more robust boolean value checking in tests

[scpubgit/stemmatology.git] / lib / Text / Tradition / Stemma.pm

diff --git a/lib/Text/Tradition/Stemma.pm b/lib/Text/Tradition/Stemma.pm
index b875e4e..24d9e84 100644 (file)
--- a/lib/Text/Tradition/Stemma.pm
+++ b/lib/Text/Tradition/Stemma.pm
@@ -107,20 +107,7 @@ has graph => (
     isa => 'Graph',
     predicate => 'has_graph',
     );
-    
-has distance_trees => (
-    is => 'ro',
-    isa => 'ArrayRef[Graph]',
-    writer => '_save_distance_trees',
-    predicate => 'has_distance_trees',
-    );
-    
-has distance_program => (
-       is => 'rw',
-       isa => 'Str',
-       default => '',
-       );
-    
+        
 sub BUILD {
     my( $self, $args ) = @_;
     # If we have been handed a dotfile, initialize it into a graph.
@@ -217,14 +204,17 @@ sub as_dot {
     return join( "\n", @dotlines );
 }
 
-=head2 editable
+=head2 editable( $linesep )
 
-Returns a version of the graph rendered in our definition format.
+Returns a version of the graph rendered in our definition format.  The
+$linesep argument defaults to newline; set it to the empty string or to
+a space if the result is to be sent via JSON.
 
 =cut
 
 sub editable {
        my $self = shift;
+       my $join = shift || "\n";
        my @dotlines;
        push( @dotlines, 'digraph stemma {' );
        my @real; # A cheap sort
@@ -246,7 +236,7 @@ sub editable {
                push( @dotlines, "  $from -> $to;" );
        }
     push( @dotlines, '}' );
-    return join( "\n", @dotlines );
+    return join( $join, @dotlines );
 }
 
 sub _make_dotline {
@@ -299,45 +289,12 @@ sub witnesses {
     return @wits;
 }
 
-=head2 distance_trees( program => $program )
-
-Returns a set of undirected graphs, which are the result of running a distance
-tree calculation program on the collation.  Currently the only supported
-program is phylip_pars.
-
-=cut
-
-#### Methods for calculating phylogenetic trees ####
-
-before 'distance_trees' => sub {
+sub hypotheticals {
     my $self = shift;
-    my %args = (
-       'program' => 'phylip_pars',
-       @_ );
-    # TODO allow specification of method for calculating distance tree
-    if( !$self->has_distance_trees
-       || $args{'program'} ne $self->distance_program ) {
-        # We need to make a tree before we can return it.
-        my $dsub = 'run_' . $args{'program'};
-        my $result = $self->$dsub(); # this might throw an error - catch it?
-               # Save the resulting trees
-               my $trees = parse_newick( $result );
-               $self->_save_distance_trees( $trees );
-               $self->distance_program( $args{'program'} );
-    }
-};
-
-=head2 run_phylip_pars
-
-Runs Phylip Pars on the collation, returning the results in Newick format.
-Used for the distance_trees calculation.
-
-=cut
-
-sub run_phylip_pars {
-       my $self = shift;
-       my $cdata = character_input( $self->collation->make_alignment_table() );
-       return phylip_pars( $cdata );
+    my @wits = grep 
+       { $self->graph->get_vertex_attribute( $_, 'class' ) eq 'hypothetical' }
+        $self->graph->vertices;
+    return @wits;
 }
 
 sub throw {