests if this mappable is found on a specific map
Returns : boolean
Args : Bio::Map::MapI
equalscodeprevnextTop
 Title   : equals
Usage : if ($mappable->equals($other_mappable)) {...}
my @equal_positions = $mappable->equals($other_mappable);
Function: Finds the positions in this mappable that are equal to any
comparison positions.
Returns : array of Bio::Map::PositionI objects
Args : arg #1 = Bio::Map::MappableI OR Bio::Map::PositionI to compare
this one to (mandatory)
arg #2 = optionally, one or more of the key => value pairs below
-map => MapI : a Bio::Map::MapI to only consider positions
on the given map
-relative => RelativeI : a Bio::Map::RelativeI to calculate in terms
of each Position's relative position to the
thing described by that Relative
less_thancodeprevnextTop
 Title   : less_than
Usage : if ($mappable->less_than($other_mappable)) {...}
my @lesser_positions = $mappable->less_than($other_mappable);
Function: Finds the positions in this mappable that are less than all
comparison positions.
Returns : array of Bio::Map::PositionI objects
Args : arg #1 = Bio::Map::MappableI OR Bio::Map::PositionI to compare
this one to (mandatory)
arg #2 = optionally, one or more of the key => value pairs below
-map => MapI : a Bio::Map::MapI to only consider positions
on the given map
-relative => RelativeI : a Bio::Map::RelativeI to calculate in terms
of each Position's relative position to the
thing described by that Relative
greater_thancodeprevnextTop
 Title   : greater_than
Usage : if ($mappable->greater_than($other_mappable)) {...}
my @greater_positions = $mappable->greater_than($other_mappable);
Function: Finds the positions in this mappable that are greater than all
comparison positions.
Returns : array of Bio::Map::PositionI objects
Args : arg #1 = Bio::Map::MappableI OR Bio::Map::PositionI to compare
this one to (mandatory)
arg #2 = optionally, one or more of the key => value pairs below
-map => MapI : a Bio::Map::MapI to only consider positions
on the given map
-relative => RelativeI : a Bio::Map::RelativeI to calculate in terms
of each Position's relative position to the
thing described by that Relative
overlapscodeprevnextTop
 Title   : overlaps
Usage : if ($mappable->overlaps($other_mappable)) {...}
my @overlapping_positions = $mappable->overlaps($other_mappable);
Function: Finds the positions in this mappable that overlap with any
comparison positions.
Returns : array of Bio::Map::PositionI objects
Args : arg #1 = Bio::Map::MappableI OR Bio::Map::PositionI to compare
this one to (mandatory)
arg #2 = optionally, one or more of the key => value pairs below
-map => MapI : a Bio::Map::MapI to only consider positions
on the given map
-relative => RelativeI : a Bio::Map::RelativeI to calculate in terms
of each Position's relative position to the
thing described by that Relative
containscodeprevnextTop
 Title   : contains
Usage : if ($mappable->contains($other_mappable)) {...}
my @container_positions = $mappable->contains($other_mappable);
Function: Finds the positions in this mappable that contain any comparison
positions.
Returns : array of Bio::Map::PositionI objects
Args : arg #1 = Bio::Map::MappableI OR Bio::Map::PositionI to compare
this one to (mandatory)
arg #2 = optionally, one or more of the key => value pairs below
-map => MapI : a Bio::Map::MapI to only consider positions
on the given map
-relative => RelativeI : a Bio::Map::RelativeI to calculate in terms
of each Position's relative position to the
thing described by that Relative
overlapping_groupscodeprevnextTop
 Title   : overlapping_groups
Usage : my @groups = $mappable->overlapping_groups($other_mappable);
my @groups = Bio::Map::Mappable->overlapping_groups(\@mappables);
Function: Look at all the positions of all the supplied mappables and group
them according to overlap.
Returns : array of array refs, each ref containing the Bio::Map::PositionI
objects that overlap with each other
Args : arg #1 = Bio::Map::MappableI OR Bio::Map::PositionI to compare
this one to, or an array ref of such objects (mandatory)
arg #2 = optionally, one or more of the key => value pairs below
-map => MapI : a Bio::Map::MapI to only consider positions
on the given map
-relative => RelativeI : a Bio::Map::RelativeI to calculate in terms
of each Position's relative position to the
thing described by that Relative
-min_pos_num => int : the minimum number of positions that must
be in a group before it will be returned
[default is 1]
-min_mappables_num => int : the minimum number of different
mappables represented by the
positions in a group before it
will be returned [default is 1]
-min_mappables_percent => number : as above, but the minimum
percentage of input mappables
[default is 0]
-min_map_num => int : the minimum number of different
maps represented by the positions
in a group before it will be
returned [default is 1]
