Raw content of Bio::EnsEMBL::Compara::GenomicAlignTree
<![CDATA[=head1 NAME
ProteinTree - DESCRIPTION of Object
=head1 SYNOPSIS
=head1 DESCRIPTION
Specific subclass of NestedSet to add functionality when the nodes of this tree
are GenomicAlign objects and the tree is a representation of a Protein derived
Phylogenetic tree
=head1 CONTACT
Contact Jessica Severin on implemetation/design detail: jessica@ebi.ac.uk
Contact Abel Ureta-Vidal on EnsEMBL compara project: abel@ebi.ac.uk
Contact Ewan Birney on EnsEMBL in general: birney@sanger.ac.uk
=head1 APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
=cut
package Bio::EnsEMBL::Compara::GenomicAlignTree;
use strict;
use Bio::EnsEMBL::Compara::BaseRelation;
use Bio::EnsEMBL::Utils::Argument;
use Bio::EnsEMBL::Utils::Exception;
use Bio::SimpleAlign;
use IO::File;
use Bio::EnsEMBL::Compara::NestedSet;
use Bio::EnsEMBL::Compara::GenomicAlignBlock;
our @ISA = qw(Bio::EnsEMBL::Compara::NestedSet Bio::EnsEMBL::Compara::GenomicAlignBlock);
# our @ISA = qw(Bio::EnsEMBL::Compara::NestedSet);
=head2 left_node_id
Arg [1] : (optional) $left_node_id
Example : $object->left_node_id($left_node_id);
Example : $left_node_id = $object->left_node_id();
Description : Getter/setter for the left_node_id attribute
Returntype : integer
Exceptions : none
Caller : general
Status : Stable
=cut
sub left_node_id {
my $self = shift;
if (@_) {
$self->{_left_node_id} = shift;
}
return $self->{_left_node_id};
}
=head2 right_node_id
Arg [1] : (optional) $right_node_id
Example : $object->right_node_id($right_node_id);
Example : $right_node_id = $object->right_node_id();
Description : Getter/setter for the right_node_id attribute
Returntype : integer
Exceptions : none
Caller : general
Status : Stable
=cut
sub right_node_id {
my $self = shift;
if (@_) {
$self->{_right_node_id} = shift;
}
return $self->{_right_node_id};
}
=head2 left_node
Arg [1] : -none-
Example : $left_node = $object->left_node();
Description : Get the left_node object from the database.
Returntype : Bio::EnsEMBL::Compara::GenomicAlignTree object
Exceptions : none
Caller : general
Status : Stable
=cut
sub left_node {
my $self = shift;
if ($self->{_left_node_id} and $self->adaptor) {
return $self->adaptor->fetch_node_by_node_id($self->{_left_node_id});
}
return undef;
}
=head2 right_node
Arg [1] : -none-
Example : $left_node = $object->right_node();
Description : Get the right_node object from the database.
Returntype : Bio::EnsEMBL::Compara::GenomicAlignTree object
Exceptions : none
Caller : general
Status : Stable
=cut
sub right_node {
my $self = shift;
if ($self->{_right_node_id} and $self->adaptor) {
return $self->adaptor->fetch_node_by_node_id($self->{_right_node_id});
}
return undef;
}
=head2 get_original_strand
Args : -none-
Example : if (!$genomic_align_tree->get_original_strand()) {
# original GenomicAlignTree has been reverse-complemented
}
Description: getter for the _orignal_strand attribute
Returntype : none
Exceptions : none
Caller : general
Status : At risk
=cut
sub get_original_strand {
my ($self) = @_;
if (!defined($self->{_original_strand})) {
$self->{_original_strand} = 1;
}
return $self->{_original_strand};
}
=head2 ancestral_genomic_align_block_id
Arg [1] : (optional) $ancestral_genomic_align_block_id
Example : $object->ancestral_genomic_align_block_id($ancestral_genomic_align_block_id);
Example : $ancestral_genomic_align_block_id = $object->ancestral_genomic_align_block_id();
Description : Getter/setter for the ancestral_genomic_align_block_id attribute
This attribute is intended for the root of the tree only!
