use Test::More;
use lib 'lib';
use Text::Tradition;
+use Text::Tradition::StemmaUtil qw/ character_input phylip_pars parse_newick /;
use XML::LibXML;
use XML::LibXML::XPathContext;
);
# 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 = $stemma->make_character_matrix();
+my $mstr = character_input( $c->alignment_table() );
## check number of rows
-is( scalar @$m, 3, "Found three witnesses in char matrix" );
+my @mlines = split( "\n", $mstr );
+my $msig = shift @mlines;
+my( $rows, $chars ) = $msig =~ /(\d+)\s+(\d+)/;
+is( $rows, 3, "Found three witnesses in char matrix" );
## check number of columns
-is( scalar( @{$m->[0]} ), 19, "Found 18 rows plus sigla in char matrix" );
+is( $chars, 18, "Found 18 rows plus sigla in char matrix" );
## check matrix
my %expected = (
'A' => 'AAAAAAAXAAAAAAAAAA',
'B' => 'AXXXAAAAAABABAABAA',
'C' => 'AXXXAAAAABAAAAAXBB',
);
-my @wits = map { shift @$_; } @$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" );
+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 installed", 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;
-
+ skip "pars not in path", 3 unless File::Which::which('pars');
+ 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" );
}