remove distance tree stuff from Stemma object

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

diff --git a/lib/Text/Tradition/Stemma.pm b/lib/Text/Tradition/Stemma.pm
index b875e4e..3969c6d 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.
@@ -299,47 +286,6 @@ 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 {
-    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 );
-}
-
 sub throw {
        Text::Tradition::Error->throw( 
                'ident' => 'Stemma error',