Returntype : int
Exceptions : none
Caller : general
Status : Stable
=cut
sub ancestral_genomic_align_block_id {
my $self = shift;
if (@_) {
$self->{_ancestral_genomic_align_block_id} = shift;
}
return $self->{_ancestral_genomic_align_block_id};
}
=head2 modern_genomic_align_block_id
Arg [1] : (optional) $modern_genomic_align_block_id
Example : $object->modern_genomic_align_block_id($modern_genomic_align_block_id);
Example : $modern_genomic_align_block_id = $object->modern_genomic_align_block_id();
Description : Getter/setter for the modern_genomic_align_block_id attribute
Returntype :
Exceptions : none
Caller : general
Status : Stable
=cut
sub modern_genomic_align_block_id {
my $self = shift;
if (@_) {
$self->{_modern_genomic_align_block_id} = shift;
}
return $self->{_modern_genomic_align_block_id};
}
=head2 genomic_align_group
Arg [1] : (optional) $genomic_align_group
Example : $object->genomic_align_group($genomic_align_group);
Example : $genomic_align_group = $object->genomic_align_group();
Description : Getter/setter for the genomic_align_group attribute
Returntype : Bio::EnsEMBL::Compara::GenomicAlignGroup object
Exceptions : none
Caller : general
Status : Stable
=cut
sub genomic_align_group {
my $self = shift;
if (@_) {
$self->{_genomic_align_group} = shift;
}
return $self->{_genomic_align_group};
}
=head2 get_all_GenomicAligns
Arg [1] : -none-
Example : $genomic_aligns = $object->get_all_GenomicAligns
Description : Getter for all the GenomicAligns contained in the
genomic_align_group object. This method is a short
cut for $object->genomic_align_group->get_all_GenomicAligns()
Returntype : listref of Bio::EnsEMBL::Compara::GenomicAlign objects
Exceptions : none
Caller : general
Status : Stable
=cut
sub get_all_GenomicAligns {
my $self = shift(@_);
return [] if (!$self->genomic_align_group);
return $self->genomic_align_group->get_all_GenomicAligns;
}
=head2 reference_genomic_align
Arg [1] : (optional) $reference_genomic_align
Example : $object->reference_genomic_align($reference_genomic_align);
Example : $reference_genomic_align = $object->reference_genomic_align();
Description : Getter/setter for the reference_genomic_align attribute
Returntype : Bio::EnsEMBL::Compara::GenomicAlign object
Exceptions : none
Caller : general
Status : Stable
=cut
sub reference_genomic_align {
my $self = shift;
if (@_) {
$self->{reference_genomic_align} = shift;
}
return $self->{reference_genomic_align};
}
=head2 reference_genomic_align_node
Arg [1] : (optional) $reference_genomic_align_node
Example : $object->reference_genomic_align_node($reference_genomic_align_node);
Example : $reference_genomic_align_node = $object->reference_genomic_align_node();
Description : Getter/setter for the reference_genomic_align_node attribute
Returntype : Bio::EnsEMBL::Compara::GenomicAlignTree object
Exceptions : none
Caller : general
Status : Stable
=cut
sub reference_genomic_align_node {
my $self = shift;
if (@_) {
$self->{reference_genomic_align_node} = shift;
}
return $self->{reference_genomic_align_node};
}
=head2 aligned_sequence
Arg [1] : -none-
Example : $aligned_sequence = $object->aligned_sequence();
Description : Get the aligned sequence for this node. When the node
contains one single sequence, it returns its aligned sequence.
For composite segments, it returns the combined aligned seq.
