package Text::Tradition::Collation;
-use Graph::Easy;
+use Encode qw( decode_utf8 );
+use File::Temp;
+use Graph;
use IPC::Run qw( run binary );
+use Text::CSV_XS;
use Text::Tradition::Collation::Reading;
+use Text::Tradition::Collation::RelationshipStore;
+use XML::LibXML;
use Moose;
-has 'graph' => (
+has 'sequence' => (
is => 'ro',
- isa => 'Graph::Easy',
+ isa => 'Graph',
+ default => sub { Graph->new() },
handles => {
- add_reading => 'add_node',
- del_reading => 'del_node',
- add_path => 'add_edge',
- del_path => 'del_edge',
- reading => 'node',
- path => 'edge',
- readings => 'nodes',
- paths => 'edges',
+ paths => 'edges',
},
- default => sub { Graph::Easy->new( undirected => 0 ) },
);
-
+
+has 'relations' => (
+ is => 'ro',
+ isa => 'Text::Tradition::Collation::RelationshipStore',
+ handles => {
+ relationships => 'relationships',
+ related_readings => 'related_readings',
+ },
+ writer => '_set_relations',
+ );
has 'tradition' => (
- is => 'rw',
- isa => 'Text::Tradition',
- );
-
-has 'svg' => (
- is => 'ro',
- isa => 'Str',
- writer => '_save_svg',
- predicate => 'has_svg',
- );
-
-has 'graphviz' => (
- is => 'ro',
- isa => 'Str',
- writer => '_save_graphviz',
- predicate => 'has_graphviz',
- );
-
-has 'graphml' => (
is => 'ro',
- isa => 'XML::LibXML::Document',
- writer => '_save_graphml',
- predicate => 'has_graphml',
+ isa => 'Text::Tradition',
+ weak_ref => 1,
);
-# Keeps track of the lemmas within the collation. At most one lemma
-# per position in the graph.
-has 'lemmata' => (
- is => 'ro',
- isa => 'HashRef[Maybe[Str]]',
+has 'readings' => (
+ isa => 'HashRef[Text::Tradition::Collation::Reading]',
+ traits => ['Hash'],
+ handles => {
+ reading => 'get',
+ _add_reading => 'set',
+ del_reading => 'delete',
+ has_reading => 'exists',
+ readings => 'values',
+ },
default => sub { {} },
- );
+ );
has 'wit_list_separator' => (
is => 'rw',
default => 'base text',
);
-has 'collapsed' => (
- is => 'rw',
- isa => 'Bool',
- );
+has 'linear' => (
+ is => 'rw',
+ isa => 'Bool',
+ default => 1,
+ );
+has 'ac_label' => (
+ is => 'rw',
+ isa => 'Str',
+ default => ' (a.c.)',
+ );
+
+has 'start' => (
+ is => 'ro',
+ isa => 'Text::Tradition::Collation::Reading',
+ writer => '_set_start',
+ weak_ref => 1,
+ );
+
+has 'end' => (
+ is => 'ro',
+ isa => 'Text::Tradition::Collation::Reading',
+ writer => '_set_end',
+ weak_ref => 1,
+ );
# The collation can be created two ways:
# 1. Collate a set of witnesses (with CollateX I guess) and process
# come through option 1.
sub BUILD {
- my( $self, $args ) = @_;
- $self->graph->use_class('node', 'Text::Tradition::Collation::Reading');
-
- # Pass through any graph-specific options.
- my $shape = exists( $args->{'shape'} ) ? $args->{'shape'} : 'ellipse';
- $self->graph->set_attribute( 'node', 'shape', $shape );
+ my $self = shift;
+ $self->_set_relations( Text::Tradition::Collation::RelationshipStore->new( 'collation' => $self ) );
+ $self->_set_start( $self->add_reading( { 'collation' => $self, 'is_start' => 1 } ) );
+ $self->_set_end( $self->add_reading( { 'collation' => $self, 'is_end' => 1 } ) );
}
-# Wrapper around add_path
+### Reading construct/destruct functions
-around add_path => sub {
- my $orig = shift;
- my $self = shift;
+sub add_reading {
+ my( $self, $reading ) = @_;
+ unless( ref( $reading ) eq 'Text::Tradition::Collation::Reading' ) {
+ my %args = %$reading;
+ $reading = Text::Tradition::Collation::Reading->new(
+ 'collation' => $self,
+ %args );
+ }
+ # First check to see if a reading with this ID exists.
+ if( $self->reading( $reading->id ) ) {
+ warn "Collation already has a reading with id " . $reading->id;
+ return undef;
+ }
+ $self->_add_reading( $reading->id => $reading );
+ # Once the reading has been added, put it in both graphs.
+ $self->sequence->add_vertex( $reading->id );
+ $self->relations->add_reading( $reading->id );
+ return $reading;
+};
- # Make sure there are three arguments
- unless( @_ == 3 ) {
- warn "Call add_path with args source, target, witness";
- return;
- }
- # Make sure the proposed path does not yet exist
- my( $source, $target, $wit ) = @_;
- $source = $self->reading( $source )
- unless ref( $source ) eq 'Text::Tradition::Collation::Reading';
- $target = $self->reading( $target )
- unless ref( $target ) eq 'Text::Tradition::Collation::Reading';
- foreach my $path ( $source->edges_to( $target ) ) {
- if( $path->label eq $wit ) {
- return;
+around del_reading => sub {
+ my $orig = shift;
+ my $self = shift;
+ my $arg = shift;
+
+ if( ref( $arg ) eq 'Text::Tradition::Collation::Reading' ) {
+ $arg = $arg->id;
}
- }
- # Do the deed
- $self->$orig( @_ );
+ # Remove the reading from the graphs.
+ $self->sequence->delete_vertex( $arg );
+ $self->relations->delete_reading( $arg );
+
+ # Carry on.
+ $self->$orig( $arg );
};
-# Wrapper around merge_nodes
+# merge_readings( $main, $to_be_deleted );
sub merge_readings {
- my $self = shift;
- my $first_node = shift;
- my $second_node = shift;
- $first_node->merge_from( $second_node );
- unshift( @_, $first_node, $second_node );
- return $self->graph->merge_nodes( @_ );
+ my $self = shift;
+
+ # We only need the IDs for adding paths to the graph, not the reading
+ # objects themselves.
+ my( $kept, $deleted, $combine_char ) = $self->_stringify_args( @_ );
+
+ # The kept reading should inherit the paths and the relationships
+ # of the deleted reading.
+ foreach my $path ( $self->sequence->edges_at( $deleted ) ) {
+ my @vector = ( $kept );
+ push( @vector, $path->[1] ) if $path->[0] eq $deleted;
+ unshift( @vector, $path->[0] ) if $path->[1] eq $deleted;
+ next if $vector[0] eq $vector[1]; # Don't add a self loop
+ my %wits = %{$self->sequence->get_edge_attributes( @$path )};
+ $self->sequence->add_edge( @vector );
+ my $fwits = $self->sequence->get_edge_attributes( @vector );
+ @wits{keys %$fwits} = values %$fwits;
+ $self->sequence->set_edge_attributes( @vector, \%wits );
+ }
+ $self->relations->merge_readings( $kept, $deleted, $combine_char );
+
+ # Do the deletion deed.
+ if( $combine_char ) {
+ my $kept_obj = $self->reading( $kept );
+ my $new_text = join( $combine_char, $kept_obj->text,
+ $self->reading( $deleted )->text );
+ $kept_obj->alter_text( $new_text );
+ }
+ $self->del_reading( $deleted );
+}
+
+
+# Helper function for manipulating the graph.
