Skip to content

Commit

Permalink
MPD/MNTD: refactor path length search into a sub
Browse files Browse the repository at this point in the history 
Substantially cleans up the calling code.
Should not make too much difference for speed
given other optimisations mean most of the
matrix is pre-populated, so this is not called
directly very often (relatively speaking).

Updates #786
  • Loading branch information
@shawnlaffan
shawnlaffan committed Apr 28, 2021
1 parent 3034465 commit d852492
Showing 1 changed file with 117 additions and 81 deletions.
198 changes: 117 additions & 81 deletions lib/Biodiverse/Indices/PhyloCom.pm
View file
Original file line number Diff line number Diff line change
Expand Up @@ -303,12 +303,22 @@ sub _calc_phylo_mpd_mntd {
my (@mpd_path_lengths, @mntd_path_lengths, @mpd_wts, @mntd_wts);


\my %last_shared_ancestor_mx = $args{PHYLO_LCA_MX}
my $last_shared_ancestor_mx = $args{PHYLO_LCA_MX}
|| croak "Argument PHYLO_LCA_MX not defined";

\my %path_cache = $args{MPD_MNTD_CUM_PATH_LENGTH_TO_ROOT_CACHE};

my $most_probable_lca_depths = $tree_ref->get_most_probable_lca_depths;

# make the code cleaner below
my %common_args_for_path_call = (
tree_ref => $tree_ref,
path_matrix => \%mx,
path_cache
=> $args{MPD_MNTD_CUM_PATH_LENGTH_TO_ROOT_CACHE},
last_shared_ancestor_mx
=> $last_shared_ancestor_mx,
most_probable_lca_depths
=> scalar $tree_ref->get_most_probable_lca_depths,
nri_nti_generation => $nri_nti_generation,
tree_is_ultrametric => $tree_is_ultrametric,
);

# Loop over all possible pairs
BY_LABEL:
Expand Down Expand Up @@ -337,82 +347,14 @@ sub _calc_phylo_mpd_mntd {
BY_LABEL2:
foreach my $label2 (@labels2) {

#my $path_length = $mx->get_defined_value_aa ($label1, $label2);
my $path_length = $mx_label1{$label2} // $mx{$label2}{$label1};

if (!defined $path_length) { # need to calculate it

# ancestor mx only really needed for non-ultrametric, non-NRI
# and is populated below
my $last_ancestor
= $last_shared_ancestor_mx{$label1}{$label2}
// $last_shared_ancestor_mx{$label2}{$label1};

my $fill_last_ancestor_cache = !$last_ancestor;

$last_ancestor
//= $tree_ref->get_last_shared_ancestor_for_nodes (
node_names => {$label1 => 1, $label2 => 1},
most_probable_lca_depths => $most_probable_lca_depths,
);
# target index is one below the last common ancestor
# last ancestor is one more than its depth from the end,
# so we subtract 2
my $ancestor_idx = -$last_ancestor->get_depth - 2;
my $path_lens1 = $path_cache{$label1}
//= $self->_get_node_cum_path_sum_to_root(
tree_ref => $tree_ref,
label => $label1,
);
$path_length += $path_lens1->[$ancestor_idx];
if ($tree_is_ultrametric) {
$path_length *= 2;
# prepopulate the matrix for the LCA
$self->_add_last_ancestor_um_path_lens_to_matrix (
matrix => \%mx,
last_ancestor => $last_ancestor,
path_length => $path_length,
);
}
elsif ($nri_nti_generation) {
$self->_add_last_ancestor_path_lens_to_matrix (
matrix => \%mx,
path_cache => \%path_cache,
last_ancestor => $last_ancestor,
tree_ref => $tree_ref,
ancestor_idx => $ancestor_idx,
);
# now grab it
$path_length = $mx{$label1}{$label2} // $mx{$label2}{$label1};
}
else {
# non-ultrametric MPD/MNTD, calc on-demand
my $path_lens2 = $path_cache{$label2}
//= $self->_get_node_cum_path_sum_to_root(
tree_ref => $tree_ref,
label => $label2,
);
$path_length += $path_lens2->[$ancestor_idx];
# try to keep the matrix triangular
# and thus speed up accesses above
if ($label1 le $label2) {
$mx{$label1}{$label2} = $path_length;
}
else {
$mx{$label2}{$label1} = $path_length;
}
if ($fill_last_ancestor_cache) {
$self->_add_to_last_ancestor_cache(
last_ancestor => $last_ancestor,
last_ancestor_mx => \%last_shared_ancestor_mx,
);
}
}
}
my $path_length
= $mx_label1{$label2}
// $mx{$label2}{$label1}
// $self->get_phylo_path_length_between_labels (
label1 => $label1,
label2 => $label2,
%common_args_for_path_call,
);

