X-Git-Url: http://git.shadowcat.co.uk/gitweb/gitweb.cgi?a=blobdiff_plain;f=t%2Fstemma.t;h=404b686bbeab8a9368c0fd1e9fbc0aaf6b1696bb;hb=ab06f3edf9045dc9a24ee138df7ae0b9bb141098;hp=6f3e7dbd54fb9106b1af90a0d6a23b40888f3cf5;hpb=68454b71e5a66972515258d6312f6355ee0536f4;p=scpubgit%2Fstemmatology.git

diff --git a/t/stemma.t b/t/stemma.t
index 6f3e7db..404b686 100644
--- a/t/stemma.t
+++ b/t/stemma.t
@@ -5,7 +5,7 @@ use File::Which;
 use Test::More;
 use lib 'lib';
 use Text::Tradition;
-use Text::Tradition::StemmaUtil qw/ phylip_pars_input /;
+use Text::Tradition::StemmaUtil qw/ character_input phylip_pars parse_newick /;
 use XML::LibXML;
 use XML::LibXML::XPathContext;
 
@@ -18,53 +18,48 @@ my $tradition = Text::Tradition->new(
     );
 # Set up some relationships
 my $c = $tradition->collation;
-$c->add_relationship( 'n25', 'n26', { 'type' => 'spelling' } );
-$c->add_relationship( 'n9', 'n23', { 'type' => 'spelling' } );
-$c->add_relationship( 'n8', 'n13', { 'type' => 'spelling' } );
+$c->add_relationship( 'n23', 'n24', { 'type' => 'spelling' } );
+$c->add_relationship( 'n9', 'n10', { 'type' => 'spelling' } );
+$c->add_relationship( 'n12', 'n13', { 'type' => 'spelling' } );
 $c->calculate_ranks();
 
-my $stemma = $tradition->add_stemma( 't/data/simple.dot' );
+my $stemma = $tradition->add_stemma( dotfile => 't/data/simple.dot' );
 
 # Test for object creation
 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 = phylip_pars_input( $c->make_alignment_table() );
+my $mstr = character_input( $c->alignment_table() );
  ## check number of rows
-my $expected = "\t3\t18\n";
-$expected .= 'A         AAAAAAAXAAAAAAAAAA
-B         AXXXAAAAAABABAABAA
-C         AXXXAAAAABAAAAAXBB';
-$expected .= "\n";
-is( $m, $expected, "Got the right pars input" );
-# is( scalar @$m, 3, "Found three witnesses in char matrix" );
-#  ## check number of columns
-# is( scalar( @{$m->[0]} ), 19, "Found 18 rows plus sigla in char matrix" );
-#  ## check matrix
-# my %expected = (
-# 	'A' => 'AAAAAAAXAAAAAAAAAA',
-# 	'B' => 'AXXXAAAAAABABAABAA',
-# 	'C' => 'AXXXAAAAABAAAAAXBB',
-# 	);
-# my @wits = map { shift @$_; } @$m;
-# map { s/\s+//g } @wits;
-# foreach my $i ( 0 .. $#wits ) {
-# 	my $w = $wits[$i];
-# 	is( join( '', @{$m->[$i]} ), $expected{$w}, "Row for witness $w is correct" );
-# }
+my @mlines = split( "\n", $mstr );
+my $msig = shift @mlines;
+my( $rows, $chars ) = $msig =~ /(\d+)\s+(\d+)/;
+is( $rows, 3, "Found three witnesses in char matrix" );
+ ## check number of columns
+is( $chars, 18, "Found 18 rows plus sigla in char matrix" );
+ ## check matrix
+my %expected = (
+	'A' => 'AAAAAAAXAAAAAAAAAA',
+	'B' => 'AXXXAAAAAABABAABAA',
+	'C' => 'AXXXAAAAABAAAAAXBB',
+	);
+foreach my $ml ( @mlines ) {
+	my( $wit, $chars ) = split( /\s+/, $ml );
+	is( $chars, $expected{$wit}, "Row for witness $wit is correct" );
+}
 
 # Test that pars runs
 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;
-    
+    my $newick = phylip_pars( $mstr );
+    ok( $newick, "pars ran successfully" );
+
+	my $trees = parse_newick( $newick );
     # Test that we get a tree
-    is( scalar @{$stemma->distance_trees}, 1, "Got a single tree" );
+    is( scalar @$trees, 1, "Got a single tree" );
     # Test that the tree has all our witnesses
-    $tree = $stemma->distance_trees->[0];
+    my $tree = $trees->[0];
     my @leaves = grep { $tree->degree( $_ ) == 1 } $tree->vertices;
     is( scalar @leaves, 3, "All witnesses in the tree" );
 }