use Encode qw( decode_utf8 );
use File::Temp;
use Graph;
-use Graph::Easy;
use IPC::Run qw( run binary );
use Text::CSV_XS;
-use Text::Tradition::Collation::Path;
use Text::Tradition::Collation::Reading;
-use Text::Tradition::Collation::Relationship;
+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',
- add_lacuna => 'add_node',
- del_reading => 'del_node',
- add_path => 'add_edge',
- del_path => 'del_edge',
- reading => 'node',
- path => 'edge',
- readings => 'nodes',
- paths => 'edges',
- relationships => 'edges',
+ paths => 'edges',
},
- default => sub { Graph::Easy->new( undirected => 0 ) },
);
-
-
-has 'tradition' => ( # TODO should this not be ro?
- is => 'rw',
- isa => 'Text::Tradition',
- );
-
-has 'svg' => (
- is => 'ro',
- isa => 'Str',
- writer => '_save_svg',
- predicate => 'has_svg',
- );
-
-has 'graphml' => (
- is => 'ro',
- isa => 'Str',
- writer => '_save_graphml',
- predicate => 'has_graphml',
- );
-
-has 'csv' => (
+
+has 'relations' => (
+ is => 'ro',
+ isa => 'Text::Tradition::Collation::RelationshipStore',
+ handles => {
+ relationships => 'relationships',
+ related_readings => 'related_readings',
+ },
+ writer => '_set_relations',
+ );
+
+has 'tradition' => (
is => 'ro',
- isa => 'Str',
- writer => '_save_csv',
- predicate => 'has_csv',
+ 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',
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');
- $self->graph->use_class('edge', 'Text::Tradition::Collation::Path');
-
- # Pass through any graph-specific options.
- my $shape = exists( $args->{'shape'} ) ? $args->{'shape'} : 'ellipse';
- $self->graph->set_attribute( 'node', 'shape', $shape );
-
- # Start and end points for all texts
- $self->start( 'INIT' );
- $self->end( 'INIT' );
+ 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 } ) );
}
-around add_lacuna => sub {
- my $orig = shift;
- my $self = shift;
- my $id = shift @_;
- my $l = $self->$orig( '#LACUNA_' . $id . '#' );
- $l->is_lacuna( 1 );
- return $l;
+### Reading construct/destruct functions
+
+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;
};
-# Wrapper around add_path
+around del_reading => sub {
+ my $orig = shift;
+ my $self = shift;
+ my $arg = shift;
+
+ if( ref( $arg ) eq 'Text::Tradition::Collation::Reading' ) {
+ $arg = $arg->id;
+ }
+ # Remove the reading from the graphs.
+ $self->sequence->delete_vertex( $arg );
+ $self->relations->delete_reading( $arg );
+
+ # Carry on.
+ $self->$orig( $arg );
+};
-around add_path => sub {
- my $orig = shift;
- my $self = shift;
+# merge_readings( $main, $to_be_deleted );
- # 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
- # NOTE 'reading' will currently return readings and segments
- 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 && $path->class eq 'edge.path' ) {
- return;
- }
- }
- # Do the deed
- $self->$orig( @_ );
-};
+sub merge_readings {
+ 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 );
+}
-# Wrapper around paths
-around paths => sub {
- my $orig = shift;
- my $self = shift;
- my @result = grep { $_->sub_class eq 'path' } $self->$orig( @_ );
- return @result;
-};
+# 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 );
+}
-around relationships => sub {
- my $orig = shift;
- my $self = shift;
- my @result = grep { $_->sub_class eq 'relationship' } $self->$orig( @_ );
- return @result;
+### 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 );
};
-# Wrapper around merge_nodes
-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( @_ );
+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, $source, $target, $label ) = @_;
- my @paths = $source->edges_to( $target );
- my @relevant = grep { $_->label eq $label } @paths;
- return scalar @relevant;
+ 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 );
}
-## Dealing with relationships between readings. This is a different
-## sort of graph edge. Return a success/failure value and a list of
-## node pairs that have been linked.