Returntype : string
Exceptions : none
Caller : general
Status : Stable
=cut
sub aligned_sequence {
my $self = shift;
return $self->genomic_align_group->aligned_sequence(@_);
}
# # =head2 group_id
# #
# # Arg [1] : integer $group_id
# # Example : my $group_id = $genomic_align_tree->group_id;
# # Example : $genomic_align_tree->group_id(1234);
# # Description: get/set for attribute group_id of the underlying
# # GenomicAlignBlock objects
# # Returntype : integer
# # Exceptions : A GenomicAlignTree is made of two GenomicAlignBlock
# # object. The method fail when gettign the value if the
# # two group_ids don't match
# # Caller : general
# #
# # =cut
# #
# # sub group_id {
# # my ($self, $group_id) = @_;
# #
# # if (defined($group_id)) {
# # $self->{'group_id'} = $group_id;
# # # Set the group_id on the genomic_align_blocks...
# # my %genomic_align_blocks;
# # foreach my $this_genomic_align_node (@{$self->get_all_sorted_genomic_align_nodes()}) {
# # my $this_genomic_align_block = $this_genomic_align_node->genomic_align->genomic_align_block;
# # if ($this_genomic_align_block and !defined($genomic_align_blocks{$this_genomic_align_block})) {
# # $this_genomic_align_block->group_id($group_id);
# # $genomic_align_blocks{$this_genomic_align_block} = 1;
# # }
# # }
# # } elsif (!defined($self->{'group_id'}) and defined($self->{adaptor})) {
# # # Try to get the ID from other sources...
# # my %group_ids;
# # my $genomic_align_block_adaptor = $self->adaptor->dba->get_GenomicAlignBlockAdaptor;
# # foreach my $this_genomic_align_node (@{$self->get_all_sorted_genomic_align_nodes()}) {
# # my $this_genomic_align_block_id = $this_genomic_align_node->genomic_align->genomic_align_block_id;
# # my $this_genomic_align_block = $genomic_align_block_adaptor->fetch_by_dbID($this_genomic_align_block_id);
# # if ($this_genomic_align_block->group_id) {
# # $group_ids{$this_genomic_align_block->group_id} = 1;
# # } else {
# # $group_ids{"undef"} = 1;
# # }
# # }
# # if (keys %group_ids == 1) {
# # if (!defined($group_ids{"undef"})) {
# # $self->{'group_id'} = (keys %group_ids)[0];
# # }
# # } else {
# # warning("Different group_ids found for this GenomicAlignTree\n");
# # }
# # }
# # return $self->{'group_id'};
# # }
=head2 name
Arg [1] : (optional) string $name
Example : $object->name($name);
Example : $name = $object->name();
Description : Getter/setter for the name attribute.
Returntype : string
Exceptions : none
Caller : general
Status : At risk
=cut
sub name {
my $self = shift;
if (@_) {
$self->{_name} = shift;
} elsif (!$self->{_name}) {
my $genomic_align_group = $self->genomic_align_group;
if (defined($self->SUPER::name()) and $self->SUPER::name() ne "") {
## Uses the name defined before blessing this object as a
## Bio::EnsEMBL::Compara::GenomicAlignTree in the Ortheus pipeline
$self->{_name} = $self->SUPER::name();
} elsif ($self->is_leaf) {
my $gdb_name;
if($genomic_align_group->genome_db->name =~ /(.)[^ ]+ (.{3})/) {
$gdb_name = "${1}${2}";
}
else {
$gdb_name = $genomic_align_group->genome_db->name();
$gdb_name =~ tr/_//;
}
$self->{_name} = $gdb_name.'_'.$genomic_align_group->dnafrag->name."_".
$genomic_align_group->dnafrag_start."_".$genomic_align_group->dnafrag_end."[".
