X-Git-Url: http://git.shadowcat.co.uk/gitweb/gitweb.cgi?a=blobdiff_plain;f=lib%2FText%2FTradition%2FStemma.pm;h=24d9e8442c3bc26d14141fe90c49f4fb2e738700;hb=88a6bac5ee5b38c4544a0cb58b67f8ee37b8b023;hp=4f98ba167c744c601837515c81c41355647f09fd;hpb=bffafb732a04df735cf154f129c1f23ba94f608a;p=scpubgit%2Fstemmatology.git diff --git a/lib/Text/Tradition/Stemma.pm b/lib/Text/Tradition/Stemma.pm index 4f98ba1..24d9e84 100644 --- a/lib/Text/Tradition/Stemma.pm +++ b/lib/Text/Tradition/Stemma.pm @@ -10,6 +10,91 @@ use Text::Tradition::Error; use Text::Tradition::StemmaUtil qw/ character_input phylip_pars parse_newick /; use Moose; +=head1 NAME + +Text::Tradition::Stemma - a representation of a I for a Text::Tradition + +=head1 SYNOPSIS + + use Text::Tradition; + my $t = Text::Tradition->new( + 'name' => 'this is a text', + 'input' => 'TEI', + 'file' => '/path/to/tei_parallel_seg_file.xml' ); + + my $s = $tradition->add_stemma( dotfile => '/path/to/stemma.dot' ); + +=head1 DESCRIPTION + +Text::Tradition is a library for representation and analysis of collated +texts, particularly medieval ones. The Collation is the central feature of +a Tradition, where the text, its sequence of readings, and its relationships +between readings are actually kept. + +=head1 DOT SYNTAX + +The easiest way to define a stemma (which is a directed acyclic graph, denoting +the scholar's hypothesis concerning which text(s) were copied from which other(s)) +is to use a special form of the 'dot' syntax of GraphViz. + +Each stemma opens with the line + + digraph Stemma { + +and continues with a list of all manuscript witnesses in the stemma, whether +extant witnesses or missing archetypes or hyparchetypes. Each of these is +listed by its sigil on its own line, e.g.: + + alpha [ class=hypothetical ] + 1 [ class=hypothetical,label=* ] + Ms4 [ class=extant ] + +Extant witnesses are listed with class=extant; missing or postulated witnesses +are listed with class=hypothetical. Anonymous hyparchetypes must be given a +unique name or number, but can be represented as anonymous with the addition +of 'label=*' to their lines. Greek letters or other special characters may be +used as names, but they must always be wrapped in double quotes. + +Links between manuscripts are then listed with arrow notation, as below. These +lines show the direction of copying, one step at a time, for the entire stemma. + + alpha -> 1 + 1 -> Ms4 + +The final line in the definition should be the closing brace: + + } + +Thus for a set of extant manuscripts A, B, and C, where A and B were copied +from the archetype O and C was copied from B, the definition would be: + + digraph Stemma { + O [ class=hypothetical] + A [ class=extant ] + B [ class=extant ] + C [ class=extant ] + O -> A + O -> B + B -> C + } + +=head1 CONSTRUCTOR + +=head2 new + +The constructor. This should generally be called from Text::Tradition, but +if called directly it takes the following options: + +=over + +=item * collation - The collation with which the stemma is associated. + +=item * dot - A filehandle open to a DOT representation of the stemma graph. + +=back + +=cut + has collation => ( is => 'ro', isa => 'Text::Tradition::Collation', @@ -22,29 +107,16 @@ 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. if( exists $args->{'dot'} ) { - $self->graph_from_dot( $args->{'dot'} ); + $self->_graph_from_dot( $args->{'dot'} ); } } -sub graph_from_dot { +sub _graph_from_dot { my( $self, $dotfh ) = @_; my $reader = Graph::Reader::Dot->new(); my $graph = $reader->read_graph( $dotfh ); @@ -60,21 +132,43 @@ sub graph_from_dot { } } +=head1 METHODS + +=head2 as_dot( \%options ) + +Returns a normal dot representation of the stemma layout, suitable for rendering +with GraphViz. Options include: + +=over + +=item * graph - A hashref of global graph options. + +=item * node - A hashref of global node options. + +=item * edge - A hashref of global edge options. + +=back + +See the