+=head2 add_relationship( $reading1, $reading2, $definition )
-sub add_relationship {
- my( $self, $source, $target, $options ) = @_;
-
- # Make sure there is not another relationship between these two
- # readings already
- $source = $self->reading( $source )
- unless ref( $source ) && $source->isa( 'Graph::Easy::Node' );
- $target = $self->reading( $target )
- unless ref( $target ) && $target->isa( 'Graph::Easy::Node' );
- foreach my $rel ( $source->edges_to( $target ), $target->edges_to( $source ) ) {
- if( $rel->class eq 'edge.relationship' ) {
- return ( undef, "Relationship already exists between these readings" );
- }
- }
- if( $options->{'equal_rank'} && !relationship_valid( $source, $target ) ) {
- return ( undef, 'Relationship creates witness loop' );
- }
+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.
- # TODO Think about positional hilarity if relationships are added after positions
- # are assigned.
-
- my @joined = ( [ $source->name, $target->name ] ); # Keep track of the nodes we join.
-
- $options->{'this_relation'} = [ $source, $target ];
- my $rel;
- eval { $rel = Text::Tradition::Collation::Relationship->new( %$options ) };
- if( $@ ) {
- return ( undef, $@ );
- }
- $self->graph->add_edge( $source, $target, $rel );
-
- # TODO Handle global relationship setting
+=cut
- return( 1, @joined );
+# 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 );
}
-sub relationship_valid {
- my( $source, $target ) = @_;
- # Check that linking the source and target in a relationship won't lead
- # to a path loop for any witness.
- my @proposed_related = ( $source, $target );
- push( @proposed_related, $source->related_readings );
- push( @proposed_related, $target->related_readings );
- my %pr_ids;
- map { $pr_ids{ $_->name } = 1 } @proposed_related;
- # The lists of 'in' and 'out' should not have any element that appears
- # in 'proposed_related'.
- foreach my $pr ( @proposed_related ) {
- foreach my $e ( grep { $_->sub_class eq 'path' } $pr->incoming ) {
- if( exists $pr_ids{ $e->from->name } ) {
- return 0;
- }
- }
- foreach my $e ( grep { $_->sub_class eq 'path' } $pr->outgoing ) {
- if( exists $pr_ids{ $e->to->name } ) {
- return 0;
- }
- }
- }
- return 1;
+=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_paths();
+ 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 );
## TODO REMOVE
# $dotfile->unlink_on_destroy(0);
binmode $dotfile, ':utf8';
- print $dotfile $self->as_dot();
+ print $dotfile $dot;
push( @cmd, $dotfile->filename );
run( \@cmd, ">", binary(), \$svg );
$svg = decode_utf8( $svg );
- $self->_save_svg( $svg );
- $self->expand_graph_paths();
return $svg;
}
+
=item B<as_dot>
-print $graph->as_dot( $view, $recalculate );
+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
=cut
sub as_dot {
- my( $self, $view ) = @_;
- $view = 'path' unless $view;
+ 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 ];\n";
+ $dot .= "\tgraph [ rankdir=LR,bgcolor=none ];\n";
$dot .= sprintf( "\tnode [ fontsize=%d, fillcolor=%s, style=%s, shape=%s ];\n",
- 11, "white", "filled", $self->graph->get_attribute( 'node', 'shape' ) );
+ 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->name eq $reading->label;
- $dot .= sprintf( "\t\"%s\" [ label=\"%s\" ];\n", $reading->name, $reading->label );
+ next if $reading->id eq $reading->text;
+ my $label = $reading->text;
+ $label =~ s/\"/\\\"/g;
+ $dot .= sprintf( "\t\"%s\" [ label=\"%s\" ];\n", $reading->id, $label );
}
-
- my @edges = $view eq 'relationship' ? $self->relationships : $self->paths;
- foreach my $edge ( @edges ) {
- my %variables = ( 'color' => '#000000',
+
+ # 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' => $edge->label,
+ 'label' => $witstr,
);
my $varopts = join( ', ', map { $_.'="'.$variables{$_}.'"' } sort keys %variables );
- $dot .= sprintf( "\t\"%s\" -> \"%s\" [ %s ];\n",