+sub _stringify_args {
+ my( $self, $first, $second, $arg ) = @_;
+ $first = $first->id
+ if ref( $first ) eq 'Text::Tradition::Collation::Reading';
+ $second = $second->id
+ if ref( $second ) eq 'Text::Tradition::Collation::Reading';
+ return( $first, $second, $arg );
+}
+
+### Path logic
+
+sub add_path {
+ my $self = shift;
+
+ # We only need the IDs for adding paths to the graph, not the reading
+ # objects themselves.
+ my( $source, $target, $wit ) = $self->_stringify_args( @_ );
+
+ # Connect the readings
+ $self->sequence->add_edge( $source, $target );
+ # Note the witness in question
+ $self->sequence->set_edge_attribute( $source, $target, $wit, 1 );
+};
+
+sub del_path {
+ my $self = shift;
+ my @args;
+ if( ref( $_[0] ) eq 'ARRAY' ) {
+ my $e = shift @_;
+ @args = ( @$e, @_ );
+ } else {
+ @args = @_;
+ }
+
+ # We only need the IDs for adding paths to the graph, not the reading
+ # objects themselves.
+ my( $source, $target, $wit ) = $self->_stringify_args( @args );
+
+ if( $self->sequence->has_edge_attribute( $source, $target, $wit ) ) {
+ $self->sequence->delete_edge_attribute( $source, $target, $wit );
+ }
+ unless( keys %{$self->sequence->get_edge_attributes( $source, $target )} ) {
+ $self->sequence->delete_edge( $source, $target );
+ }
+}
+
+
+# Extra graph-alike utility
+sub has_path {
+ my $self = shift;
+ my( $source, $target, $wit ) = $self->_stringify_args( @_ );
+ return undef unless $self->sequence->has_edge( $source, $target );
+ return $self->sequence->has_edge_attribute( $source, $target, $wit );
+}
+
+=head2 add_relationship( $reading1, $reading2, $definition )
+
+Adds the specified relationship between the two readings. A relationship
+is transitive (i.e. undirected); the options for its definition may be found
+in Text::Tradition::Collation::Relationship.
+
+=cut
+
+# Wouldn't it be lovely if edges could be objects, and all this type checking
+# and attribute management could be done via Moose?
+
+sub add_relationship {
+ my $self = shift;
+ my( $source, $target, $opts ) = $self->_stringify_args( @_ );
+ my( $ret, @vectors ) = $self->relations->add_relationship( $source,
+ $self->reading( $source ), $target, $self->reading( $target ), $opts );
+ # Force a full rank recalculation every time. Yuck.
+ $self->calculate_ranks() if $ret && $self->end->has_rank;
+ return( $ret, @vectors );
+}
+
+=head2 reading_witnesses( $reading )
+
+Return a list of sigils corresponding to the witnesses in which the reading appears.
+
+=cut
+
+sub reading_witnesses {
+ my( $self, $reading ) = @_;
+ # We need only check either the incoming or the outgoing edges; I have
+ # arbitrarily chosen "incoming". Thus, special-case the start node.
+ if( $reading eq $self->start ) {
+ return map { $_->sigil } $self->tradition->witnesses;
+ }
+ my %all_witnesses;
+ foreach my $e ( $self->sequence->edges_to( $reading ) ) {
+ my $wits = $self->sequence->get_edge_attributes( @$e );
+ @all_witnesses{ keys %$wits } = 1;
+ }
+ return keys %all_witnesses;
}
=head2 Output method(s)
=item B<as_svg>
-print $graph->as_svg( $recalculate );
+print $collation->as_svg();
-Returns an SVG string that represents the graph. Uses GraphViz to do
-this, because Graph::Easy doesn\'t cope well with long graphs. Unless
-$recalculate is passed (and is a true value), the method will return a
-cached copy of the SVG after the first call to the method.
+Returns an SVG string that represents the graph, via as_dot and graphviz.
=cut
sub as_svg {
- my( $self, $recalc ) = @_;
- return $self->svg if $self->has_svg;
+ my( $self ) = @_;
+
+ my @cmd = qw/dot -Tsvg/;
+ my( $svg, $err );
+ my $dotfile = File::Temp->new();
+ ## TODO REMOVE
+ # $dotfile->unlink_on_destroy(0);
+ binmode $dotfile, ':utf8';
+ print $dotfile $self->as_dot();
+ push( @cmd, $dotfile->filename );
+ run( \@cmd, ">", binary(), \$svg );
+ $svg = decode_utf8( $svg );
+ return $svg;
+}
+
+=item B<svg_subgraph>
+
+print $collation->svg_subgraph( $from, $to )
+
+Returns an SVG string that represents the portion of the graph given by the
+specified range. The $from and $to variables refer to ranks within the graph.
+
+=cut
+
+sub svg_subgraph {
+ my( $self, $from, $to ) = @_;
- $self->collapse_graph_edges();
- $self->_save_graphviz( $self->graph->as_graphviz() )
- unless( $self->has_graphviz && !$recalc );
+ my $dot = $self->as_dot( $from, $to );
+ unless( $dot ) {
+ warn "Could not output a graph with range $from - $to";
+ return;
+ }
my @cmd = qw/dot -Tsvg/;
my( $svg, $err );
- my $in = $self->graphviz;
- run( \@cmd, \$in, ">", binary(), \$svg );
- $self->{'svg'} = $svg;
- $self->expand_graph_edges();
+ 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 );
+ $svg = decode_utf8( $svg );
return $svg;
}
+
+=item B<as_dot>
+
+print $collation->as_dot();
+
+Returns a string that is the collation graph expressed in dot
+(i.e. GraphViz) format. The 'view' argument determines what kind of
+graph is produced.
+ * 'path': a graph of witness paths through the collation (DEFAULT)
+ * 'relationship': a graph of how collation readings relate to
+ each other
+
+=cut
+
+sub as_dot {
+ my( $self, $startrank, $endrank ) = @_;
+
+ # Check the arguments
+ if( $startrank ) {
+ return if $endrank && $startrank > $endrank;
+ return if $startrank > $self->end->rank;
+ }
+ if( defined $endrank ) {
+ return if $endrank < 0;
+ }
+
+ # TODO consider making some of these things configurable
+ my $graph_name = $self->tradition->name;
+ $graph_name =~ s/[^\w\s]//g;
+ $graph_name = join( '_', split( /\s+/, $graph_name ) );
+ my $dot = sprintf( "digraph %s {\n", $graph_name );
+ $dot .= "\tedge [ arrowhead=open ];\n";
+ $dot .= "\tgraph [ rankdir=LR,bgcolor=none ];\n";
+ $dot .= sprintf( "\tnode [ fontsize=%d, fillcolor=%s, style=%s, shape=%s ];\n",
+ 11, "white", "filled", "ellipse" );
+
+ # Output substitute start/end readings if necessary
+ if( $startrank ) {
+ $dot .= "\t\"#SUBSTART#\" [ label=\"...\" ];\n";
+ }
+ if( $endrank ) {
+ $dot .= "\t\"#SUBEND#\" [ label=\"...\" ];\n";
+ }
+ my %used; # Keep track of the readings that actually appear in the graph
+ my %subedges;
+ my %subend;
+ foreach my $reading ( $self->readings ) {
+ # Only output readings within our rank range.