push @path_lengths_this_node, $path_length;

Expand Down Expand Up @@ -475,6 +417,100 @@ sub _calc_phylo_mpd_mntd {
return wantarray ? %results : \%results;
}


sub get_phylo_path_length_between_labels {
my ($self, %args) = @_;

my $label1 = $args{label1};
my $label2 = $args{label2};
my $tree_ref = $args{tree_ref};
my $tree_is_ultrametric
= exists $args{tree_is_ultrametric}
? $args{tree_is_ultrametric}
: $tree_ref->is_ultrametric;

my $nri_nti_generation = $args{nri_nti_generation};

\my %mx = $args{path_matrix};
\my %path_cache = $args{path_cache};
\my %last_shared_ancestor_mx
= $args{last_shared_ancestor_mx};

# ancestor mx only really needed for non-ultrametric, non-NRI
# and is populated below
my $last_ancestor
= $last_shared_ancestor_mx{$label1}{$label2}
// $last_shared_ancestor_mx{$label2}{$label1};

my $fill_last_ancestor_cache = !$last_ancestor;

$last_ancestor
//= $tree_ref->get_last_shared_ancestor_for_nodes (
node_names => {$label1 => 1, $label2 => 1},
most_probable_lca_depths => $args{most_probable_lca_depths},
);
# target index is one below the last common ancestor
# last ancestor is one more than its depth from the end,
# so we subtract 2
my $ancestor_idx = -$last_ancestor->get_depth - 2;
my $path_lens1 = $path_cache{$label1}
//= $self->_get_node_cum_path_sum_to_root(
tree_ref => $tree_ref,
label => $label1,
);
my $path_length = $path_lens1->[$ancestor_idx];
if ($tree_is_ultrametric) {
$path_length *= 2;
# prepopulate the matrix for the LCA
$self->_add_last_ancestor_um_path_lens_to_matrix (
matrix => \%mx,
last_ancestor => $last_ancestor,
path_length => $path_length,
);
}
elsif ($nri_nti_generation) {
$self->_add_last_ancestor_path_lens_to_matrix (
matrix => \%mx,
path_cache => \%path_cache,
last_ancestor => $last_ancestor,
tree_ref => $tree_ref,
ancestor_idx => $ancestor_idx,
);
# now grab it
$path_length = $mx{$label1}{$label2} // $mx{$label2}{$label1};
}
else {
# non-ultrametric MPD/MNTD, calc on-demand
my $path_lens2 = $path_cache{$label2}
//= $self->_get_node_cum_path_sum_to_root(
tree_ref => $tree_ref,
label => $label2,
);
$path_length += $path_lens2->[$ancestor_idx];
# try to keep the matrix triangular
# and thus speed up accesses above
if ($label1 le $label2) {
$mx{$label1}{$label2} = $path_length;
}
else {
$mx{$label2}{$label1} = $path_length;
}
if ($fill_last_ancestor_cache) {
$self->_add_to_last_ancestor_cache(
last_ancestor => $last_ancestor,
last_ancestor_mx => \%last_shared_ancestor_mx,
);
}
}
return $path_length;
}
# For an ultrametric tree,
# populate the matrix for all pairs
# that share this common ancestor,
Expand Down

0 comments on commit d852492

Please sign in to comment.