-min_map_percent => number : as above, but the minimum
percentage of maps known by the
input mappables [default is 0]
-require_self => 1|0 : require that at least one of the
calling object's positions be in
each group [default is 1, has no
effect when the second usage form
is used]
-required => \@mappables : require that at least one position
for each mappable supplied in this
array ref be in each group
disconnected_intersectionscodeprevnextTop
 Title   : disconnected_intersections
Usage : @positions = $mappable->disconnected_intersections($other_mappable);
@positions = Bio::Map::Mappable->disconnected_intersections(\@mappables);
Function: Make the positions that are at the intersection of each group of
overlapping positions, considering all the positions of the supplied
mappables.
Returns : new Bio::Map::Mappable who's positions on maps are the calculated
disconnected unions
Args : arg #1 = Bio::Map::MappableI OR Bio::Map::PositionI to compare
this one to, or an array ref of such objects (mandatory)
arg #2 = optionally, one or more of the key => value pairs below
-map => MapI : a Bio::Map::MapI to only consider positions
on the given map
-relative => RelativeI : a Bio::Map::RelativeI to calculate in terms
of each Position's relative position to the
thing described by that Relative
-min_pos_num => int : the minimum number of positions that must
be in a group before the intersection will
be calculated and returned [default is 1]
-min_mappables_num => int : the minimum number of different
mappables represented by the
positions in a group before the
intersection will be calculated
and returned [default is 1]
-min_mappables_percent => number : as above, but the minimum
percentage of input mappables
[default is 0]
-min_map_num => int : the minimum number of different
maps represented by the positions
in a group before the intersection
will be calculated and returned
[default is 1]
-min_map_percent => number : as above, but the minimum
percentage of maps known by the
input mappables [default is 0]
-require_self => 1|0 : require that at least one of the
calling object's positions be in
each group [default is 1, has no
effect when the second usage form
is used]
-required => \@mappables : require that at least one position
for each mappable supplied in this
array ref be in each group
disconnected_unionscodeprevnextTop
 Title   : disconnected_unions
Usage : my @positions = $mappable->disconnected_unions($other_mappable);
my @positions = Bio::Map::Mappable->disconnected_unions(\@mappables);
Function: Make the positions that are the union of each group of overlapping
positions, considering all the positions of the supplied mappables.
Returns : new Bio::Map::Mappable who's positions on maps are the calculated
disconnected unions
Args : arg #1 = Bio::Map::MappableI OR Bio::Map::PositionI to compare
this one to, or an array ref of such objects (mandatory)
arg #2 = optionally, one or more of the key => value pairs below
-map => MapI : a Bio::Map::MapI to only consider positions
on the given map
-relative => RelativeI : a Bio::Map::RelativeI to calculate in terms
of each Position's relative position to the
thing described by that Relative
-min_pos_num => int : the minimum number of positions that must
be in a group before the union will be
calculated and returned [default is 1]
-min_mappables_num => int : the minimum number of different
mappables represented by the
positions in a group before the
union will be calculated and
returned [default is 1]
-min_mappables_percent => number : as above, but the minimum
percentage of input mappables
[default is 0]
-min_map_num => int : the minimum number of different
maps represented by the positions
in a group before the union will
be calculated and returned
[default is 1]
-min_map_percent => number : as above, but the minimum
percentage of maps known by the
input mappables [default is 0]
-require_self => 1|0 : require that at least one of the
calling object's positions be in
each group [default is 1, has no
effect when the second usage form
is used]
-required => \@mappables : require that at least one position
for each mappable supplied in this
array ref be in each group
tuplecodeprevnextTop
 Title   : tuple
Usage : Do Not Use!
Function: tuple was supposed to be a private method; this method no longer
does anything
Returns : warning
Args : none
Status : deprecated, will be removed in next version
annotationcodeprevnextTop
 Title   : annotation
Usage : $mappable->annotation($an_col);
my $an_col = $mappable->annotation();
Function: Get the annotation collection (see Bio::AnnotationCollectionI)
for this annotatable object.
Returns : a Bio::AnnotationCollectionI implementing object, or undef
Args : none to get, OR
a Bio::AnnotationCollectionI implementing object to set
Methods code
newdescriptionprevnextTop
sub new {
    my ($class, @args) = @_;
    my $self = $class->SUPER::new(@args);
    