+ next if $startrank && $reading->rank < $startrank;
+ next if $endrank && $reading->rank > $endrank;
+ $used{$reading->id} = 1;
+ $subedges{$reading->id} = '#SUBSTART#'
+ if $startrank && $startrank == $reading->rank;
+ $subedges{$reading->id} = '#SUBEND#'
+ if $endrank && $endrank == $reading->rank;
+ # Need not output nodes without separate labels
+ next if $reading->id eq $reading->text;
+ my $label = $reading->text;
+ $label =~ s/\"/\\\"/g;
+ $dot .= sprintf( "\t\"%s\" [ label=\"%s\" ];\n", $reading->id, $label );
+ }
+
+ # Add substitute start and end edges if necessary
+ foreach my $node ( keys %subedges ) {
+ my @vector = ( $subedges{$node}, $node );
+ @vector = reverse( @vector ) if $vector[0] =~ /END/;
+ my $witstr = join( ', ', sort $self->reading_witnesses( $self->reading( $node ) ) );
+ my %variables = ( 'color' => '#000000',
+ 'fontcolor' => '#000000',
+ 'label' => $witstr,
+ );
+ my $varopts = join( ', ', map { $_.'="'.$variables{$_}.'"' } sort keys %variables );
+ $dot .= sprintf( "\t\"%s\" -> \"%s\" [ %s ];\n", @vector, $varopts );
+ }
+
+ # Add the real edges
+ my @edges = $self->paths;
+ foreach my $edge ( @edges ) {
+ # Do we need to output this edge?
+ if( $used{$edge->[0]} && $used{$edge->[1]} ) {;
+ my %variables = ( 'color' => '#000000',
+ 'fontcolor' => '#000000',
+ 'label' => join( ', ', $self->path_display_label( $edge ) ),
+ );
+ my $varopts = join( ', ', map { $_.'="'.$variables{$_}.'"' } sort keys %variables );
+ # Account for the rank gap if necessary
+ my $rankgap = $self->reading( $edge->[1] )->rank
+ - $self->reading( $edge->[0] )->rank;
+ $varopts .= ", minlen=$rankgap" if $rankgap > 1;
+ $dot .= sprintf( "\t\"%s\" -> \"%s\" [ %s ];\n",
+ $edge->[0], $edge->[1], $varopts );
+ }
+ }
+
+ $dot .= "}\n";
+ return $dot;
+}
+
+sub path_witnesses {
+ my( $self, @edge ) = @_;
+ # If edge is an arrayref, cope.
+ if( @edge == 1 && ref( $edge[0] ) eq 'ARRAY' ) {
+ my $e = shift @edge;
+ @edge = @$e;
+ }
+ my @wits = keys %{$self->sequence->get_edge_attributes( @edge )};
+ return sort @wits;
+}
+
+sub path_display_label {
+ my( $self, $edge ) = @_;
+ my @wits = $self->path_witnesses( $edge );
+ my $maj = scalar( $self->tradition->witnesses ) * 0.6;
+ if( scalar @wits > $maj ) {
+ return 'majority';
+ } else {
+ return join( ', ', @wits );
+ }
+}
+
+
=item B<as_graphml>
-print $graph->as_graphml( $recalculate )
+print $collation->as_graphml( $recalculate )
Returns a GraphML representation of the collation graph, with
transposition information and position information. Unless
=cut
sub as_graphml {
- my( $self, $recalc ) = @_;
- return $self->graphml if $self->has_graphml;
+ my( $self ) = @_;
# Some namespaces
my $graphml_ns = 'http://graphml.graphdrawing.org/xmlns';
my $xsi_ns = 'http://www.w3.org/2001/XMLSchema-instance';
my $graphml_schema = 'http://graphml.graphdrawing.org/xmlns ' .
- 'http://graphml.graphdrawing.org/xmlns/1.0/graphml.xsd';
+ 'http://graphml.graphdrawing.org/xmlns/1.0/graphml.xsd';
# Create the document and root node
my $graphml = XML::LibXML->createDocument( "1.0", "UTF-8" );
$root->setNamespace( $xsi_ns, 'xsi', 0 );
$root->setAttributeNS( $xsi_ns, 'schemaLocation', $graphml_schema );
+ # Add the data keys for the graph
+ my %graph_data_keys;
+ my $gdi = 0;
+ my @graph_attributes = qw/ version wit_list_separator baselabel linear ac_label /;
+ foreach my $datum ( @graph_attributes ) {
+ $graph_data_keys{$datum} = 'dg'.$gdi++;
+ my $key = $root->addNewChild( $graphml_ns, 'key' );
+ $key->setAttribute( 'attr.name', $datum );
+ $key->setAttribute( 'attr.type', $key eq 'linear' ? 'boolean' : 'string' );
+ $key->setAttribute( 'for', 'graph' );
+ $key->setAttribute( 'id', $graph_data_keys{$datum} );
+ }
+
# Add the data keys for nodes
- my @node_data = ( 'name', 'token', 'identical', 'position' );
- foreach my $ndi ( 0 .. $#node_data ) {
- my $key = $root->addNewChild( $graphml_ns, 'key' );
- $key->setAttribute( 'attr.name', $node_data[$ndi] );
- $key->setAttribute( 'attr.type', 'string' );
- $key->setAttribute( 'for', 'node' );
- $key->setAttribute( 'id', 'd'.$ndi );
+ my %node_data_keys;
+ my $ndi = 0;
+ my %node_data = (
+ id => 'string',
+ text => 'string',
+ rank => 'string',
+ is_start => 'boolean',
+ is_end => 'boolean',
+ is_lacuna => 'boolean',
+ );
+ foreach my $datum ( keys %node_data ) {
+ $node_data_keys{$datum} = 'dn'.$ndi++;
+ my $key = $root->addNewChild( $graphml_ns, 'key' );
+ $key->setAttribute( 'attr.name', $datum );
+ $key->setAttribute( 'attr.type', $node_data{$datum} );
+ $key->setAttribute( 'for', 'node' );
+ $key->setAttribute( 'id', $node_data_keys{$datum} );
}
- # Add the data keys for edges
- my %wit_hash;
- my $wit_ctr = 0;
- foreach my $wit ( @{$self->tradition->witnesses} ) {
- my $wit_key = 'w' . $wit_ctr++;
- $wit_hash{$wit} = $wit_key;
- my $key = $root->addNewChild( $graphml_ns, 'key' );
- $key->setAttribute( 'attr.name', $wit );
- $key->setAttribute( 'attr.type', 'string' );
- $key->setAttribute( 'for', 'edge' );
- $key->setAttribute( 'id', $wit_key );
+ # Add the data keys for edges, i.e. witnesses
+ my $edi = 0;
+ my %edge_data_keys;
+ my %edge_data = (
+ class => 'string', # Class, deprecated soon
+ witness => 'string', # ID/label for a path
+ relationship => 'string', # ID/label for a relationship
+ extra => 'boolean', # Path key
+ colocated => 'boolean', # Relationship key
+ non_correctable => 'boolean', # Relationship key
+ non_independent => 'boolean', # Relationship key
+ );
+ foreach my $datum ( keys %edge_data ) {
+ $edge_data_keys{$datum} = 'de'.$edi++;
+ my $key = $root->addNewChild( $graphml_ns, 'key' );
+ $key->setAttribute( 'attr.name', $datum );
+ $key->setAttribute( 'attr.type', $edge_data{$datum} );
+ $key->setAttribute( 'for', 'edge' );
+ $key->setAttribute( 'id', $edge_data_keys{$datum} );
}
- # Add the graph, its nodes, and its edges
- $self->collapse_graph_edges();
- my $graph = $root->addNewChild( $graphml_ns, 'graph' );
- $graph->setAttribute( 'edgedefault', 'directed' );
- $graph->setAttribute( 'id', 'g0' ); # TODO make this meaningful
- $graph->setAttribute( 'parse.edgeids', 'canonical' );
- $graph->setAttribute( 'parse.edges', $self->edges() );
- $graph->setAttribute( 'parse.nodeids', 'canonical' );
- $graph->setAttribute( 'parse.nodes', $self->nodes() );
- $graph->setAttribute( 'parse.order', 'nodesfirst' );
+ # Add the collation graph itself
+ my $sgraph = $root->addNewChild( $graphml_ns, 'graph' );
+ $sgraph->setAttribute( 'edgedefault', 'directed' );
+ $sgraph->setAttribute( 'id', $self->tradition->name );
