use Graph::Reader::Dot;
use IPC::Run qw/ run binary /;
use Text::Tradition::Error;
-use Text::Tradition::StemmaUtil qw/ character_input phylip_pars parse_newick /;
use Moose;
=head1 NAME
=item * dot - A filehandle open to a DOT representation of the stemma graph.
+=item * graph - If no DOT specification is given, you can pass a Graph object
+instead. The vertices of the graph should have an attribute 'class' set to
+either of the values 'extant' or 'hypothetical'.
+
+=item * is_undirected - If the graph specification (or graph object) is for an
+undirected graph (e.g. a phylogenetic tree), this should be set.
+
=back
=begin testing
use_ok( 'Text::Tradition::Stemma' );
# Try to create a bad graph
+TODO: {
+ local $TODO = "cannot use stdout redirection trick with FastCGI";
my $baddotfh;
-open( $baddotfh, 't/data/besoin_bad.dot' ) or die "Could not open test dotfile";
-try {
- my $stemma = Text::Tradition::Stemma->new( dot => $baddotfh );
- ok( 0, "Created broken stemma from dotfile with syntax error" );
-} catch( Text::Tradition::Error $e ) {
- like( $e->message, qr/^Error trying to parse/, "Syntax error in dot threw exception" );
+ open( $baddotfh, 't/data/besoin_bad.dot' ) or die "Could not open test dotfile";
+ try {
+ my $stemma = Text::Tradition::Stemma->new( dot => $baddotfh );
+ ok( 0, "Created broken stemma from dotfile with syntax error" );
+ } catch( Text::Tradition::Error $e ) {
+ like( $e->message, qr/^Error trying to parse/, "Syntax error in dot threw exception" );
+ }
}
# Create a good graph
}
ok( $found_unicode_sigil, "Found a correctly encoded Unicode sigil" );
+# TODO Create stemma from graph, create stemma from undirected graph,
+# create stemma from incompletely-specified graph
+
=end testing
=cut
has collation => (
is => 'ro',
isa => 'Text::Tradition::Collation',
- clearer => 'clear_collation',
+ clearer => 'clear_collation', # interim measure to remove refs in DB
weak_ref => 1,
);
isa => 'Graph',
predicate => 'has_graph',
);
+
+has is_undirected => (
+ is => 'ro',
+ isa => 'Bool',
+ default => undef,
+ writer => 'set_undirected',
+ );
sub BUILD {
my( $self, $args ) = @_;
# If we have been handed a dotfile, initialize it into a graph.
if( exists $args->{'dot'} ) {
$self->_graph_from_dot( $args->{'dot'} );
- }
+ } else {
+ }
}
+before 'graph' => sub {
+ my $self = shift;
+ if( @_ ) {
+ # Make sure all unclassed graph nodes are marked extant.
+ my $g = $_[0];
+ throw( "Cannot set graph to a non-Graph object" )
+ unless ref( $g ) eq 'Graph';
+ foreach my $v ( $g->vertices ) {
+ unless( $g->has_vertex_attribute( $v, 'class' ) ) {
+ $g->set_vertex_attribute( $v, 'class', 'extant' );
+ }
+ }
+ $self->set_undirected( $g->is_undirected );
+ }
+};
+
sub _graph_from_dot {
my( $self, $dotfh ) = @_;
my $reader = Graph::Reader::Dot->new();
throw( "Failed to create graph from dot" );
}
$self->graph( $graph );
- # Go through the nodes and set any non-hypothetical node to extant.
- foreach my $v ( $self->graph->vertices ) {
- $self->graph->set_vertex_attribute( $v, 'class', 'extant' )
- unless $self->graph->has_vertex_attribute( $v, 'class' );
- }
}
=head1 METHODS
@edgeopts{ keys %{$opts->{'edge'}} } = values %{$opts->{'edge'}}
if $opts->{'edge'};
+ my $gdecl = $graph->is_directed ? 'digraph' : 'graph';
my @dotlines;
- push( @dotlines, 'digraph stemma {' );
+ push( @dotlines, "$gdecl stemma {" );
## Print out the global attributes
push( @dotlines, _make_dotline( 'graph', %graphopts ) ) if keys %graphopts;
push( @dotlines, _make_dotline( 'edge', %edgeopts ) ) if keys %edgeopts;