(($genomic_align_group->dnafrag_strand eq "-1")?"-":"+")."]";
} else {
$self->{_name} = join("-", map {
my $name = $_->genomic_align_group->genome_db->name;
if($name =~ /(.)[^ ]+ (.{3})/) {
$name = "$1$2";
}
else {
$name =~ tr/_//;
}
$name;
} @{$self->get_all_leaves})."[".scalar(@{$self->get_all_leaves})."]";
}
}
return $self->{_name};
}
=head2 get_all_sorted_genomic_align_nodes
Arg [1] : (optional) Bio::EnsEMBL::Compara::GenomicAlignTree $reference_genomic_align_node
Example : $object->get_all_sorted_genomic_align_nodes($ref_genomic_align_node);
Example : $nodes = $object->get_all_sorted_genomic_align_nodes();
Description : If ref_genomic_align_node is set, sorts the tree based on the
reference_genomic_align_node
If ref_genomic_align_node is not set, sorts the tree based on
the species name
Returntype : Bio::EnsEMBL::Compara::GenomicAlignTree
Exceptions : none
Caller : general
Status : At risk
=cut
sub get_all_sorted_genomic_align_nodes {
my ($self, $reference_genomic_align_node) = @_;
my $sorted_genomic_align_nodes = [];
if (!$reference_genomic_align_node and $self->reference_genomic_align_node) {
$reference_genomic_align_node = $self->reference_genomic_align_node;
}
my $children = $self->children;
if (@$children >= 1) {
$children = [sort _sort_children @$children];
push(@$sorted_genomic_align_nodes, @{$children->[0]->get_all_sorted_genomic_align_nodes(
$reference_genomic_align_node)});
push(@$sorted_genomic_align_nodes, $self);
for (my $i = 1; $i < @$children; $i++) {
push(@$sorted_genomic_align_nodes, @{$children->[$i]->get_all_sorted_genomic_align_nodes(
$reference_genomic_align_node)});
}
} elsif (@$children == 0) {
push(@$sorted_genomic_align_nodes, $self);
}
return $sorted_genomic_align_nodes;
}
=head2 restrict_between_alignment_positions
Arg[1] : [optional] int $start, refers to the start of the alignment
Arg[2] : [optional] int $end, refers to the start of the alignment
Arg[3] : [optional] boolean $skip_empty_GenomicAligns
Example : none
Description: restrict this GenomicAlignBlock. It returns a new object unless no
restriction is needed. In that case, it returns the original unchanged
object.
This method uses coordinates relative to the alignment itself.
For instance if you have an alignment like:
1 1 2 2 3
1 5 0 5 0 5 0
AAC--CTTGTGGTA-CTACTT-----ACTTT
AACCCCTT-TGGTATCTACTTACCTAACTTT
and you restrict it between 5 and 25, you will get back a
object containing the following alignment:
1 1
1 5 0 5
CTTGTGGTA-CTACTT----
CTT-TGGTATCTACTTACCT
See restrict_between_reference_positions() elsewhere in this document
for an alternative method using absolute genomic coordinates.
NB: This method works only for GenomicAlignBlock which have been
fetched from the DB as it is adjusting the dnafrag coordinates
and the cigar_line only and not the actual sequences stored in the
object if any. If you want to restrict an object with no coordinates
a simple substr() will do!
