reduce calls to TreeNode->get_length

The Tree class has a method to get a hash of lengths.
This is cached so later calls are very cheap.

By using this we can avoid many repeated calls
to the get_length method.  As fast as it is,
they can add up across randomisations.

lib/Biodiverse/Indices/Phylogenetic.pm

@@ -1783,14 +1783,14 @@ sub get_inverse_range_weighted_path_lengths {
     my %args = @_;
 
     my $tree = $args{tree_ref};
-    my $node_ranges = $args{node_range};
-
+    \my %node_ranges = $args{node_range};
+    \my %node_length_hash = $tree->get_node_length_hash;
+
     my %range_weighted;
-
-    foreach my $node ($tree->get_node_refs) {
-        my $name = $node->get_name;
-        next if !$node_ranges->{$name};
-        $range_weighted{$name} = $node->get_length / $node_ranges->{$name};
+
+    foreach my $name (keys %node_length_hash) {
+        next if !$node_ranges{$name};
+        $range_weighted{$name} = $node_length_hash{$name} / $node_ranges{$name};
     }
 
     my %results = (inverse_range_weighted_node_lengths => \%range_weighted);

lib/Biodiverse/Indices/PhylogeneticRelative.pm

@@ -656,21 +656,20 @@ sub get_metadata_get_trimmed_tree_eq_branch_lengths_node_length_hash {
     return $metadata_class->new(\%metadata);
 }
 
-#  should just be a wrapper around Tree::get_node_length_hash
 sub get_trimmed_tree_eq_branch_lengths_node_length_hash {
     my $self = shift;
     my %args = @_;
 
     my $tree_ref = $args{TREE_REF_EQUALISED_BRANCHES_TRIMMED}
       // croak 'Missing TREE_REF_EQUALISED_BRANCHES_TRIMMED arg';
-    my $node_hash = $tree_ref->get_node_hash;
-
-    my (%len_hash, $nonzero_length);
-    foreach my $node_name (keys %$node_hash) {
-        my $node_ref = $node_hash->{$node_name};
-        my $length   = $node_ref->get_length;
-        $len_hash{$node_name} = $length;
-        $nonzero_length ||= $length;
+
+    \my %len_hash = $tree_ref->get_node_length_hash;
+
+    my $nonzero_length;
+
+    foreach my $len (values %len_hash) {
+        $nonzero_length ||= $len;
+        last if $len;
     }
 
     my %results = (
@@ -737,14 +736,14 @@ sub get_trimmed_tree_range_inverse_hash_nonzero_len {
     my %args = @_;
 
     my $tree        = $args{trimmed_tree};
-    my $node_ranges = $args{node_range};
+    \my %node_ranges = $args{node_range};
+    \my %length_hash = $tree->get_node_length_hash;
 
     my %range_weighted;
 
-    foreach my $name (keys %$node_ranges) {
-        my $range = $node_ranges->{$name} || next;
-        my $numerator = $tree->get_node_ref_aa($name)->get_length ? 1 : 0;
-        $range_weighted{$name} = $numerator / $range;
+    foreach my $name (keys %node_ranges) {
+        my $range = $node_ranges{$name} || next;
+        $range_weighted{$name} = ($length_hash{$name} ? 1 : 0) / $range;
     }
 
     my %results = (trimmed_tree_range_inverse_hash_nonzero_len => \%range_weighted);

lib/Biodiverse/Tree.pm

@@ -3095,20 +3095,17 @@ sub clone_tree_with_equalised_branch_lengths {
 
     my $name = $args{name} // ( $self->get_param('NAME') . ' EQ' );
 
-    my $non_zero_len = $args{node_length};
+    my $non_zero_len = $args{node_length}
+     // ($self->get_total_tree_length / ( $self->get_nonzero_length_count || 1 ));
 
-    if ( !defined $non_zero_len ) {
-        # my $non_zero_node_count = grep { $_->get_length } $self->get_node_refs;
-        #  this caches
-        my $non_zero_node_count = $self->get_nonzero_length_count;
-        $non_zero_len =
-          $self->get_total_tree_length / ( $non_zero_node_count || 1 );
-    }
+    \my %orig_node_length_hash = $self->get_node_length_hash;
 
     my $new_tree = $self->clone_without_caches;
+    \my %new_node_hash = $new_tree->get_node_hash;
 
-    foreach my $node ( $new_tree->get_node_refs ) {
-        $node->set_length_aa ( $node->get_length ? $non_zero_len : 0 );
+    foreach my $name ( keys %new_node_hash ) {
+        my $node = $new_node_hash{$name};
+        $node->set_length_aa ( $orig_node_length_hash{$name} ? $non_zero_len : 0 );
     }
     $new_tree->rename( new_name => $name );