package Text::Tradition::Stemma;
-use File::chdir;
+use Bio::Phylo::IO;
+use Encode qw( decode_utf8 );
use File::Temp;
-use IPC::Run qw/ run /;
+use Graph;
+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;
-use Text::Tradition::Collation::Position;
+
+=head1 NAME
+
+Text::Tradition::Stemma - a representation of a I<stemma codicum> 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 Stemma is a representation of the
+copying relationships between the witnesses in a Tradition, modelled with
+a connected rooted directed acyclic graph (CRDAG).
+
+=head1 DOT SYNTAX
+
+The easiest way to define a stemma 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',
required => 1,
+ weak_ref => 1,
);
-has character_matrix => (
- is => 'ro',
- isa => 'ArrayRef[ArrayRef[Str]]',
- writer => '_save_character_matrix',
- predicate => 'has_character_matrix',
+has graph => (
+ is => 'rw',
+ isa => 'Graph',
+ predicate => 'has_graph',
);
-
-sub make_character_matrix {
- my $self = shift;
- unless( $self->collation->linear ) {
- warn "Need a linear graph in order to make an alignment table";
- return;
- }
- my @all_pos = sort { Text::Tradition::Collation::Position::str_cmp( $a, $b ) }
- $self->collation->possible_positions;
- my $table = [];
- my $characters = {};
- map { $characters->{$_} = {} } @all_pos;
- foreach my $wit ( @{$self->collation->tradition->witnesses} ) {
- # First implementation: make dumb alignment table, caring about
- # nothing except which reading is in which position.
- push( @$table, [ $wit->sigil, make_witness_row( $characters, $wit->path,
- \@all_pos ) ] );
- if( $wit->has_ante_corr ) {
- push( @$table, [ $wit->sigil . "_ac",
- make_witness_row( $characters, $wit->uncorrected_path,
- \@all_pos ) ] );
- }
+
+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->_save_character_matrix( $table );
}
-sub make_witness_row {
- my( $characters, $path, $positions ) = @_;
- my @row;
- my $pathdrift = 0;
- foreach my $i( 0 .. $#{$positions} ) {
- if( $path->[$i-$pathdrift]->position->minref eq $positions->[$i] ) {
- push( @row, get_character( $path->[$i-$pathdrift], $characters ) );
+sub _graph_from_dot {
+ my( $self, $dotfh ) = @_;
+ my $reader = Graph::Reader::Dot->new();
+ my $graph = $reader->read_graph( $dotfh );
+ if( $graph ) {
+ $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' );
+ }
} else {
- push( @row, 'X' );
- $pathdrift++;
+ throw( "Failed to parse dot in $dotfh" );
}
- $i++;
- }
- return @row;
}
+
+=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 ) = @_;
+
+ ## See if we are including any a.c. witnesses in this graph.
+ my $graph = $self->graph;
+ if( exists $opts->{'layerwits'} ) {
+ my $extant = {};
+ map { $extant->{$_} = 1 } $self->witnesses;
+ $graph = $self->situation_graph( $extant, $opts->{'layerwits'} );
+ }
+
+ # Get default and specified options
+ my %graphopts = (
+ # 'ratio' => 1,
+ );
+ my %nodeopts = (
+ 'fontsize' => 11,
+ 'style' => 'filled',
+ 'fillcolor' => 'white',
+ 'color' => 'white',
+ 'shape' => 'ellipse', # Shape for the extant nodes
+ );
+ my %edgeopts = (
+ 'arrowhead' => 'none',
+ );
+ @graphopts{ keys %{$opts->{'graph'}} } = values %{$opts->{'graph'}}
+ if $opts->{'graph'};
+ @nodeopts{ keys %{$opts->{'node'}} } = values %{$opts->{'node'}}
+ if $opts->{'node'};
+ @edgeopts{ keys %{$opts->{'edge'}} } = values %{$opts->{'edge'}}
+ if $opts->{'edge'};
+
+ my @dotlines;
+ push( @dotlines, 'digraph stemma {' );
+ ## Print out the global attributes
+ push( @dotlines, _make_dotline( 'graph', %graphopts ) ) if keys %graphopts;
+ push( @dotlines, _make_dotline( 'edge', %edgeopts ) ) if keys %edgeopts;
+ push( @dotlines, _make_dotline( 'node', %nodeopts ) ) if keys %nodeopts;
+
+ # Add each of the nodes.
