add clear_witness functionality, use it, and update Collation pod

[scpubgit/stemmatology.git] / t / stemma.t

diff --git a/t/stemma.t b/t/stemma.t
index 95b25e3..8d2fd6e 100644 (file)
--- a/t/stemma.t
+++ b/t/stemma.t
@@ -1,9 +1,11 @@
 #!/usr/bin/perl
 
 use strict; use warnings;
+use File::Which;
 use Test::More;
 use lib 'lib';
 use Text::Tradition;
+use Text::Tradition::StemmaUtil qw/ make_character_matrix /;
 use XML::LibXML;
 use XML::LibXML::XPathContext;
 
@@ -28,7 +30,7 @@ ok( $stemma->isa( 'Text::Tradition::Stemma' ), 'Got the right sort of object' );
 is( $stemma->graph, '1-2,1-A,2-B,2-C', "Got the correct graph" );
 
 # Test for character matrix creation
-my $m = $stemma->make_character_matrix();
+my $m = make_character_matrix( $c->make_alignment_table() );
  ## check number of rows
 is( scalar @$m, 3, "Found three witnesses in char matrix" );
  ## check number of columns
@@ -47,16 +49,19 @@ foreach my $i ( 0 .. $#wits ) {
 }
 
 # Test that pars runs
-my( $status, $tree ) = $stemma->run_phylip_pars();
-ok( $status, "pars ran successfully" );
-print STDERR "Error was $tree\n" unless $status;
-
-# Test that we get a tree
-is( scalar @{$stemma->distance_trees}, 1, "Got a single tree" );
-# Test that the tree has all our witnesses
-$tree = $stemma->distance_trees->[0];
-my @leaves = grep { $tree->degree( $_ ) == 1 } $tree->vertices;
-is( scalar @leaves, 3, "All witnesses in the tree" );
+SKIP: {
+    skip "pars not in path", 3 unless File::Which::which('pars');
+    my( $status, $tree ) = $stemma->run_phylip_pars();
+    ok( $status, "pars ran successfully" );
+    print STDERR "Error was $tree\n" unless $status;
+    
+    # Test that we get a tree
+    is( scalar @{$stemma->distance_trees}, 1, "Got a single tree" );
+    # Test that the tree has all our witnesses
+    $tree = $stemma->distance_trees->[0];
+    my @leaves = grep { $tree->degree( $_ ) == 1 } $tree->vertices;
+    is( scalar @leaves, 3, "All witnesses in the tree" );
+}
 
 # Test our dot output
 my $display = $stemma->as_dot();
@@ -67,4 +72,4 @@ my $editable = $stemma->editable();
 ok( $editable =~ /digraph/, "Got a dot edit graph" );
 ok( $editable =~ /hypothetical/, "Graph contains an edit class" );
 
-done_testing();
\ No newline at end of file
+done_testing();