+ $sgraph->setAttribute( 'parse.edgeids', 'canonical' );
+ $sgraph->setAttribute( 'parse.edges', scalar($self->paths) );
+ $sgraph->setAttribute( 'parse.nodeids', 'canonical' );
+ $sgraph->setAttribute( 'parse.nodes', scalar($self->readings) );
+ $sgraph->setAttribute( 'parse.order', 'nodesfirst' );
+
+ # Collation attribute data
+ foreach my $datum ( @graph_attributes ) {
+ my $value = $datum eq 'version' ? '3.0' : $self->$datum;
+ _add_graphml_data( $sgraph, $graph_data_keys{$datum}, $value );
+ }
my $node_ctr = 0;
my %node_hash;
- foreach my $n ( $self->readings ) {
- my %this_node_data = ();
- foreach my $ndi ( 0 .. $#node_data ) {
- my $value;
- $this_node_data{'d'.$ndi} = $n->name if $node_data[$ndi] eq 'name';
- $this_node_data{'d'.$ndi} = $n->label
- if $node_data[$ndi] eq 'token';
- $this_node_data{'d'.$ndi} = $n->primary->name if $n->has_primary;
- $this_node_data{'d'.$ndi} =
- $self->{'positions'}->node_position( $n )
- if $node_data[$ndi] eq 'position';
- }
- my $node_el = $graph->addNewChild( $graphml_ns, 'node' );
- my $node_xmlid = 'n' . $node_ctr++;
- $node_hash{ $n->name } = $node_xmlid;
- $node_el->setAttribute( 'id', $node_xmlid );
-
- foreach my $dk ( keys %this_node_data ) {
- my $d_el = $node_el->addNewChild( $graphml_ns, 'data' );
- $d_el->setAttribute( 'key', $dk );
- $d_el->appendTextChild( $this_node_data{$dk} );
- }
+ # Add our readings to the graph
+ foreach my $n ( sort { $a->id cmp $b->id } $self->readings ) {
+ # Add to the main graph
+ my $node_el = $sgraph->addNewChild( $graphml_ns, 'node' );
+ my $node_xmlid = 'n' . $node_ctr++;
+ $node_hash{ $n->id } = $node_xmlid;
+ $node_el->setAttribute( 'id', $node_xmlid );
+ foreach my $d ( keys %node_data ) {
+ my $nval = $n->$d;
+ _add_graphml_data( $node_el, $node_data_keys{$d}, $nval )
+ if defined $nval;
+ }
}
- foreach my $e ( $self->paths() ) {
- my( $name, $from, $to ) = ( $e->name,
- $node_hash{ $e->from()->name() },
- $node_hash{ $e->to()->name() } );
- my $edge_el = $graph->addNewChild( $graphml_ns, 'edge' );
- $edge_el->setAttribute( 'source', $from );
- $edge_el->setAttribute( 'target', $to );
- $edge_el->setAttribute( 'id', $name );
- # TODO Got to add the witnesses
- }
+ # Add the path edges to the sequence graph
+ my $edge_ctr = 0;
+ foreach my $e ( sort { $a->[0] cmp $b->[0] } $self->sequence->edges() ) {
+ # We add an edge in the graphml for every witness in $e.
+ foreach my $wit ( $self->path_witnesses( $e ) ) {
+ my( $id, $from, $to ) = ( 'e'.$edge_ctr++,
+ $node_hash{ $e->[0] },
+ $node_hash{ $e->[1] } );
+ my $edge_el = $sgraph->addNewChild( $graphml_ns, 'edge' );
+ $edge_el->setAttribute( 'source', $from );
+ $edge_el->setAttribute( 'target', $to );
+ $edge_el->setAttribute( 'id', $id );
+
+ # It's a witness path, so add the witness
+ my $base = $wit;
+ my $key = $edge_data_keys{'witness'};
+ # Is this an ante-corr witness?
+ my $aclabel = $self->ac_label;
+ if( $wit =~ /^(.*)\Q$aclabel\E$/ ) {
+ # Keep the base witness
+ $base = $1;
+ # ...and record that this is an 'extra' reading path
+ _add_graphml_data( $edge_el, $edge_data_keys{'extra'}, $aclabel );
+ }
+ _add_graphml_data( $edge_el, $edge_data_keys{'witness'}, $base );
+ _add_graphml_data( $edge_el, $edge_data_keys{'class'}, 'path' );
+ }
+ }
+
+ # Add the relationship graph to the XML
+ $self->relations->as_graphml( $root );
- # Return the thing
- $self->_save_graphml( $graphml );
- $self->expand_graph_edges();
- return $graphml;
+ # Save and return the thing
+ my $result = decode_utf8( $graphml->toString(1) );
+ return $result;
}
-sub collapse_graph_edges {
- my $self = shift;
- # Our collation graph has an edge per witness. This is great for
- # calculation purposes, but terrible for display. Thus we want to
- # display only one edge between any two nodes.
-
- return if $self->collapsed;
-
- print STDERR "Collapsing path edges in graph...\n";
-
- # Don't list out every witness if we have more than half to list.
- my $majority = int( scalar( @{$self->tradition->witnesses} ) / 2 ) + 1;
- foreach my $node( $self->readings ) {
- my $newlabels = {};
- # We will visit each node, so we only look ahead.
- foreach my $edge ( $node->outgoing() ) {
- add_hash_entry( $newlabels, $edge->to->name, $edge->name );
- $self->del_path( $edge );
- }
+sub _add_graphml_data {
+ my( $el, $key, $value ) = @_;
+ return unless defined $value;
+ my $data_el = $el->addNewChild( $el->namespaceURI, 'data' );
+ $data_el->setAttribute( 'key', $key );
+ $data_el->appendText( $value );
+}
- foreach my $newdest ( keys %$newlabels ) {
- my $label;
- my @compressed_wits = ();
- if( @{$newlabels->{$newdest}} < $majority ) {
- $label = join( ', ', @{$newlabels->{$newdest}} );
- } else {
- ## TODO FIX THIS HACK
- my @aclabels;
- foreach my $wit ( @{$newlabels->{$newdest}} ) {
- if( $wit =~ /^(.*?)(\s*\(?a\.\s*c\.\)?)$/ ) {
- push( @aclabels, $wit );
- } else {
- push( @compressed_wits, $wit );
- }
- }
- $label = join( ', ', 'majority', @aclabels );
- }
-
- my $newedge =
- $self->add_path( $node, $self->reading( $newdest ), $label );
- if( @compressed_wits ) {
- ## TODO fix this hack too.
- $newedge->set_attribute( 'class',
- join( '|', @compressed_wits ) );
- }
- }
+=item B<as_csv>
+
+print $collation->as_csv( $recalculate )
+
+Returns a CSV alignment table representation of the collation graph, one
+row per witness (or witness uncorrected.)
+
+=cut
+
+sub as_csv {
+ my( $self ) = @_;
+ my $table = $self->make_alignment_table;
+ my $csv = Text::CSV_XS->new( { binary => 1, quote_null => 0 } );
+ my @result;
+ # Make the header row
+ $csv->combine( map { $_->{'witness'} } @{$table->{'alignment'}} );
+ push( @result, decode_utf8( $csv->string ) );
+ # Make the rest of the rows
+ foreach my $idx ( 0 .. $table->{'length'} - 1 ) {
+ my @rowobjs = map { $_->{'tokens'}->[$idx] } @{$table->{'alignment'}};
+ my @row = map { $_ ? $_->{'t'} : $_ } @rowobjs;
+ $csv->combine( @row );
+ push( @result, decode_utf8( $csv->string ) );
+ }
+ return join( "\n", @result );
+}
+
+=item B<make_alignment_table>
+
+my $table = $collation->make_alignment_table( $use_refs, \@wits_to_include )
+
+Return a reference to an alignment table, in a slightly enhanced CollateX
+format which looks like this:
+
+ $table = { alignment => [ { witness => "SIGIL",
+ tokens => [ { t => "READINGTEXT" }, ... ] },
+ { witness => "SIG2",
+ tokens => [ { t => "READINGTEXT" }, ... ] },
+ ... ],
+ length => TEXTLEN };
+
+If $use_refs is set to 1, the reading object is returned in the table
+instead of READINGTEXT; if not, the text of the reading is returned.