# Add each of our edges.
foreach my $e ( $graph->edges ) {
my( $from, $to ) = map { _dotquote( $_ ) } @$e;
- push( @dotlines, " $from -> $to;" );
+ my $connector = $graph->is_directed ? '->' : '--';
+ push( @dotlines, " $from $connector $to;" );
}
push( @dotlines, '}' );
# Create the graph
my $join = ( $opts && exists $opts->{'linesep'} ) ? $opts->{'linesep'} : "\n";
+ my $gdecl = $graph->is_undirected ? 'graph' : 'digraph';
my @dotlines;
- push( @dotlines, 'digraph stemma {' );
+ push( @dotlines, "$gdecl stemma {" );
my @real; # A cheap sort
foreach my $n ( sort $graph->vertices ) {
my $c = $graph->get_vertex_attribute( $n, 'class' );
}
foreach my $e ( sort _by_vertex $graph->edges ) {
my( $from, $to ) = map { _dotquote( $_ ) } @$e;
- push( @dotlines, " $from -> $to;" );
+ my $conn = $graph->is_undirected ? '--' : '->';
+ push( @dotlines, " $from $conn $to;" );
}
push( @dotlines, '}' );
return join( $join, @dotlines );
=head2 situation_graph( $extant, $layered )
-Returns a graph which is the original stemma with all witnesses not in the
-%$extant hash marked as hypothetical, and witness layers added to the graph
-according to the list in @$layered. A layered (a.c.) witness is added as a
-parent of its main version, and additionally shares all other parents and
-children with that version.
+Returns a graph which is the original stemma graph with all witnesses not
+in the %$extant hash marked as hypothetical, and witness layers added to
+the graph according to the list in @$layered. A layered (a.c.) witness is
+added as a parent of its main version, and additionally shares all other
+parents and children with that version.
=cut
sub as_svg {
my( $self, $opts ) = @_;
my $dot = $self->as_dot( $opts );
- my @cmd = qw/dot -Tsvg/;
+ my @cmd = ( '-Tsvg' );
+ unshift( @cmd, $self->is_undirected ? 'neato' : 'dot' );
my $svg;
my $dotfile = File::Temp->new();
## TODO REMOVE
my( $ew, $eh ) = @{$opts->{'size'}};
# If the graph is wider than it is tall, set width to ew and remove height.
# Otherwise set height to eh and remove width.
+ # TODO Also scale the viewbox
my $width = $svgdoc->documentElement->getAttribute('width');
my $height = $svgdoc->documentElement->getAttribute('height');
$width =~ s/\D+//g;
return @wits;
}
+=head2 root( $root_vertex ) {
+
+If the stemma graph is undirected, make it directed with $root_vertex at the root.
+If it is directed, re-root it.
+
+=cut
+
+sub root_graph {
+ my( $self, $rootvertex ) = @_;
+ my $graph;
+ if( $self->is_undirected ) {
+ $graph = $self->graph;
+ } else {
+ # Make an undirected version of this graph.
+ $graph = $self->graph->undirected_copy();
+ }
+ my $rooted = Graph->new();
+ $rooted->add_vertex( $rootvertex );
+ my @next = ( $rootvertex );
+ while( @next ) {
+ my @children;
+ foreach my $v ( @next ) {
+ # Place its not-placed neighbors (ergo children) in the tree
+ # and connect them
+ foreach my $n ( grep { !$rooted->has_vertex( $_ ) }
+ $graph->neighbors( $v ) ) {
+ $rooted->add_vertex( $n );
+ $rooted->add_edge( $v, $n );
+ push( @children, $n );
+ }
+ }
+ @next = @children;
+ }
+ # Set the vertex classes
+ map { $rooted->set_vertex_attribute( $_, 'class', 'hypothetical' ) }
+ $self->graph->hypotheticals;
+ map { $rooted->set_vertex_class( $_, 'class', 'extant' ) }
+ $self->graph->witnesses;
+ return $rooted;
+}
+
+
sub throw {
Text::Tradition::Error->throw(
'ident' => 'Stemma error',
projects / scpubgit/stemmatology.git / blobdiff