Returntype : Bio::EnsEMBL::Compara::GenomicAlignBlock object
Exceptions : none
Caller : general
Status : At risk
=cut
sub restrict_between_alignment_positions {
my ($self, $start, $end, $skip_empty_GenomicAligns, $reference_genomic_align) = @_;
my $genomic_align_tree;
$genomic_align_tree = $self->copy();
$genomic_align_tree->adaptor($self->adaptor);
foreach my $this_node (@{$genomic_align_tree->get_all_nodes}) {
my $genomic_align_group = $this_node->genomic_align_group;
next if (!$genomic_align_group);
my $new_genomic_aligns = [];
foreach my $this_genomic_align (@{$genomic_align_group->get_all_GenomicAligns}) {
my $restricted_genomic_align = $this_genomic_align->restrict($start, $end);
if ($genomic_align_tree->reference_genomic_align eq $this_genomic_align) {
## Update the reference_genomic_align
$genomic_align_tree->reference_genomic_align($restricted_genomic_align);
$genomic_align_tree->reference_genomic_align_node($this_node);
}
if (!$skip_empty_GenomicAligns or
$restricted_genomic_align->dnafrag_start <= $restricted_genomic_align->dnafrag_end
) {
## Always skip composite segments outside of the range of restriction
## The cigar_line will contain only X's
next if ($restricted_genomic_align->cigar_line =~ /^\d*X$/);
$restricted_genomic_align->genomic_align_block($genomic_align_tree);
push(@$new_genomic_aligns, $restricted_genomic_align);
}
}
if (@$new_genomic_aligns) {
$genomic_align_group->{genomic_align_array} = undef;
foreach my $this_genomic_align (@$new_genomic_aligns) {
$genomic_align_group->add_GenomicAlign($this_genomic_align);
}
} else {
$this_node->disavow_parent();
my $reference_genomic_align = $genomic_align_tree->reference_genomic_align;
my $reference_genomic_align_node = $genomic_align_tree->reference_genomic_align_node;
$genomic_align_tree = $genomic_align_tree->minimize_tree();
## Make sure links are not broken after tree minimization
$genomic_align_tree->reference_genomic_align($reference_genomic_align);
$genomic_align_tree->reference_genomic_align->genomic_align_block($genomic_align_tree);
$genomic_align_tree->reference_genomic_align_node($reference_genomic_align_node);
}
}
return $genomic_align_tree;
}
=head2 restrict_between_reference_positions
Arg[1] : [optional] int $start, refers to the reference_dnafrag
Arg[2] : [optional] int $end, refers to the reference_dnafrag
Arg[3] : [optional] Bio::EnsEMBL::Compara::GenomicAlign $reference_GenomicAlign
Arg[4] : [optional] boolean $skip_empty_GenomicAligns [ALWAYS FALSE]
Example : none
Description: restrict this GenomicAlignBlock. It returns a new object unless no
restriction is needed. In that case, it returns the original unchanged
object
It might be the case that the restricted region coincide with a gap
in one or several GenomicAligns. By default these GenomicAligns are
returned with a dnafrag_end equals to its dnafrag_start + 1. For instance,
a GenomicAlign with dnafrag_start = 12345 and dnafrag_end = 12344
correspond to a block which goes on this region from before 12345 to
after 12344, ie just between 12344 and 12345. You can choose to remove
these empty GenomicAligns by setting $skip_empty_GenomicAligns to any
true value.
Returntype : Bio::EnsEMBL::Compara::GenomicAlignBlock object in scalar context. In
list context, returns the previous object and the start and end
positions of the restriction in alignment coordinates (from 1 to
alignment_length)
Exceptions : return undef if reference positions lie outside of the alignment
Caller : general
Status : At risk
=cut
sub restrict_between_reference_positions {
my ($self, $start, $end, $reference_genomic_align, $skip_empty_GenomicAligns) = @_;
my $genomic_align_tree;
$reference_genomic_align ||= $self->reference_genomic_align;
throw("A reference Bio::EnsEMBL::Compara::GenomicAlignTree must be given")