- $edge->from->name, $edge->to->name, $varopts );
+ $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';
# Add the data keys for the graph
my %graph_data_keys;
my $gdi = 0;
- my @graph_attributes = qw/ wit_list_separator baselabel linear ac_label /;
+ 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' );
# Add the data keys for nodes
my %node_data_keys;
my $ndi = 0;
- foreach my $datum ( qw/ name reading identical rank class / ) {
+ 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', 'string' );
+ $key->setAttribute( 'attr.type', $node_data{$datum} );
$key->setAttribute( 'for', 'node' );
$key->setAttribute( 'id', $node_data_keys{$datum} );
}
# Add the data keys for edges, i.e. witnesses
my $edi = 0;
my %edge_data_keys;
- my @string_keys = qw/ class witness relationship /;
- my @bool_keys = qw/ extra equal_rank non_correctable non_independent /;
- foreach my $edge_key( @string_keys ) {
- $edge_data_keys{$edge_key} = 'de'.$edi++;
+ 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', $edge_key );
- $key->setAttribute( 'attr.type', 'string' );
- $key->setAttribute( 'for', 'edge' );
- $key->setAttribute( 'id', $edge_data_keys{$edge_key} );
- }
- foreach my $edge_key( @bool_keys ) {
- $edge_data_keys{$edge_key} = 'de'.$edi++;
- my $key = $root->addNewChild( $graphml_ns, 'key' );
- $key->setAttribute( 'attr.name', $edge_key );
- $key->setAttribute( 'attr.type', 'boolean' );
+ $key->setAttribute( 'attr.name', $datum );
+ $key->setAttribute( 'attr.type', $edge_data{$datum} );
$key->setAttribute( 'for', 'edge' );
- $key->setAttribute( 'id', $edge_data_keys{$edge_key} );
+ $key->setAttribute( 'id', $edge_data_keys{$datum} );
}
-
- # Add the graph, its nodes, and its edges
- my $graph = $root->addNewChild( $graphml_ns, 'graph' );
- $graph->setAttribute( 'edgedefault', 'directed' );
- $graph->setAttribute( 'id', $self->tradition->name );
- $graph->setAttribute( 'parse.edgeids', 'canonical' );
- $graph->setAttribute( 'parse.edges', scalar($self->paths) );
- $graph->setAttribute( 'parse.nodeids', 'canonical' );
- $graph->setAttribute( 'parse.nodes', scalar($self->readings) );
- $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 ) {
- _add_graphml_data( $graph, $graph_data_keys{$datum}, $self->$datum );
+ 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;
# Add our readings to the graph
- foreach my $n ( sort { $a->name cmp $b->name } $self->readings ) {
- my $node_el = $graph->addNewChild( $graphml_ns, 'node' );
+ 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->name } = $node_xmlid;
+ $node_hash{ $n->id } = $node_xmlid;
$node_el->setAttribute( 'id', $node_xmlid );
- _add_graphml_data( $node_el, $node_data_keys{'name'}, $n->name );
- _add_graphml_data( $node_el, $node_data_keys{'reading'}, $n->label );
- _add_graphml_data( $node_el, $node_data_keys{'rank'}, $n->rank )
- if $n->has_rank;
- _add_graphml_data( $node_el, $node_data_keys{'class'}, $n->sub_class );
- _add_graphml_data( $node_el, $node_data_keys{'identical'}, $n->primary->name )
- if $n->has_primary && $n->primary ne $n;
+ foreach my $d ( keys %node_data ) {
+ my $nval = $n->$d;
+ _add_graphml_data( $node_el, $node_data_keys{$d}, $nval )
+ if defined $nval;
+ }
}
- # Add the path and relationship edges
+ # Add the path edges to the sequence graph
my $edge_ctr = 0;
- foreach my $e ( sort { $a->from->name cmp $b->from->name } $self->graph->edges() ) {
- my( $name, $from, $to ) = ( 'e'.$edge_ctr++,
- $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 );
- # Add the edge class
- _add_graphml_data( $edge_el, $edge_data_keys{'class'}, $e->sub_class );
-
- # For some classes we have extra information to save.
- if( $e->sub_class eq 'path' ) {
- # It's a witness path, so add the witness
- my $base = $e->label;
- my $key = $edge_data_keys{'witness_main'};
- # Is this an ante-corr witness?