+If $wits_to_include is set to a hashref, only the witnesses whose sigil
+keys have a true hash value will be included.
+
+=cut
+
+sub make_alignment_table {
+ my( $self, $noderefs, $include ) = @_;
+ unless( $self->linear ) {
+ warn "Need a linear graph in order to make an alignment table";
+ return;
+ }
+ my $table = { 'alignment' => [], 'length' => $self->end->rank - 1 };
+ my @all_pos = ( 1 .. $self->end->rank - 1 );
+ foreach my $wit ( sort { $a->sigil cmp $b->sigil } $self->tradition->witnesses ) {
+ if( $include ) {
+ next unless $include->{$wit->sigil};
+ }
+ # print STDERR "Making witness row(s) for " . $wit->sigil . "\n";
+ my @wit_path = $self->reading_sequence( $self->start, $self->end, $wit->sigil );
+ my @row = _make_witness_row( \@wit_path, \@all_pos, $noderefs );
+ push( @{$table->{'alignment'}},
+ { 'witness' => $wit->sigil, 'tokens' => \@row } );
+ if( $wit->is_layered ) {
+ my @wit_ac_path = $self->reading_sequence( $self->start, $self->end,
+ $wit->sigil.$self->ac_label, $wit->sigil );
+ my @ac_row = _make_witness_row( \@wit_ac_path, \@all_pos, $noderefs );
+ push( @{$table->{'alignment'}},
+ { 'witness' => $wit->sigil.$self->ac_label, 'tokens' => \@ac_row } );
+ }
}
+ return $table;
+}
- $self->collapsed( 1 );
+sub _make_witness_row {
+ my( $path, $positions, $noderefs ) = @_;
+ my %char_hash;
+ map { $char_hash{$_} = undef } @$positions;
+ my $debug = 0;
+ foreach my $rdg ( @$path ) {
+ my $rtext = $rdg->text;
+ $rtext = '#LACUNA#' if $rdg->is_lacuna;
+ print STDERR "rank " . $rdg->rank . "\n" if $debug;
+ # print STDERR "No rank for " . $rdg->id . "\n" unless defined $rdg->rank;
+ $char_hash{$rdg->rank} = $noderefs ? { 't' => $rdg }
+ : { 't' => $rtext };
+ }
+ my @row = map { $char_hash{$_} } @$positions;
+ # Fill in lacuna markers for undef spots in the row
+ my $last_el = shift @row;
+ my @filled_row = ( $last_el );
+ foreach my $el ( @row ) {
+ # If we are using node reference, make the lacuna node appear many times
+ # in the table. If not, use the lacuna tag.
+ if( $last_el && _el_is_lacuna( $last_el ) && !defined $el ) {
+ $el = $noderefs ? $last_el : { 't' => '#LACUNA#' };
+ }
+ push( @filled_row, $el );
+ $last_el = $el;
+ }
+ return @filled_row;
}
-sub expand_graph_edges {
- my $self = shift;
- # Our collation graph has only one edge between any two nodes.
- # This is great for display, but not so great for analysis.
- # Expand this so that each witness has its own edge between any
- # two reading nodes.
- return unless $self->collapsed;
-
- print STDERR "Expanding path edges in graph...\n";
-
- foreach my $edge( $self->paths ) {
- my $from = $edge->from;
- my $to = $edge->to;
- my @wits = split( /, /, $edge->label );
- if( grep { $_ eq 'majority' } @wits ) {
- push( @wits, split( /\|/, $edge->get_attribute( 'class' ) ) );
- }
- $self->del_path( $edge );
- foreach ( @wits ) {
- $self->add_path( $from, $to, $_ );
- }
+# Tiny utility function to say if a table element is a lacuna
+sub _el_is_lacuna {
+ my $el = shift;
+ return 1 if $el->{'t'} eq '#LACUNA#';
+ return 1 if ref( $el->{'t'} ) eq 'Text::Tradition::Collation::Reading'
+ && $el->{'t'}->is_lacuna;
+ return 0;
+}
+
+# Helper to turn the witnesses along columns rather than rows. Assumes
+# equal-sized rows.
+sub _turn_table {
+ my( $table ) = @_;
+ my $result = [];
+ return $result unless scalar @$table;
+ my $nrows = scalar @{$table->[0]};
+ foreach my $idx ( 0 .. $nrows - 1 ) {
+ foreach my $wit ( 0 .. $#{$table} ) {
+ $result->[$idx]->[$wit] = $table->[$wit]->[$idx];
+ }
}
- $self->collapsed( 0 );
+ return $result;
}
=back
Returns the beginning of the collation, a meta-reading with label '#START#'.
-=cut
+=item B<end>
+
+my $end = $collation->end();
+
+Returns the end of the collation, a meta-reading with label '#END#'.
-sub start {
- # Return the beginning reading of the graph.
- my $self = shift;
- my( $new_start ) = @_;
- if( $new_start ) {
- $self->del_reading( '#START#' );
- $self->graph->rename_node( $new_start, '#START#' );
- }
- return $self->reading('#START#');
-}
=item B<reading_sequence>
-my @readings = $graph->reading_sequence( $first, $last, $path[, $alt_path] );
+my @readings = $collation->reading_sequence( $first, $last, $path[, $alt_path] );
Returns the ordered list of readings, starting with $first and ending
with $last, along the given witness path. If no path is specified,
=cut
+# TODO Think about returning some lazy-eval iterator.
+
sub reading_sequence {
my( $self, $start, $end, $witness, $backup ) = @_;
my @readings = ( $start );
my %seen;
my $n = $start;
- while( $n && $n ne $end ) {
- if( exists( $seen{$n->name()} ) ) {
- warn "Detected loop at " . $n->name();
- last;
- }
- $seen{$n->name()} = 1;
-
- my $next = $self->next_reading( $n, $witness, $backup );
- warn "Did not find any path for $witness from reading " . $n->name
- unless $next;
- push( @readings, $next );
- $n = $next;
+ while( $n && $n->id ne $end->id ) {
+ if( exists( $seen{$n->id} ) ) {
+ warn "Detected loop at " . $n->id;
+ last;
+ }
+ $seen{$n->id} = 1;
+
+ my $next = $self->next_reading( $n, $witness, $backup );
+ unless( $next ) {
+ warn "Did not find any path for $witness from reading " . $n->id;
+ last;
+ }
+ push( @readings, $next );
+ $n = $next;
}
# Check that the last reading is our end reading.
my $last = $readings[$#readings];
- warn "Last reading found from " . $start->label() .
- " for witness $witness is not the end!"
- unless $last eq $end;
+ warn "Last reading found from " . $start->text .
+ " for witness $witness is not the end!"