if (!$reference_genomic_align);
my @restricted_genomic_align_tree_params = $self->SUPER::restrict_between_reference_positions($start, $end, $reference_genomic_align, $skip_empty_GenomicAligns);
my $restricted_genomic_align_tree = $restricted_genomic_align_tree_params[0];
#return $self if (!$restricted_genomic_align_tree or $restricted_genomic_align_tree eq $self);
return wantarray ? @restricted_genomic_align_tree_params : $restricted_genomic_align_tree;
}
=head2 copy
Arg : none
Example : my $new_tree = $this_tree->copy()
Description : Create a copy of this Bio::EnsEMBL::Compara::GenomicAlignTree
object
Returntype : Bio::EnsEMBL::Compara::GenomicAlignTree
Exceptions : none
Caller : general
Status : At risk
=cut
sub copy {
my $self = shift(@_);
my $new_copy = $self->SUPER::copy();
$new_copy->genomic_align_group($self->genomic_align_group->copy) if ($self->genomic_align_group);
$new_copy->reference_genomic_align($self->reference_genomic_align) if ($self->reference_genomic_align);
$new_copy->reference_genomic_align_node($self->reference_genomic_align_node) if ($self->reference_genomic_align_node);
return $new_copy;
}
=head2 print
Arg : none
Example : print()
Description : Print the fields in a Bio::EnsEMBL::Compara::GenomicAlignTree
Returntype : none
Exceptions : none
Caller : general
Status : At risk
=cut
sub print {
my $self = shift(@_);
my $level = shift;
my $reference_genomic_align = shift;
if (!$level) {
print STDERR $self->newick_format(), "\n";
$reference_genomic_align = ($self->reference_genomic_align or "");
}
$level++;
my $mark = "- ";
if (grep {$_ eq $reference_genomic_align} @{$self->get_all_GenomicAligns}) {
$mark = "* ";
}
print STDERR " " x $level, $mark,
"[", $self->node_id, "/", ($self->get_original_strand?"+":"-"), "] ",
$self->genomic_align_group->genome_db->name,":",
$self->genomic_align_group->dnafrag->name,":",
$self->genomic_align_group->dnafrag_start,":",
$self->genomic_align_group->dnafrag_end,":",
$self->genomic_align_group->dnafrag_strand,":",
" (", ($self->left_node_id?$self->left_node->node_id."/".$self->left_node->root->node_id:"...."),
" - ", ($self->right_node_id?$self->right_node->node_id."/".$self->right_node->root->node_id:"...."),")\n";
foreach my $this_genomic_align (@{$self->get_all_GenomicAligns}) {
if ($this_genomic_align eq $reference_genomic_align) {
print " " x 8, "* ", $this_genomic_align->aligned_sequence("+FAKE_SEQ"), "\n";
} else {
print " " x 10, $this_genomic_align->aligned_sequence("+FAKE_SEQ"), "\n";
}
}
foreach my $node (sort _sort_children @{$self->children}) {
$node->print($level, $reference_genomic_align);
}
$level--;
}
=head2 get_all_nodes_from_leaves_to_this
Arg[1] : Bio::EnsEMBL::Compara::GenomicAlignTree $all_nodes
Example : my $all_nodes = get_all_nodes_from_leaves_to_this()
Description :
Returntype : Bio::EnsEMBL::Compara::GenomicAlignTree object
Exceptions : none
Caller : general
Status : At risk
=cut
sub get_all_nodes_from_leaves_to_this {
my $self = shift(@_);
my $all_nodes = (shift or []);
foreach my $node (sort _sort_children @{$self->children}) {
$all_nodes = $node->get_all_nodes_from_leaves_to_this($all_nodes);
}
push(@$all_nodes, $self);
return $all_nodes;
}
=head2 get_all_leaves
Title : get_all_leaves
Usage : my @leaves = @{$tree->get_all_leaves};
Function: searching from the given starting node, searches and creates list
of all leaves in this subtree and returns by reference.
This method overwrites the parent method because it sorts
the leaves according to their node_id. Here, we use this method
to get all leaves in another sorting function. Not only it doesn't
make much sense to sort something that will be sorted again, but
it can also produce some Perl errors as sort methods uses $a and
$b which are package global variables.