    my ($name, $id) = $self->_rearrange([qw(NAME ID)], @args);
    $self->name($name) if $name;
    $self->id($id) if $id;
    
    return $self;
}
namedescriptionprevnextTop
sub name {
    my $self = shift;
    if (@_) { $self->{_name} = shift }
    return $self->{_name} || '';
}
iddescriptionprevnextTop
sub id {
    my $self = shift;
    if (@_) { $self->{_id} = shift }
    return $self->{_id} || return;
}
in_mapdescriptionprevnextTop
sub in_map {
	my ($self, $query_map) = @_;
	$self->throw("Must supply an argument") unless $query_map;
    $self->throw("This is [$query_map], not an object") unless ref($query_map);
    $self->throw("This is [$query_map], not a Bio::Map::MapI object") unless $query_map->isa('Bio::Map::MapI');
    
    foreach my $map ($self->known_maps) {
        ($map eq $query_map) && return 1;
    }
    
    return 0;
}
equalsdescriptionprevnextTop
sub equals {
    my $self = shift;
    return $self->_compare('equals', @_);
}
less_thandescriptionprevnextTop
sub less_than {
    my $self = shift;
    return $self->_compare('less_than', @_);
}
greater_thandescriptionprevnextTop
sub greater_than {
    my $self = shift;
    return $self->_compare('greater_than', @_);
}
overlapsdescriptionprevnextTop
sub overlaps {
    my $self = shift;
    return $self->_compare('overlaps', @_);
}
containsdescriptionprevnextTop
sub contains {
    my $self = shift;
    return $self->_compare('contains', @_);
}
overlapping_groupsdescriptionprevnextTop
sub overlapping_groups {
    my $self = shift;
    return $self->_compare('overlapping_groups', @_);
}
disconnected_intersectionsdescriptionprevnextTop
sub disconnected_intersections {
    my $self = shift;
    return $self->_compare('intersection', @_);
}
disconnected_unionsdescriptionprevnextTop
sub disconnected_unions {
    my $self = shift;
    return $self->_compare('union', @_);
}

# do a RangeI-related comparison by calling the corresponding PositionI method
# on all the requested Positions of our Mappables
}
_comparedescriptionprevnextTop
sub _compare {
    my ($self, $method, $input, @extra_args) = @_;
    $self->throw("Must supply an object or array ref of them") unless ref($input);
    $self->throw("Wrong number of extra args (should be key => value pairs)") unless @extra_args % 2 == 0;
    my @compares = ref($input) eq 'ARRAY' ? @{$input} : ($input);
    