+ unless $last->id eq $end->id;
return @readings;
}
=item B<next_reading>
-my $next_reading = $graph->next_reading( $reading, $witpath );
+my $next_reading = $collation->next_reading( $reading, $witpath );
Returns the reading that follows the given reading along the given witness
path.
sub next_reading {
# Return the successor via the corresponding path.
my $self = shift;
- return $self->_find_linked_reading( 'next', @_ );
+ my $answer = $self->_find_linked_reading( 'next', @_ );
+ return undef unless $answer;
+ return $self->reading( $answer );
}
=item B<prior_reading>
-my $prior_reading = $graph->prior_reading( $reading, $witpath );
+my $prior_reading = $collation->prior_reading( $reading, $witpath );
Returns the reading that precedes the given reading along the given witness
path.
sub prior_reading {
# Return the predecessor via the corresponding path.
my $self = shift;
- return $self->_find_linked_reading( 'prior', @_ );
+ my $answer = $self->_find_linked_reading( 'prior', @_ );
+ return $self->reading( $answer );
}
sub _find_linked_reading {
my( $self, $direction, $node, $path, $alt_path ) = @_;
my @linked_paths = $direction eq 'next'
- ? $node->outgoing() : $node->incoming();
+ ? $self->sequence->edges_from( $node )
+ : $self->sequence->edges_to( $node );
return undef unless scalar( @linked_paths );
# We have to find the linked path that contains all of the
# witnesses supplied in $path.
my( @path_wits, @alt_path_wits );
- @path_wits = $self->witnesses_of_label( $path ) if $path;
- @alt_path_wits = $self->witnesses_of_label( $alt_path ) if $alt_path;
+ @path_wits = sort( $self->witnesses_of_label( $path ) ) if $path;
+ @alt_path_wits = sort( $self->witnesses_of_label( $alt_path ) ) if $alt_path;
my $base_le;
my $alt_le;
foreach my $le ( @linked_paths ) {
- if( $le->name eq $self->baselabel ) {
- $base_le = $le;
- } else {
- my @le_wits = $self->witnesses_of_label( $le->name );
- if( _is_within( \@path_wits, \@le_wits ) ) {
- # This is the right path.
- return $direction eq 'next' ? $le->to() : $le->from();
- } elsif( _is_within( \@alt_path_wits, \@le_wits ) ) {
- $alt_le = $le;
- }
- }
+ if( $self->sequence->has_edge_attribute( @$le, $self->baselabel ) ) {
+ $base_le = $le;
+ }
+ my @le_wits = $self->path_witnesses( $le );
+ if( _is_within( \@path_wits, \@le_wits ) ) {
+ # This is the right path.
+ return $direction eq 'next' ? $le->[1] : $le->[0];
+ } elsif( _is_within( \@alt_path_wits, \@le_wits ) ) {
+ $alt_le = $le;
+ }
}
# Got this far? Return the alternate path if it exists.
- return $direction eq 'next' ? $alt_le->to() : $alt_le->from()
- if $alt_le;
+ return $direction eq 'next' ? $alt_le->[1] : $alt_le->[0]
+ if $alt_le;
# Got this far? Return the base path if it exists.
- return $direction eq 'next' ? $base_le->to() : $base_le->from()
- if $base_le;
+ return $direction eq 'next' ? $base_le->[1] : $base_le->[0]
+ if $base_le;
# Got this far? We have no appropriate path.
- warn "Could not find $direction node from " . $node->label
- . " along path $path";
+ warn "Could not find $direction node from " . $node->id
+ . " along path $path";
return undef;
}
my( $set1, $set2 ) = @_;
my $ret = @$set1; # will be 0, i.e. false, if set1 is empty
foreach my $el ( @$set1 ) {
- $ret = 0 unless grep { /^\Q$el\E$/ } @$set2;
+ $ret = 0 unless grep { /^\Q$el\E$/ } @$set2;
}
return $ret;
}
## INITIALIZATION METHODS - for use by parsers
-# Walk the paths for each witness in the graph, and return the nodes
-# that the graph has in common. If $using_base is true, some
-# different logic is needed.
-
-sub walk_witness_paths {
- my( $self, $end ) = @_;
- # For each witness, walk the path through the graph.
- # Then we need to find the common nodes.
- # TODO This method is going to fall down if we have a very gappy
- # text in the collation.
- my $paths = {};
- my @common_readings;
- foreach my $wit ( @{$self->tradition->witnesses} ) {
- my $curr_reading = $self->start;
- my @wit_path = $self->reading_sequence( $self->start, $end,
- $wit->sigil );
- $wit->path( \@wit_path );
-
- # Detect the common readings.
- @common_readings = _find_common( \@common_readings, \@wit_path );
- }
-
- # Mark all the nodes as either common or not.
- foreach my $cn ( @common_readings ) {
- print STDERR "Setting " . $cn->name . " / " . $cn->label
- . " as common node\n";
- $cn->make_common;
- }
- foreach my $n ( $self->readings() ) {
- $n->make_variant unless $n->is_common;
- }
- # Return an array of the common nodes in order.
- return @common_readings;
-}
-
-sub _find_common {
- my( $common_readings, $new_path ) = @_;
- my @cr;
- if( @$common_readings ) {
- foreach my $n ( @$new_path ) {
- push( @cr, $n ) if grep { $_ eq $n } @$common_readings;
- }
- } else {
- push( @cr, @$new_path );
- }
- return @cr;
-}
-sub _remove_common {
- my( $common_readings, $divergence ) = @_;
- my @cr;
- my %diverged;
- map { $diverged{$_->name} = 1 } @$divergence;
- foreach( @$common_readings ) {
- push( @cr, $_ ) unless $diverged{$_->name};
- }
- return @cr;
-}
-
-
-# An alternative to walk_witness_paths, for use when a collation is
-# constructed from a base text and an apparatus. We have the
-# sequences of readings and just need to add path edges.
+# For use when a collation is constructed from a base text and an apparatus.
+# We have the sequences of readings and just need to add path edges.
+# When we are done, clear out the witness path attributes, as they are no
+# longer needed.
+# TODO Find a way to replace the witness path attributes with encapsulated functions?
sub make_witness_paths {
my( $self ) = @_;
-
- my @common_readings;
- foreach my $wit ( @{$self->tradition->witnesses} ) {
- $self->make_witness_path( $wit );
- @common_readings = _find_common( \@common_readings, $wit->path );
-
- # If we have pre-corrected readings, we need to add paths
- # for those as well.
- if( $wit->has_ante_corr ) {
- my @path = @{$wit->path};
- foreach my $ac ( @{$wit->ante_corr} ) {
- # my( $offset, $length, $items ) = @$ac;
- # Figure out where the path needs to start and
- # end its divergence.
- my $start = $ac->[0] - 1;
- my $end = $ac->[0] + $ac->[1];
- my @chain;
- push( @chain, $path[$start] );
- push( @chain, @{$ac->[2]} );
- push( @chain, $path[$end] );
- $self->make_path_uncorrection( $wit->sigil, @chain );
- }
- @common_readings = _find_common( \@common_readings,
- $wit->uncorrected_path );
- }
+ foreach my $wit ( $self->tradition->witnesses ) {
+ # print STDERR "Making path for " . $wit->sigil . "\n";
+ $self->make_witness_path( $wit );
}
- return @common_readings;
}
sub make_witness_path {
my( $self, $wit ) = @_;
my @chain = @{$wit->path};
- $self->connect_readings_for_witness( $wit->sigil, @chain );
-}
-
-sub make_path_uncorrection {
- my( $self, $sig, @chain ) = @_;
- $sig .= ' (a.c.)';
- $self->connect_readings_for_witness( $sig, @chain );
-}
-
-sub connect_readings_for_witness {
- my( $self, $sig, @chain ) = @_;
+ my $sig = $wit->sigil;
foreach my $idx ( 0 .. $#chain-1 ) {
- $self->add_path( $chain[$idx], $chain[$idx+1], $sig );
+ $self->add_path( $chain[$idx], $chain[$idx+1], $sig );
}
+ if( $wit->is_layered ) {
+ @chain = @{$wit->uncorrected_path};
+ foreach my $idx( 0 .. $#chain-1 ) {
+ my $source = $chain[$idx];
+ my $target = $chain[$idx+1];
+ $self->add_path( $source, $target, $sig.$self->ac_label )
+ unless $self->has_path( $source, $target, $sig );
+ }
+ }
+ $wit->clear_path;
+ $wit->clear_uncorrected_path;
}
-
-sub common_readings {
+sub calculate_ranks {
my $self = shift;
- my @common = grep { $_->is_common } $self->readings();
- return sort { _cmp_position( $a->position, $b->position ) } @common;
-}
-
-# Calculate the relative positions of nodes in the graph, if they
-# were not given to us.