GraphViz documentation for the list of available options. + +=cut + sub as_dot { my( $self, $opts ) = @_; # Get default and specified options - my %graphopts = (); + my %graphopts = ( + # 'ratio' => 1, + ); my %nodeopts = ( 'fontsize' => 11, - 'hshape' => 'plaintext', # Shape for the hypothetical nodes - 'htext' => '*', 'style' => 'filled', 'fillcolor' => 'white', + 'color' => 'white', 'shape' => 'ellipse', # Shape for the extant nodes ); my %edgeopts = ( - 'arrowhead' => 'open', + 'arrowhead' => 'none', ); @graphopts{ keys %{$opts->{'graph'}} } = values %{$opts->{'graph'}} if $opts->{'graph'}; @@ -88,16 +182,13 @@ sub as_dot { ## Print out the global attributes push( @dotlines, _make_dotline( 'graph', %graphopts ) ) if keys %graphopts; push( @dotlines, _make_dotline( 'edge', %edgeopts ) ) if keys %edgeopts; - ## Delete our special attributes from the node set before continuing - my $hshape = delete $nodeopts{'hshape'}; - my $htext = delete $nodeopts{'htext'}; push( @dotlines, _make_dotline( 'node', %nodeopts ) ) if keys %nodeopts; # Add each of the nodes. foreach my $n ( $self->graph->vertices ) { - if( $self->graph->get_vertex_attribute( $n, 'class' ) eq 'hypothetical' ) { - # Apply our display settings for hypothetical nodes. - push( @dotlines, _make_dotline( $n, 'shape' => $hshape, 'label' => $htext ) ); + if( $self->graph->has_vertex_attribute( $n, 'label' ) ) { + my $ltext = $self->graph->get_vertex_attribute( $n, 'label' ); + push( @dotlines, _make_dotline( $n, 'label' => $ltext ) ); } else { # Use the default display settings. push( @dotlines, " $n;" ); @@ -113,11 +204,17 @@ sub as_dot { return join( "\n", @dotlines ); } +=head2 editable( $linesep ) + +Returns a version of the graph rendered in our definition format. The +$linesep argument defaults to newline; set it to the empty string or to +a space if the result is to be sent via JSON. + +=cut -# Another version of dot output meant for graph editing, thus -# much simpler. sub editable { my $self = shift; + my $join = shift || "\n"; my @dotlines; push( @dotlines, 'digraph stemma {' ); my @real; # A cheap sort @@ -139,7 +236,7 @@ sub editable { push( @dotlines, " $from -> $to;" ); } push( @dotlines, '}' ); - return join( "\n", @dotlines ); + return join( $join, @dotlines ); } sub _make_dotline { @@ -157,7 +254,12 @@ sub _by_vertex { return $a->[0].$a->[1] cmp $b->[0].$b->[1]; } -# Render the stemma as SVG. +=head2 as_svg + +Returns an SVG representation of the graph, calling as_dot first. + +=cut + sub as_svg { my( $self, $opts ) = @_; my $dot = $self->as_dot( $opts ); @@ -174,6 +276,12 @@ sub as_svg { return $svg; } +=head2 witnesses + +Returns a list of the extant witnesses represented in the stemma. + +=cut + sub witnesses { my $self = shift; my @wits = grep { $self->graph->get_vertex_attribute( $_, 'class' ) eq 'extant' } @@ -181,34 +289,12 @@ sub witnesses { return @wits; } -#### Methods for calculating phylogenetic trees #### - -before 'distance_trees' => sub { +sub hypotheticals { 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( $ok, $result ) = $self->$dsub(); - if( $ok ) { - # Save the resulting trees - my $trees = parse_newick( $result ); - $self->_save_distance_trees( $trees ); - $self->distance_program( $args{'program'} ); - } else { - throw( "Failed to calculate distance trees: $result" ); - } - } -}; - -sub run_phylip_pars { - my $self = shift; - my $cdata = character_input( $self->collation->make_alignment_table() ); - return phylip_pars( $cdata ); + my @wits = grep + { $self->graph->get_vertex_attribute( $_, 'class' ) eq 'hypothetical' } + $self->graph->vertices; + return @wits; } sub throw { @@ -223,3 +309,13 @@ no Moose; __PACKAGE__->meta->make_immutable; 1; + +=head1 LICENSE + +This package is free software and is provided "as is" without express +or implied warranty. You can redistribute it and/or modify it under +the same terms as Perl itself. + +=head1 AUTHOR + +Tara L Andrews Eaurum@cpan.orgE