+ foreach my $n ( $graph->vertices ) {
+ if( $graph->has_vertex_attribute( $n, 'label' ) ) {
+ my $ltext = $graph->get_vertex_attribute( $n, 'label' );
+ push( @dotlines, _make_dotline( $n, 'label' => $ltext ) );
+ } else {
+ # Use the default display settings.
+ $n = _dotquote( $n );
+ push( @dotlines, " $n;" );
+ }
+ }
+ # Add each of our edges.
+ foreach my $e ( $graph->edges ) {
+ my( $from, $to ) = map { _dotquote( $_ ) } @$e;
+ push( @dotlines, " $from -> $to;" );
+ }
+ push( @dotlines, '}' );
+ return join( "\n", @dotlines );
+}
+
+=head2 editable( $opts )
-sub get_character {
- my( $reading, $characters ) = @_;
- my $this_pos = $characters->{$reading->position->minref};
- # This is a simple algorithm that treats every reading as different.
- # Eventually we will want to be able to specify how relationships
- # affect the character matrix.
- my $text = $reading->text;
- unless( exists $this_pos->{$text} ) {
- # We need to find what the next character is here, and record it.
- my @all_chr = sort { $a <=> $b } values( %$this_pos );
- if( @all_chr == 8 ) {
- warn "Already have eight variants at position "
- . $reading->position->minref . "; not adding " . $reading->text;
- return '?';
+=head2 editable_graph( $graph, $opts )
+
+Returns a version of the graph rendered in our definition format. The
+output separates statements with a newline; set $opts->{'linesep'} to the
+empty string or to a space if the result is to be sent via JSON.
+
+If a situational version of the stemma is required, the arguments for
+situation_graph should be passed via $opts->{'extant'} and $opts->{'layerwits'}.
+
+=cut
+
+sub editable {
+ my( $self, $opts ) = @_;
+ my $graph = $self->graph;
+ ## See if we need an editable version of a situational graph.
+ if( exists $opts->{'layerwits'} || exists $opts->{'extant'} ) {
+ my $extant = delete $opts->{'extant'} || {};
+ my $layerwits = delete $opts->{'layerwits'} || [];
+ $graph = $self->situation_graph( $extant, $layerwits );
}
- $this_pos->{$text} = scalar @all_chr;
+ return editable_graph( $graph, $opts );
+}
+
+sub editable_graph {
+ my( $graph, $opts ) = @_;
+
+ # Create the graph
+ my $join = ( $opts && exists $opts->{'linesep'} ) ? $opts->{'linesep'} : "\n";
+ my @dotlines;
+ push( @dotlines, 'digraph stemma {' );
+ my @real; # A cheap sort
+ foreach my $n ( sort $graph->vertices ) {
+ my $c = $graph->get_vertex_attribute( $n, 'class' );
+ $c = 'extant' unless $c;
+ if( $c eq 'extant' ) {
+ push( @real, $n );
+ } else {
+ push( @dotlines, _make_dotline( $n, 'class' => $c ) );
+ }
}
- return $this_pos->{$text};
+ # Now do the real ones
+ foreach my $n ( @real ) {
+ push( @dotlines, _make_dotline( $n, 'class' => 'extant' ) );
+ }
+ foreach my $e ( sort _by_vertex $graph->edges ) {
+ my( $from, $to ) = map { _dotquote( $_ ) } @$e;
+ push( @dotlines, " $from -> $to;" );
+ }
+ push( @dotlines, '}' );
+ return join( $join, @dotlines );
+}
+
+sub _make_dotline {
+ my( $obj, %attr ) = @_;
+ my @pairs;
+ foreach my $k ( keys %attr ) {
+ my $v = _dotquote( $attr{$k} );
+ push( @pairs, "$k=$v" );
+ }
+ return sprintf( " %s [ %s ];", _dotquote( $obj ), join( ', ', @pairs ) );
+}
+
+sub _dotquote {
+ my( $str ) = @_;
+ return $str if $str =~ /^[A-Za-z0-9]+$/;
+ $str =~ s/\"/\\\"/g;
+ $str = '"' . $str . '"';
+ return $str;
+}
+
+sub _by_vertex {
+ return $a->[0].$a->[1] cmp $b->[0].$b->[1];
+}
+
+=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.