- my $aclabel = $self->ac_label;
- if( $e->label =~ /^(.*)\Q$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'}, 'true' );
- }
- _add_graphml_data( $edge_el, $edge_data_keys{'witness'}, $base );
- } elsif( $e->sub_class eq 'relationship' ) {
- # It's a relationship, so save the relationship data
- _add_graphml_data( $edge_el, $edge_data_keys{'relationship'}, $e->label );
- _add_graphml_data( $edge_el, $edge_data_keys{'equal_rank'}, $e->equal_rank );
- _add_graphml_data( $edge_el, $edge_data_keys{'non_correctable'}, $e->non_correctable );
- _add_graphml_data( $edge_el, $edge_data_keys{'non_independent'}, $e->non_independent );
- }
- }
+ 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 );
# Save and return the thing
my $result = decode_utf8( $graphml->toString(1) );
- $self->_save_graphml( $result );
return $result;
}
=item B<as_csv>
-print $graph->as_csv( $recalculate )
+print $collation->as_csv( $recalculate )
Returns a CSV alignment table representation of the collation graph, one
-row per witness (or witness uncorrected.) Unless $recalculate is passed
-(and is a true value), the method will return a cached copy of the CSV
-after the first call to the method.
+row per witness (or witness uncorrected.)
=cut
sub as_csv {
- my( $self, $recalc ) = @_;
- return $self->csv if $self->has_csv;
+ my( $self ) = @_;
my $table = $self->make_alignment_table;
my $csv = Text::CSV_XS->new( { binary => 1, quote_null => 0 } );
my @result;
- foreach my $row ( @$table ) {
- $csv->combine( @$row );
+ # 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 ) );
}
- $self->_save_csv( join( "\n", @result ) );
- return $self->csv;
+ return join( "\n", @result );
}
-# Make an alignment table - $noderefs controls whether the objects
-# in the table are the nodes or simply their readings.
+=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 ) = @_;
warn "Need a linear graph in order to make an alignment table";
return;
}
- my $table;
- my @all_pos = ( 0 .. $self->end->rank - 1 );
- foreach my $wit ( $self->tradition->witnesses ) {
+ 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 @row = _make_witness_row( $wit->path, \@all_pos, $noderefs );
- unshift( @row, $wit->sigil );
- push( @$table, \@row );
- if( $wit->has_ante_corr ) {
- my @ac_row = _make_witness_row( $wit->uncorrected_path, \@all_pos, $noderefs );
- unshift( @ac_row, $wit->sigil . $self->ac_label );
- push( @$table, \@ac_row );
+ 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 } );
}
}
-
- if( $include ) {
- my $winnowed = [];
- # Winnow out the rows for any witness not included.
- foreach my $row ( @$table ) {
- next unless $include->{$row->[0]};
- push( @$winnowed, $row );
- }
- $table = $winnowed;
- }
-
- # Return a table where the witnesses read in columns rather than rows.
- my $turned = _turn_table( $table );
- # TODO We should really go through and delete empty rows.
- return $turned;
+ return $table;
}
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 "No rank for " . $rdg->name . "\n" unless defined $rdg->rank;
- $char_hash{$rdg->rank} = $noderefs ? $rdg : $rtext;
+ 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
# 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 : '#LACUNA#';
+ $el = $noderefs ? $last_el : { 't' => '#LACUNA#' };
}
push( @filled_row, $el );
$last_el = $el;
# Tiny utility function to say if a table element is a lacuna
sub _el_is_lacuna {
my $el = shift;
- return 1 if $el eq '#LACUNA#';
- return 1 if ref( $el ) eq 'Text::Tradition::Collation::Reading'
- && $el->is_lacuna;
+ return 1 if $el->{'t'} eq '#LACUNA#';
+ return 1 if ref( $el->{'t'} ) eq 'Text::Tradition::Collation::Reading'
+ && $el->{'t'}->is_lacuna;
return 0;
}
return $result;
}
-
-sub collapse_graph_paths {
- my $self = shift;
- # Our collation graph has an path per witness. This is great for
- # calculation purposes, but terrible for display. Thus we want to
- # display only one path between any two nodes.
-
- return if $self->collapsed;
-
- print STDERR "Collapsing witness paths 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;
- # But don't compress if there are only a few witnesses.
- $majority = 4 if $majority < 4;
- foreach my $node ( $self->readings ) {
- my $newlabels = {};
- # We will visit each node, so we only look ahead.