-sub calculate_positions {
- my( $self, @ordered_common ) = @_;
-
- # We have to calculate the position identifiers for each word,
- # keyed on the common nodes. This will be 'fun'. The end result
- # is a hash per witness, whose key is the word node and whose
- # value is its position in the text. Common nodes are always N,1
- # so have identical positions in each text.
-
- my $node_pos = {};
- foreach my $wit ( @{$self->tradition->witnesses} ) {
- print STDERR "Calculating positions in " . $wit->sigil . "\n";
- _update_positions_from_path( $wit->path, @ordered_common );
- _update_positions_from_path( $wit->uncorrected_path, @ordered_common )
- if $wit->has_ante_corr;
- }
-
- # DEBUG
- foreach my $r ( $self->readings() ) {
- print STDERR "Reading " . $r->name . "/" . $r->label . " has no position\n"
- unless( $r->has_position );
+ # Walk a version of the graph where every node linked by a relationship
+ # edge is fundamentally the same node, and do a topological ranking on
+ # the nodes in this graph.
+ my $topo_graph = Graph->new();
+ my %rel_containers;
+ my $rel_ctr = 0;
+ # Add the nodes
+ foreach my $r ( $self->readings ) {
+ next if exists $rel_containers{$r->id};
+ my @rels = $r->related_readings( 'colocated' );
+ if( @rels ) {
+ # Make a relationship container.
+ push( @rels, $r );
+ my $rn = 'rel_container_' . $rel_ctr++;
+ $topo_graph->add_vertex( $rn );
+ foreach( @rels ) {
+ $rel_containers{$_->id} = $rn;
+ }
+ } else {
+ # Add a new node to mirror the old node.
+ $rel_containers{$r->id} = $r->id;
+ $topo_graph->add_vertex( $r->id );
+ }
}
- $self->init_lemmata();
-}
-
-sub _update_positions_from_path {
- my( $path, @ordered_common ) = @_;
-
- # First we walk the given path, making a matrix for the witness
- # that corresponds to its eventual position identifier. Common
- # nodes always start a new row, and are thus always in the first
- # column.
- my $wit_matrix = [];
- my $cn = 0; # We should hit the common readings in order.
- my $row = [];
- foreach my $wn ( @{$path} ) {
- if( $wn eq $ordered_common[$cn] ) {
- # Set up to look for the next common node, and
- # start a new row of words.
- $cn++;
- push( @$wit_matrix, $row ) if scalar( @$row );
- $row = [];
- }
- push( @$row, $wn );
+ # Add the edges.
+ foreach my $r ( $self->readings ) {
+ foreach my $n ( $self->sequence->successors( $r->id ) ) {
+ my( $tfrom, $tto ) = ( $rel_containers{$r->id},
+ $rel_containers{$n} );
+ $DB::single = 1 unless $tfrom && $tto;
+ $topo_graph->add_edge( $tfrom, $tto );
+ }
}
- push( @$wit_matrix, $row ); # Push the last row onto the matrix
-
- # Now we have a matrix per witness, so that each row in the
- # matrix begins with a common node, and continues with all the
- # variant words that appear in the witness. We turn this into
- # real positions in row,cell format. But we need some
- # trickery in order to make sure that each node gets assigned
- # to only one position.
- foreach my $li ( 1..scalar(@$wit_matrix) ) {
- foreach my $di ( 1..scalar(@{$wit_matrix->[$li-1]}) ) {
- my $reading = $wit_matrix->[$li-1]->[$di-1];
- my $position = "$li,$di";
- $DB::single = 1 unless ref( $reading ) eq 'Text::Tradition::Collation::Reading';
-
- # If we have seen this node before, we need to compare
- # its position with what went before.
- unless( $reading->has_position &&
- _cmp_position( $position, $reading->position ) < 1 ) {
- # The new position ID replaces the old one.
- $reading->position( $position );
- } # otherwise, the old position needs to stay.
- }
+ # Now do the rankings, starting with the start node.
+ my $topo_start = $rel_containers{$self->start->id};
+ my $node_ranks = { $topo_start => 0 };
+ my @curr_origin = ( $topo_start );
+ # A little iterative function.
+ while( @curr_origin ) {
+ @curr_origin = _assign_rank( $topo_graph, $node_ranks, @curr_origin );
}
-}
-
-sub _cmp_position {
- my( $a, $b ) = @_;
- if ( $a && $b ) {
- my @pos_a = split(/,/, $a );
- my @pos_b = split(/,/, $b );
-
- my $big_cmp = $pos_a[0] <=> $pos_b[0];
- return $big_cmp if $big_cmp;
- # else
- return $pos_a[1] <=> $pos_b[1];
- } elsif ( $b ) { # a is undefined
- return -1;
- } elsif ( $a ) { # b is undefined
- return 1;
+ # Transfer our rankings from the topological graph to the real one.
+ foreach my $r ( $self->readings ) {
+ if( defined $node_ranks->{$rel_containers{$r->id}} ) {
+ $r->rank( $node_ranks->{$rel_containers{$r->id}} );
+ } else {
+ $DB::single = 1;
+ die "No rank calculated for node " . $r->id
+ . " - do you have a cycle in the graph?";
+ }
}
- return 0; # they are both undefined
-}
-
-sub all_positions {
- my $self = shift;
- my %positions = ();
- map { $positions{$_->position} = 1 } $self->readings;
- my @answer = sort { _cmp_position( $a, $b ) } keys( %positions );
- return @answer;
}
-sub readings_at_position {
- my( $self, $pos ) = @_;
- my @answer = grep { $_->position eq $pos } $self->readings;
- return @answer;
+sub _assign_rank {
+ my( $graph, $node_ranks, @current_nodes ) = @_;
+ # Look at each of the children of @current_nodes. If all the child's
+ # parents have a rank, assign it the highest rank + 1 and add it to
+ # @next_nodes. Otherwise skip it; we will return when the highest-ranked
+ # parent gets a rank.
+ my @next_nodes;
+ foreach my $c ( @current_nodes ) {
+ warn "Current reading $c has no rank!"
+ unless exists $node_ranks->{$c};
+ # print STDERR "Looking at child of node $c, rank "
+ # . $node_ranks->{$c} . "\n";
+ foreach my $child ( $graph->successors( $c ) ) {
+ next if exists $node_ranks->{$child};
+ my $highest_rank = -1;
+ my $skip = 0;
+ foreach my $parent ( $graph->predecessors( $child ) ) {
+ if( exists $node_ranks->{$parent} ) {
+ $highest_rank = $node_ranks->{$parent}
+ if $highest_rank <= $node_ranks->{$parent};
+ } else {
+ $skip = 1;
+ last;
+ }
+ }
+ next if $skip;
+ my $c_rank = $highest_rank + 1;
+ # print STDERR "Assigning rank $c_rank to node $child \n";
+ $node_ranks->{$child} = $c_rank;
+ push( @next_nodes, $child );
+ }
+ }
+ return @next_nodes;
}
-## Lemmatizer functions
-
-sub init_lemmata {
+# Another method to make up for rough collation methods. If the same reading
+# appears multiple times at the same rank, collapse the nodes.
+sub flatten_ranks {
my $self = shift;
-
- foreach my $position ( $self->all_positions ) {
- $self->lemmata->{$position} = undef;
- }
-
- foreach my $cr ( $self->common_readings ) {
- $self->lemmata->{$cr->position} = $cr->name;
+ my %unique_rank_rdg;
+ foreach my $rdg ( $self->readings ) {
+ next unless $rdg->has_rank;
+ my $key = $rdg->rank . "||" . $rdg->text;
+ if( exists $unique_rank_rdg{$key} ) {
+ # Combine!