+
+=cut
+
+sub situation_graph {
+ my( $self, $extant, $layerwits ) = @_;
+
+ my $graph = $self->graph->copy;
+ foreach my $vertex ( $graph->vertices ) {
+ # Set as extant any vertex that is extant in the stemma AND
+ # exists in the $extant hash.
+ my $class = 'hypothetical';
+ $class = 'extant' if exists $extant->{$vertex} && $extant->{$vertex} &&
+ $self->graph->get_vertex_attribute( $vertex, 'class' ) ne 'hypothetical';
+ $graph->set_vertex_attribute( $vertex, 'class', $class );
+ }
+
+ # For each 'layered' witness in the layerwits array, add it to the graph
+ # as an ancestor of the 'main' witness, and otherwise with the same parent/
+ # child links as its main analogue.
+ # TOOD Handle case where B is copied from A but corrected from C
+ my $aclabel = $self->collation->ac_label;
+ foreach my $lw ( @$layerwits ) {
+ # Add the layered witness and set it with the same attributes as
+ # its 'main' analogue
+ throw( "Cannot add a layer to a hypothetical witness $lw" )
+ unless $graph->get_vertex_attribute( $lw, 'class' ) eq 'extant';
+ my $lwac = $lw . $aclabel;
+ $graph->add_vertex( $lwac );
+ $graph->set_vertex_attributes( $lwac,
+ $graph->get_vertex_attributes( $lw ) );
+
+ # Set it as ancestor to the main witness
+ $graph->add_edge( $lwac, $lw );
+
+ # Give it the same ancestors and descendants as the main witness has,
+ # bearing in mind that those ancestors and descendants might also just
+ # have had a layered witness defined.
+ foreach my $v ( $graph->predecessors( $lw ) ) {
+ next if $v eq $lwac; # Don't add a loop
+ $graph->add_edge( $v, $lwac );
+ $graph->add_edge( $v.$aclabel, $lwac )
+ if $graph->has_vertex( $v.$aclabel );
+ }
+ foreach my $v ( $graph->successors( $lw ) ) {
+ next if $v eq $lwac; # but this shouldn't occur
+ $graph->add_edge( $lwac, $v );
+ $graph->add_edge( $lwac, $v.$aclabel )
+ if $graph->has_vertex( $v.$aclabel );
+ }
+ }
+ return $graph;
+}
+
+=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 );
+ my @cmd = qw/dot -Tsvg/;
+ my $svg;
+ my $dotfile = File::Temp->new();
+ ## TODO REMOVE
+ # $dotfile->unlink_on_destroy(0);
+ binmode $dotfile, ':utf8';
+ print $dotfile $dot;
+ push( @cmd, $dotfile->filename );
+ run( \@cmd, ">", binary(), \$svg );
+ # HACK: Parse the SVG and change the dimensions.
+ # Get rid of width and height attributes to allow scaling.
+ if( $opts->{'size'} ) {
+ require XML::LibXML;
+ my $parser = XML::LibXML->new();
+ my $svgdoc = $parser->parse_string( decode_utf8( $svg ) );
+ 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.
+ my $width = $svgdoc->documentElement->getAttribute('width');
+ my $height = $svgdoc->documentElement->getAttribute('height');
+ $width =~ s/\D+//g;
+ $height =~ s/\D+//g;
+ my( $remove, $keep, $val );
+ if( $width > $height ) {
+ $remove = 'height';
+ $keep = 'width';
+ $val = $ew . 'px';
+ } else {
+ $remove = 'width';
+ $keep = 'height';
+ $val = $eh . 'px';
+ }
+ $svgdoc->documentElement->removeAttribute( $remove );
+ $svgdoc->documentElement->setAttribute( $keep, $val );
+ $svg = $svgdoc->toString();
+ }
+ # Return the result
+ return decode_utf8( $svg );
}
-sub run_pars {
+=head2 witnesses
+
+Returns a list of the extant witnesses represented in the stemma.