Example :
Returns : reference to list of NestedSet objects (all leaves)
Args : none
Status : At risk
=cut
sub get_all_leaves {
my $self = shift;
my $leaves = {};
$self->_recursive_get_all_leaves($leaves);
my @leaf_list = values(%{$leaves});
return \@leaf_list;
}
=head2 _sort_children
Arg : none
Example : sort _sort_children @$children
Description : sort function for sorting the nodes of a Bio::EnsEMBL::Compara::GenomicAlignTree object
Returntype : int (-1,0,1)
Exceptions : none
Caller : general
Status : At risk
=cut
sub _sort_children {
my $reference_genomic_align;
if (defined ($a->root) && defined($b->root) && $a->root eq $b->root and $a->root->reference_genomic_align) {
$reference_genomic_align = $a->root->reference_genomic_align;
}
## Reference GenomicAlign based sorting
if ($reference_genomic_align) {
if (grep {$_ eq $reference_genomic_align} map {@{$_->get_all_GenomicAligns}}
@{$a->get_all_nodes}) {
return -1;
} elsif (grep {$_ eq $reference_genomic_align} map {@{$_->get_all_GenomicAligns}}
@{$b->get_all_nodes}) {
return 1;
}
}
## Species name based sorting
my $species_a = $a->_name_for_sorting;
my $species_b = $b->_name_for_sorting;
return $species_a cmp $species_b;
}
=head2 _name_for_sorting
Arg : none
Example : my $species_a = $a->_name_for_sorting;
Description : if the node is a leaf, create a name based on the species
name, dnafrag name, group_id and the start position. If the
node is an internal node, create a name based on the species
name, dnafrag name and the start position
Returntype : string
Exceptions : none
Caller : _sort_children
Status : At risk
=cut
sub _name_for_sorting {
my ($self) = @_;
my $name;
if ($self->is_leaf) {
$name = sprintf("%s.%s.%s.%020d",
$self->genomic_align_group->genome_db->name,
$self->genomic_align_group->dnafrag->name,
($self->genomic_align_group->dbID or
$self->genomic_align_group->{original_dbID} or 0),
$self->genomic_align_group->dnafrag_start);
} else {
$name = join(" - ", sort map {sprintf("%s.%s.%020d",
$_->genomic_align_group->genome_db->name,
$_->genomic_align_group->dnafrag->name,
$_->genomic_align_group->dnafrag_start)} @{$self->get_all_leaves});
}
return $name;
}
=head2 reverse_complement
Args : none
Example : none
Description: reverse complement the tree,
modifying dnafrag_strand and cigar_line of each GenomicAlign in consequence
Returntype : none
Exceptions : none
Caller : general
Status : At risk
=cut
sub reverse_complement {
my ($self) = @_;
if (defined($self->{_original_strand})) {
$self->{_original_strand} = 1 - $self->{_original_strand};
} else {
$self->{_original_strand} = 0;
}
foreach my $this_node (@{$self->get_all_nodes}) {
my $genomic_align_group = $this_node->genomic_align_group;
next if (!$genomic_align_group);
my $gas = $genomic_align_group->get_all_GenomicAligns;
foreach my $ga (@{$gas}) {
$ga->reverse_complement;
}
}
}
sub length {
my ($self, $length) = @_;
if (defined($length)) {
$self->{'length'} = $length;
} elsif (!defined($self->{'length'})) {
# Try to get the ID from other sources...
if (defined($self->{'adaptor'}) and defined($self->dbID)) {
# ...from the database, using the dbID of the Bio::Ensembl::Compara::GenomicAlignBlock object
$self->adaptor->retrieve_all_direct_attributes($self);
} elsif (@{$self->get_all_GenomicAligns} and $self->get_all_GenomicAligns->[0]->aligned_sequence("+FAKE_SEQ")) {
$self->{'length'} = CORE::length($self->get_all_GenomicAligns->[0]->aligned_sequence("+FAKE_SEQ"));
} else {
foreach my $this_node (@{$self->get_all_nodes}) {
my $genomic_align_group = $this_node->genomic_align_group;
next if (!$genomic_align_group);
$self->{'length'} = CORE::length($genomic_align_group->get_all_GenomicAligns->[0]->aligned_sequence("+FAKE_SEQ"));
last;
}
}
}
return $self->{'length'};
}
1;
]]>