- foreach my $edge ( $node->outgoing() ) {
- next unless $edge->class eq 'edge.path';
- add_hash_entry( $newlabels, $edge->to->name, $edge->name );
- $self->del_path( $edge );
- }
-
- foreach my $newdest ( keys %$newlabels ) {
- my $label;
- my @compressed_wits = @{$newlabels->{$newdest}};
- if( @compressed_wits < $majority ) {
- $label = join( ', ', sort( @{$newlabels->{$newdest}} ) );
- } else {
- ## TODO FIX THIS HACK
- my @aclabels;
- foreach my $wit ( @compressed_wits ) {
- push( @aclabels, $wit ) if( $wit =~ /^(.*?)(\s*\(?a\.\s*c\.\)?)$/ );
- }
- $label = join( ', ', 'majority', sort( @aclabels ) );
- }
-
- my $newpath = $self->add_path( $node, $self->reading( $newdest ), $label );
- $newpath->hidden_witnesses( \@compressed_wits );
- }
- }
-
- $self->collapsed( 1 );
-}
-
-sub expand_graph_paths {
- my $self = shift;
- # Our collation graph has only one path between any two nodes.
- # This is great for display, but not so great for analysis.
- # Expand this so that each witness has its own path between any
- # two reading nodes.
- return unless $self->collapsed;
-
- print STDERR "Expanding witness paths in graph...\n";
- foreach my $path( $self->paths ) {
- my $from = $path->from;
- my $to = $path->to;
- warn sprintf( "No hidden witnesses on %s -> %s ?", $from->name, $to->name )
- unless $path->has_hidden_witnesses;
- my @wits = @{$path->hidden_witnesses};
- $self->del_path( $path );
- foreach ( @wits ) {
- $self->add_path( $from, $to, $_ );
- }
- }
- $self->collapsed( 0 );
-}
-
=back
=head2 Navigation methods
Returns the beginning of the collation, a meta-reading with label '#START#'.
-=cut
-
-sub start {
- # Return the beginning reading of the graph.
- my( $self, $new_start ) = @_;
- my $start = $self->reading( '#START#' );
- if( ref( $new_start ) eq 'Text::Tradition::Collation::Reading' ) {
- # Replace the existing start node.
- $self->del_reading( '#START#' );
- $self->graph->rename_node( $new_start, '#START#' );
- $start = $new_start;
- } elsif ( $new_start && $new_start eq 'INIT' ) {
- # Make a new start node.
- $start = $self->add_reading( '#START#' );
- }
- # Make sure the start node is a meta node
- $start->is_meta( 1 );
- # Make sure the start node has a start position.
- unless( $start->has_rank ) {
- $start->rank( '0' );
- }
- return $start;
-}
-
=item B<end>
my $end = $collation->end();
Returns the end of the collation, a meta-reading with label '#END#'.
-=cut
-
-sub end {
- my $self = shift;
- my( $new_end ) = @_;
- my $end = $self->reading( '#END#' );
- if( ref( $new_end ) eq 'Text::Tradition::Collation::Reading' ) {
- $self->del_reading( '#END#' );
- $self->graph->rename_node( $new_end, '#END#' );
- $end = $new_end
- } elsif ( $new_end && $new_end eq 'INIT' ) {
- # Make a new start node.
- $end = $self->add_reading( '#END#' );
- }
- # Make sure the start node is a meta node
- $end->is_meta( 1 );
- return $end;
-}
=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,
my @readings = ( $start );
my %seen;
my $n = $start;
- while( $n && $n ne $end ) {
- if( exists( $seen{$n->name()} ) ) {
- warn "Detected loop at " . $n->name();
+ while( $n && $n->id ne $end->id ) {
+ if( exists( $seen{$n->id} ) ) {
+ warn "Detected loop at " . $n->id;
last;
}
- $seen{$n->name()} = 1;
+ $seen{$n->id} = 1;
my $next = $self->next_reading( $n, $witness, $backup );
- warn "Did not find any path for $witness from reading " . $n->name
- unless $next;
+ 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() .
+ warn "Last reading found from " . $start->text .
" for witness $witness is not the end!"
- unless $last eq $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 ) {
+ if( $self->sequence->has_edge_attribute( @$le, $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;
- }
}
+ 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()
+ 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()
+ 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
+ warn "Could not find $direction node from " . $node->id
. " along path $path";
return undef;
}
## 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.
-# NOTE This does not create paths; it merely finds common readings.