+ # print STDERR "Combining readings at same rank: $key\n";
+ $self->merge_readings( $unique_rank_rdg{$key}, $rdg );
+ } else {
+ $unique_rank_rdg{$key} = $rdg;
+ }
}
}
-
-=item B<lemma_readings>
-
-my @state = $graph->lemma_readings( @readings_delemmatized );
-Takes a list of readings that have just been delemmatized, and returns
-a set of tuples of the form ['reading', 'state'] that indicates what
-changes need to be made to the graph.
-
-=over
-=item *
+## Utility functions
+
+# Return the string that joins together a list of witnesses for
+# display on a single path.
+sub witnesses_of_label {
+ my( $self, $label ) = @_;
+ my $regex = $self->wit_list_separator;
+ my @answer = split( /\Q$regex\E/, $label );
+ return @answer;
+}
-A state of 1 means 'lemmatize this reading'
+=begin testing
-=item *
+use Text::Tradition;
-A state of 0 means 'delemmatize this reading'
+my $cxfile = 't/data/Collatex-16.xml';
+my $t = Text::Tradition->new(
+ 'name' => 'inline',
+ 'input' => 'CollateX',
+ 'file' => $cxfile,
+ );
+my $c = $t->collation;
-=item *
+is( $c->common_predecessor( $c->reading('n9'), $c->reading('n23') )->id,
+ 'n20', "Found correct common predecessor" );
+is( $c->common_successor( $c->reading('n9'), $c->reading('n23') )->id,
+ '#END#', "Found correct common successor" );
-A state of undef means 'an ellipsis belongs in the text here because
-no decision has been made / an earlier decision was backed out'
+is( $c->common_predecessor( $c->reading('n19'), $c->reading('n17') )->id,
+ 'n16', "Found correct common predecessor for readings on same path" );
+is( $c->common_successor( $c->reading('n21'), $c->reading('n26') )->id,
+ '#END#', "Found correct common successor for readings on same path" );
-=back
+=end testing
=cut
-sub lemma_readings {
- my( $self, @toggled_off_nodes ) = @_;
-
- # First get the positions of those nodes which have been
- # toggled off.
- my $positions_off = {};
- map { $positions_off->{ $_->position } = $_->name } @toggled_off_nodes;
-
- # Now for each position, we have to see if a node is on, and we
- # have to see if a node has been turned off.
- my @answer;
- foreach my $pos ( $self->all_positions() ) {
- # Find the state of this position. If there is an active node,
- # its name will be the state; otherwise the state will be 0
- # (nothing at this position) or undef (ellipsis at this position)
- my $active = $self->lemmata->{$pos};
-
- # Is there a formerly active node that was toggled off?
- if( exists( $positions_off->{$pos} ) ) {
- my $off_node = $positions_off->{$pos};
- if( $active && $active ne $off_node) {
- push( @answer, [ $off_node, 0 ], [ $active, 1 ] );
- } else {
- push( @answer, [ $off_node, $active ] );
- }
-
- # No formerly active node, so we just see if there is a currently
- # active one.
- } elsif( $active ) {
- # Push the active node, whatever it is.
- push( @answer, [ $active, 1 ] );
- } else {
- # Push the state that is there. Arbitrarily use the first node
- # at that position.
- my @pos_nodes = $self->readings_at_position( $pos );
- push( @answer, [ $pos_nodes[0]->name, $self->lemmata->{$pos} ] );
- }
- }
-
- return @answer;
+## Return the closest reading that is a predecessor of both the given readings.
+sub common_predecessor {
+ my $self = shift;
+ return $self->common_in_path( @_, 'predecessors' );
}
-=item B<toggle_reading>
-
-my @readings_delemmatized = $graph->toggle_reading( $reading_name );
-
-Takes a reading node name, and either lemmatizes or de-lemmatizes
-it. Returns a list of all readings that are de-lemmatized as a result
-of the toggle.
-
-=cut
-
-sub toggle_reading {
- my( $self, $rname ) = @_;
-
- return unless $rname;
- my $reading = $self->reading( $rname );
- if( !$reading || $reading->is_common() ) {
- # Do nothing, it's a common node.
- return;
- }
-
- my $pos = $reading->position;
- my $old_state = $self->lemmata->{$pos};
- my @readings_off;
- if( $old_state && $old_state eq $rname ) {
- # Turn off the node. We turn on no others by default.
- push( @readings_off, $reading );
- } else {
- # Turn on the node.
- $self->lemmata->{$pos} = $rname;
- # Any other 'on' readings in the same position should be off.
- push( @readings_off, $self->same_position_as( $reading ) );
- # Any node that is an identical transposed one should be off.
- push( @readings_off, $reading->identical_readings );
- }
- @readings_off = unique_list( @readings_off );
-
- # Turn off the readings that need to be turned off.
- my @readings_delemmatized;
- foreach my $n ( @readings_off ) {
- my $state = $self->lemmata->{$n->position};
- if( $state && $state eq $n->name ) {
- # this reading is still on, so turn it off
- push( @readings_delemmatized, $n );
- my $new_state = undef;
- if( $n eq $reading ) {
- # This is the reading that was clicked, so if there are no
- # other readings there, turn off the position. In all other
- # cases, restore the ellipsis.
- my @other_n = $self->same_position_as( $n );
- $new_state = 0 unless @other_n;
- }
- $self->lemmata->{$n->position} = $new_state;
- } elsif( $old_state && $old_state eq $n->name ) {
- # another reading has already been turned on here
- push( @readings_delemmatized, $n );
- } # else some other reading was on anyway, so pass.
- }
- return @readings_delemmatized;
+sub common_successor {
+ my $self = shift;
+ return $self->common_in_path( @_, 'successors' );
}
-sub same_position_as {
- my( $self, $reading ) = @_;
- my $pos = $reading->position;
- my @same = grep { $_ ne $reading } $self->readings_at_position( $reading->position );
- return @same;
+sub common_in_path {
+ my( $self, $r1, $r2, $dir ) = @_;
+ my $iter = $r1->rank > $r2->rank ? $r1->rank : $r2->rank;
+ $iter = $self->end->rank - $iter if $dir eq 'successors';
+ my @candidates;
+ my @last_checked = ( $r1, $r2 );
+ my %all_seen;
+ while( !@candidates ) {
+ my @new_lc;
+ foreach my $lc ( @last_checked ) {
+ foreach my $p ( $lc->$dir ) {
+ if( $all_seen{$p->id} ) {
+ push( @candidates, $p );
+ } else {
+ $all_seen{$p->id} = 1;
+ push( @new_lc, $p );
+ }
+ }
+ }
+ @last_checked = @new_lc;
+ }
+ my @answer = sort { $a->rank <=> $b->rank } @candidates;
+ return $dir eq 'predecessors' ? pop( @answer ) : shift ( @answer );
}
-# Return the string that joins together a list of witnesses for
-# display on a single path.
-sub path_label {
- my $self = shift;
- return join( $self->wit_list_separator, @_ );
-}
+no Moose;
+__PACKAGE__->meta->make_immutable;
-sub witnesses_of_label {
- my( $self, $label ) = @_;
- my $regex = $self->wit_list_separator;
- my @answer = split( /\Q$regex\E/, $label );
- return @answer;
-}
+=head1 BUGS / TODO
-sub unique_list {
- my( @list ) = @_;
- my %h;
- map { $h{$_->name} = $_ } @list;
- return values( %h );
-}
+=over
-sub add_hash_entry {
- my( $hash, $key, $entry ) = @_;
- if( exists $hash->{$key} ) {
- push( @{$hash->{$key}}, $entry );
- } else {
- $hash->{$key} = [ $entry ];
- }
-}
+=item * Think about making Relationship objects again
-no Moose;
-__PACKAGE__->meta->make_immutable;
+=back