+
+=cut
+
+sub witnesses {
my $self = shift;
- $self->make_character_matrix unless $self->has_character_matrix;
-
- # Set up a temporary directory for all the default Phylip files.
- my $phylip_dir = File::Temp->newdir();
-
- # We need an infile, and we need a command input file.
- $DB::single = 1;
- open( MATRIX, ">$phylip_dir/infile" ) or die "Could not write $phylip_dir/infile";
- my $rows = scalar @{$self->character_matrix};
- my $columns = scalar @{$self->character_matrix->[0]} - 1;
- print MATRIX "\t$rows\t$columns\n";
- foreach my $row ( @{$self->character_matrix} ) {
- my $wit = shift @$row;
- my $chars = join( '', @$row );
- print MATRIX sprintf( "%-10s%s\n", $wit, $chars );
- }
- close MATRIX;
-
- open( CMD, ">$phylip_dir/cmdfile" ) or die "Could not write $phylip_dir/cmdfile";
- ## TODO any configuration parameters we want to set here
-# U Search for best tree? Yes
-# S Search option? More thorough search
-# V Number of trees to save? 100
-# J Randomize input order of species? No. Use input order
-# O Outgroup root? No, use as outgroup species 1
-# T Use Threshold parsimony? No, use ordinary parsimony
-# W Sites weighted? No
-# M Analyze multiple data sets? No
-# I Input species interleaved? Yes
-# 0 Terminal type (IBM PC, ANSI, none)? ANSI
-# 1 Print out the data at start of run No
-# 2 Print indications of progress of run Yes
-# 3 Print out tree Yes
-# 4 Print out steps in each site No
-# 5 Print character at all nodes of tree No
-# 6 Write out trees onto tree file? Yes
- print CMD "Y\n";
- close CMD;
-
- # And then we run the program.
- ### HACKY HACKY
- my $PHYLIP_PATH = '/Users/tla/Projects/phylip-3.69/exe';
- my $program = "pars";
- if( $^O eq 'darwin' ) {
- $program = "$PHYLIP_PATH/$program.app/Contents/MacOS/$program";
- } else {
- $program = "$PHYLIP_PATH/$program";
- }
+ my @wits = grep { $self->graph->get_vertex_attribute( $_, 'class' ) eq 'extant' }
+ $self->graph->vertices;
+ return @wits;
+}
- {
- # We need to run it in our temporary directory where we have created
- # all the expected files.
- local $CWD = $phylip_dir;
- my @cmd = ( $program );
- run \@cmd, '<', 'cmdfile', '>', '/dev/null';
- }
- # Now our output should be in 'outfile' and our tree in 'outtree',
- # both in the temp directory.
-
- my @outtree;
- if( -f "$phylip_dir/outtree" ) {
- open( TREE, "$phylip_dir/outtree" ) or die "Could not open outtree for read";
- @outtree = <TREE>;
- close TREE;
- }
- return( 1, join( '', @outtree ) ) if @outtree;
-
- my @error;
- if( -f "$phylip_dir/output" ) {
- open( OUTPUT, "$phylip_dir/output" ) or die "Could not open output for read";
- @error = <OUTPUT>;
- close OUTPUT;
- } else {
- push( @error, "Neither outtree nor output file was produced!" );
- }
- return( undef, join( '', @error ) );
+=head2 hypotheticals
+
+Returns a list of the hypothetical witnesses represented in the stemma.
+
+=cut
+
+sub hypotheticals {
+ my $self = shift;
+ my @wits = grep
+ { $self->graph->get_vertex_attribute( $_, 'class' ) eq 'hypothetical' }
+ $self->graph->vertices;
+ return @wits;
+}
+
+sub throw {
+ Text::Tradition::Error->throw(
+ 'ident' => 'Stemma error',
+ 'message' => $_[0],
+ );
}
+
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 E<lt>aurum@cpan.orgE<gt>