-
-sub walk_witness_paths {
- my( $self ) = @_;
- # 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, $self->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;
-}
-
# 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 ) = @_;
foreach my $wit ( $self->tradition->witnesses ) {
- print STDERR "Making path for " . $wit->sigil . "\n";
+ # print STDERR "Making path for " . $wit->sigil . "\n";
$self->make_witness_path( $wit );
}
}
foreach my $idx ( 0 .. $#chain-1 ) {
$self->add_path( $chain[$idx], $chain[$idx+1], $sig );
}
- if( $wit->has_ante_corr ) {
+ if( $wit->is_layered ) {
@chain = @{$wit->uncorrected_path};
foreach my $idx( 0 .. $#chain-1 ) {
my $source = $chain[$idx];
unless $self->has_path( $source, $target, $sig );
}
}
+ $wit->clear_path;
+ $wit->clear_uncorrected_path;
}
sub calculate_ranks {
my $rel_ctr = 0;
# Add the nodes
foreach my $r ( $self->readings ) {
- next if exists $rel_containers{$r->name};
+ next if exists $rel_containers{$r->id};
my @rels = $r->related_readings( 'colocated' );
if( @rels ) {
# Make a relationship container.
my $rn = 'rel_container_' . $rel_ctr++;
$topo_graph->add_vertex( $rn );
foreach( @rels ) {
- $rel_containers{$_->name} = $rn;
+ $rel_containers{$_->id} = $rn;
}
} else {
# Add a new node to mirror the old node.
- $rel_containers{$r->name} = $r->name;
- $topo_graph->add_vertex( $r->name );
+ $rel_containers{$r->id} = $r->id;
+ $topo_graph->add_vertex( $r->id );
}
}
- # Add the edges. Need only one edge between any pair of nodes.
+ # Add the edges.
foreach my $r ( $self->readings ) {
- foreach my $n ( $r->neighbor_readings( 'forward' ) ) {
- my( $tfrom, $tto ) = ( $rel_containers{$r->name},
- $rel_containers{$n->name} );
- $topo_graph->add_edge( $tfrom, $tto )
- unless $topo_graph->has_edge( $tfrom, $tto );
+ 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 );
}
}
# Now do the rankings, starting with the start node.
- my $topo_start = $rel_containers{$self->start->name};
+ my $topo_start = $rel_containers{$self->start->id};
my $node_ranks = { $topo_start => 0 };
my @curr_origin = ( $topo_start );
# A little iterative function.
}
# Transfer our rankings from the topological graph to the real one.
foreach my $r ( $self->readings ) {
- if( defined $node_ranks->{$rel_containers{$r->name}} ) {
- $r->rank( $node_ranks->{$rel_containers{$r->name}} );
+ 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->name
+ die "No rank calculated for node " . $r->id
. " - do you have a cycle in the graph?";
}
}
my $key = $rdg->rank . "||" . $rdg->text;
if( exists $unique_rank_rdg{$key} ) {
# Combine!
- print STDERR "Combining readings at same rank: $key\n";
+ # print STDERR "Combining readings at same rank: $key\n";
$self->merge_readings( $unique_rank_rdg{$key}, $rdg );
} else {
$unique_rank_rdg{$key} = $rdg;
# 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, @_ );
-}
-
sub witnesses_of_label {
my( $self, $label ) = @_;
my $regex = $self->wit_list_separator;
return @answer;
}
-sub add_hash_entry {
- my( $hash, $key, $entry ) = @_;
- if( exists $hash->{$key} ) {
- push( @{$hash->{$key}}, $entry );
- } else {
- $hash->{$key} = [ $entry ];
- }
+=begin testing
+
+use Text::Tradition;
+
+my $cxfile = 't/data/Collatex-16.xml';
+my $t = Text::Tradition->new(
+ 'name' => 'inline',
+ 'input' => 'CollateX',
+ 'file' => $cxfile,
+ );
+my $c = $t->collation;
+
+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" );
+
+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" );
+
+=end testing
+
+=cut
+
+## 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' );
+}
+
+sub common_successor {
+ my $self = shift;
+ return $self->common_in_path( @_, 'successors' );
+}
+
+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 );
}
no Moose;
=over
-=item * Rationalize edge classes
-
-=item * Port the internal graph from Graph::Easy to Graph
+=item * Think about making Relationship objects again
=back
projects / scpubgit/stemmatology.git / blobdiff