    my %args = (-map => undef, -relative => undef, -min_pos_num => 1,
                -min_mappables_num => 1, -min_mappables_percent => 0,
                -min_map_num => 1, -min_map_percent => 0,
                -require_self => 0, -required => undef, -min_overlap_percent => 0, @extra_args);
    my $map = $args{-map};
    my $rel = $args{-relative};
    my $overlap = $args{-min_overlap_percent};
    my $min_pos_num = $args{-min_pos_num};
    my $min_pables_num = $args{-min_mappables_num};
    if ($args{-min_mappables_percent}) {
        my $mn = (@compares + (ref($self) ? 1 : 0)) / 100 * $args{-min_mappables_percent};
if ($mn > $min_pables_num) { $min_pables_num = $mn; } } my $min_map_num = $args{-min_map_num}; if ($args{-min_map_percent}) { my %known_maps; foreach my $pable (@compares, ref($self) ? ($self) : ()) { foreach my $known ($pable->known_maps) { $known_maps{$known->unique_id} = 1; } } my $mn = scalar(keys %known_maps) / 100 * $args{-min_map_percent};
if ($mn > $min_map_num) { $min_map_num = $mn; } } my %required = map { $_ => 1 } $args{-required} ? @{$args{-required}} : (); my (@mine, @yours); if (ref($self)) { @mine = $self->get_positions($map); if ($args{-require_self}) { @mine > 0 or return; $required{$self} = 1; } } my @required = keys %required; foreach my $compare (@compares) { if ($compare->isa('Bio::Map::PositionI')) { push(@yours, $compare); } elsif ($compare->isa('Bio::Map::MappableI')) { push(@yours, $compare->get_positions($map)); } else { $self->throw("This is [$compare], not a Bio::Map::MappableI or Bio::Map::PositionI"); } } @yours > 0 or return; my @ok; SWITCH: for ($method) { /equals|overlaps|contains/ && do { @mine > 0 or return; foreach my $my_pos (@mine) { foreach my $your_pos (@yours) { if ($my_pos->$method($your_pos, undef, $rel)) { push(@ok, $my_pos); last; } } } last SWITCH; }; /less_than|greater_than/ && do { @mine > 0 or return; if ($method eq 'greater_than') { @mine = map { $_->[1] } sort { $b->[0] <=> $a->[0] } map { [$_->end($_->absolute_relative), $_] } @mine; @yours = map { $_->[1] } sort { $b->[0] <=> $a->[0] } map { [$_->end($_->absolute_relative), $_] } @yours; } my $test_pos = shift(@yours); foreach my $my_pos (@mine) { if ($my_pos->$method($test_pos, $rel)) { push(@ok, $my_pos); } else { last; } } if ($method eq 'greater_than') { @ok = map { $_->[1] } sort { $a->[0] <=> $b->[0] } map { [$_->sortable, $_] } @ok; } last SWITCH; }; /overlapping_groups|intersection|union/ && do { my @positions = (@mine, @yours); my $start_pos = shift(@positions); my $dr_able = $start_pos->disconnected_ranges(\@positions, $rel, $overlap) || return; my @disconnected_ranges = $dr_able->get_positions; #print "got ", scalar(@disconnected_ranges), " disconnected_ranges, first has range ", $disconnected_ranges[0]->toString, "\n";
#use Benchmark qw(:all);
#my $t0 = new Benchmark;
my %all_groups; my %done_ranges; for my $i (0..$#disconnected_ranges) { my $range = $disconnected_ranges[$i]; my $range_string = $range->toString; next if $done_ranges{$range_string}; $done_ranges{$range_string} = 1; foreach my $pos ($start_pos, @positions) { if ($pos->overlaps($range, undef, $rel)) { $all_groups{$range_string}->{$pos} = $pos; } } } #my $t1 = new Benchmark;
#my $td = timediff($t1, $t0);
#print "grouping took: ",timestr($td),"\n";
# purge the temporary working (not $dr_able->purge_positions since
# that removes the element from each position, but leaves it on
# the map. *** need complete purge that removes position from
# memory...
foreach my $pos (@disconnected_ranges) { my $map = $pos->map || next; $map->purge_positions($pos); } my @groups; GROUPS: foreach my $group_range (keys %all_groups) { # sort keys %all_groups might help, but causes test fails
my $group = $all_groups{$group_range}; my @group = values %{$group}; #print "* in group $group_range, there are ", scalar(@group), " members\n";
@group >= $min_pos_num or next; @group >= $min_pables_num or next; # shortcut before having to work it out properly
@group >= $min_map_num or next; # shortcut before having to work it out properly
my %mappables; foreach my $pos (@group) { my $mappable = $pos->element || next; $mappables{$mappable} = 1; } keys %mappables >= $min_pables_num or next; my %maps; foreach my $pos (@group) { my $map = $pos->map || next; $maps{$map->unique_id} = 1; } keys %maps >= $min_map_num or next; foreach my $required (@required) { exists $mappables{$required} or next GROUPS; } my @sorted = map { $_->[1] } sort { $a->[0] <=> $b->[0] } map { [$_->sortable, $_] } @group; push(@groups,\@ sorted); } if ($method eq 'overlapping_groups') { return @groups; } else { foreach my $group (@groups) { my $start_pos = shift(@{$group}); unless (@{$group}) { # we'll consider the 'intersection' or 'union' of just
# one position as the position itself
push(@ok, Bio::Map::Position->new(-map => $start_pos->map, -start => $start_pos->start, -end => $start_pos->end)); } else { my @rel_arg = $method eq 'intersection' ? (undef, $rel) : ($rel); my $result = $start_pos->$method($group, @rel_arg) || next; push(@ok, $result->get_positions); } } # assign all the positions to a result mappable
my $result = $self->new(); $result->add_position(@ok) if @ok; # add_position can actually take a list
return $result; } last SWITCH; }; $self->throw("Unknown method '$method'"); } return @ok;
}
tupledescriptionprevnextTop
sub tuple {
    my $self = shift;
    $self->warn("The tuple method was supposed to be a private method, don't call it!");
}
annotationdescriptionprevnextTop
sub annotation {
    my $self = shift;
    if (@_) { $self->{_annotation} = shift }
    return $self->{_annotation} || return;
}

1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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
Support Top
Please direct usage questions or support issues to the mailing list:
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.
Reporting BugsTop
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://redmine.open-bio.org/projects/bioperl/
AUTHOR - Sendu BalaTop
Email bix@sendu.me.uk
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
Comparison methodsTop