GUI: Add menu option to merge tree knuckle nodes

Updates #814
shawnlaffan · Sep 12, 2022 · aefb514 · aefb514
1 parent 2baf4e8
commit aefb514
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diff --git a/bin/ui/wndMain.ui b/bin/ui/wndMain.ui
@@ -542,6 +542,14 @@ Assumes a dissimilarity matrix, so take care.</property>
             <signal handler="on_trim_tree_to_lca" name="activate"/>
           </object>
         </child>
+        <child>
+          <object class="GtkAction" id="menu_merge_tree_knuckle_nodes">
+            <property name="name">menu_merge_tree_knuckle_nodes</property>
+            <property name="tooltip" translatable="yes">Merge single-child (knuckle) nodes with their children</property>
+            <property name="label" translatable="yes">Merge knuckle nodes</property>
+            <signal handler="on_tree_merge_knuckle_nodes" name="activate"/>
+          </object>
+        </child>
         <child>
           <object class="GtkAction" id="menu_range_weight_tree_branches">
             <property name="name">menu_range_weight_tree_branches</property>
@@ -808,6 +816,7 @@ This cannot be undone.  </property>
           <menuitem action="menu_convert_phylogeny_to_matrix"/>
           <menuitem action="menu_trim_tree_to_basedata"/>
           <menuitem action="menu_trim_tree_to_lca"/>
+          <menuitem action="menu_merge_tree_knuckle_nodes"/>
           <menuitem action="menu_range_weight_tree_branches"/>
           <menuitem action="menu_equalise_tree_branches"/>
           <menuitem action="menu_rescale_tree_branches2"/>

diff --git a/lib/Biodiverse/GUI/Callbacks.pm b/lib/Biodiverse/GUI/Callbacks.pm
@@ -349,6 +349,9 @@ my %data_funcs = (
     on_trim_tree_to_lca => {
         METHOD => 'do_trim_tree_to_lca',
     },
+    on_tree_merge_knuckle_nodes => {
+        METHOD => 'do_tree_merge_knuckle_nodes',
+    },
     on_trim_matrix_to_basedata => {
         METHOD => 'do_trim_matrix_to_basedata',
     },

diff --git a/lib/Biodiverse/GUI/GUIManager.pm b/lib/Biodiverse/GUI/GUIManager.pm
@@ -1944,6 +1944,75 @@ sub do_trim_tree_to_lca {
 }
 
 
+#  too much duplicated code in here
+sub do_tree_merge_knuckle_nodes {
+    my $self = shift;
+    my %args = @_;
+
+    my $phylogeny = $self->{project}->get_selected_phylogeny;
+
+    if ( !defined $phylogeny ) {
+        Biodiverse::GUI::YesNoCancel->run(
+            {
+                header      => 'no tree selected',
+                hide_yes    => 1,
+                hide_no     => 1,
+                hide_cancel => 1,
+            }
+        );
+
+        return 0;
+    }
+
+    # Show the Get Name dialog
+    my ( $dlgxml, $dlg ) = $self->get_dlg_duplicate();
+    $dlg->set_transient_for( $self->get_object('wndMain') );
+
+    my $txt_name = $dlgxml->get_object('txtName');
+    my $name     = $phylogeny->get_param('NAME');
+
+    my $suffix = $args{suffix} || '_noknuckles';
+
+    # If ends with $suffix followed by a number then increment it
+    if ( $name =~ /(.*_$suffix)([0-9]+)$/ ) {
+        $name = $1 . ( $2 + 1 );
+    }
+    else {
+        $name .= "_${suffix}1";
+    }
+    $txt_name->set_text($name);
+
+    my $response    = $dlg->run();
+    my $chosen_name = $txt_name->get_text;
+
+    $dlg->destroy;
+
+    return if $response ne 'ok';    #  they chickened out
+
+    #  could be more efficient?
+    my $new_tree = $phylogeny->clone;
+    $new_tree->delete_cached_values;
+    $new_tree->merge_knuckle_nodes;
+
+    $new_tree->set_param( NAME => $chosen_name );
+
+    #  now we add it if it is not already in the list
+    #  otherwise we select it
+    my $phylogenies = $self->{project}->get_phylogeny_list;
+
+    my $in_list = grep { $_ eq $new_tree } @$phylogenies;
+
+    if ($in_list) {
+        $self->{project}->select_phylogeny($new_tree);
+    }
+    else {
+        $self->{project}->add_phylogeny( $new_tree, 0 );
+    }
+
+    return;
+}
+
+
 sub do_tree_equalise_branch_lengths {
     my $self = shift;
     my %args = @_;