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::Tradition::Collation::Path;
-use Text::Tradition::Collation::Position;
+use Text::CSV_XS;
use Text::Tradition::Collation::Reading;
-use Text::Tradition::Collation::Relationship;
-use Text::Tradition::Collation::Segment;
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',
- segments => '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 'relations' => (
+ is => 'ro',
+ isa => 'Graph',
+ default => sub { Graph->new( undirected => 1 ) },
+ handles => {
+ relationships => 'edges',
+ },
+ );
-has 'graphml' => (
+has 'tradition' => (
is => 'ro',
- isa => 'Str',
- 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',
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 );
+ my $self = shift;
+ $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_vertex( $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
- # 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;
+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_vertex( $arg );
+
+ # Carry on.
+ $self->$orig( $arg );
};
-# Wrapper around paths
-around paths => sub {
- my $orig = shift;
- my $self = shift;
+# merge_readings( $main, $to_be_deleted );
- my @result = grep { $_->sub_class eq 'path' } $self->$orig( @_ );
- return @result;
-};
+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 );
+ }
+ foreach my $rel ( $self->relations->edges_at( $deleted ) ) {
+ my @vector = ( $kept );
+ push( @vector, $rel->[0] eq $deleted ? $rel->[1] : $rel->[0] );
+ next if $vector[0] eq $vector[1]; # Don't add a self loop
+ # Is there a relationship here already? If so, keep it.
+ # TODO Warn about conflicting relationships
+ next if $self->relations->has_edge( @vector );
+ # If not, adopt the relationship that would be deleted.
+ $self->relations->add_edge( @vector );
+ my $attr = $self->relations->get_edge_attributes( @$rel );
+ $self->relations->set_edge_attributes( @vector, $attr );
+ }
+
+ # 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 );
+}
-around relationships => sub {
- my $orig = shift;
- my $self = shift;
- my @result = grep { $_->sub_class eq 'relationship' } $self->$orig( @_ );
- return @result;
-};
-around readings => sub {
- my $orig = shift;
- my $self = shift;
- my @result = grep { $_->sub_class ne 'segment' } $self->$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 segments => sub {
- my $orig = shift;
- my $self = shift;
- my @result = grep { $_->sub_class eq 'segment' } $self->$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 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 );
-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( @_ );
+ 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 groups of readings, i.e. segments.
+### Relationship logic
-sub add_segment {
- my( $self, @items ) = @_;
- my $segment = Text::Tradition::Collation::Segment->new( 'members' => \@items );
- return $segment;
-}
+=head2 add_relationship( $reading1, $reading2, $definition )
-## 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.
+Adds the specified relationship between the two readings. A relationship
+is transitive (i.e. undirected), and must have the following attributes
+specified in the hashref $definition:
-sub add_relationship {
- my( $self, $source, $target, $options ) = @_;
+=over 4
+
+=item * type - Can be one of spelling, orthographic, grammatical, meaning, repetition, transposition. The first three are only valid relationships between readings that occur at the same point in the text.
+
+=item * non_correctable - (Optional) True if the reading would not have been corrected independently.
+=item * non_independent - (Optional) True if the variant is unlikely to have occurred independently in unrelated witnesses.
+
+=item * global - (Optional) A meta-attribute, to set the same relationship between readings with the same text whenever they occur in the same place.
+
+=back
+
+=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, $options ) = $self->_stringify_args( @_ );
+
+ # Check the options
+ if( !defined $options->{'type'} ||
+ $options->{'type'} !~ /^(spelling|orthographic|grammatical|meaning|lexical|repetition|transposition)$/i ) {
+ my $t = $options->{'type'} ? $options->{'type'} : '';
+ return( undef, "Invalid or missing type " . $options->{'type'} );
+ }
+ unless ( $options->{'type'} =~ /^(repetition|transposition)$/ ) {
+ $options->{'colocated'} = 1;
+ }
+
# Make sure there is not another relationship between these two
- # readings or segments 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" );
+ # readings already
+ if( $self->relations->has_edge( $source, $target ) ) {
+ return ( undef, "Relationship already exists between these readings" );
+ }
+ if( !$self->relationship_valid( $source, $target, $options->{'type'} ) ) {
+ return ( undef, 'Relationship creates witness loop' );
+ }
+
+ my @vector = ( $source, $target );
+ $self->relations->add_edge( @vector );
+ $self->relations->set_edge_attributes( @vector, $options );
+
+ # TODO Handle global relationship setting
+
+ return( 1, @vector );
+}
+
+sub relationship_valid {
+ my( $self, $source, $target, $rel ) = @_;
+ if( $rel eq 'repetition' ) {
+ return 1;
+ } elsif ( $rel eq 'transposition' ) {
+ # Check that the two readings do not appear in the same witness.
+ my %seen_wits;
+ map { $seen_wits{$_} = 1 } $self->reading_witnesses( $source );
+ foreach my $w ( $self->reading_witnesses( $target ) ) {
+ return 0 if $seen_wits{$w};
+ }
+ return 1;
} else {
- return ( undef, "There is a witness path between these readings" );
+ # Check that linking the source and target in a relationship won't lead
+ # to a path loop for any witness. First make a lookup table of all the
+ # readings related to either the source or the target.
+ my @proposed_related = ( $source, $target );
+ push( @proposed_related, $self->related_readings( $source, 'colocated' ) );
+ push( @proposed_related, $self->related_readings( $target, 'colocated' ) );
+ my %pr_ids;
+ map { $pr_ids{ $_ } = 1 } @proposed_related;
+
+ # None of these proposed related readings should have a neighbor that
+ # is also in proposed_related.
+ foreach my $pr ( keys %pr_ids ) {
+ foreach my $neighbor( $self->sequence->neighbors( $pr ) ) {
+ return 0 if exists $pr_ids{$neighbor};
+ }
+ }
+ return 1;
}
- }
+}
- if( $source->has_position && $target->has_position ) {
- unless( grep { $_ eq $target } $self->same_position_as( $source ) ) {
- return( undef, "Cannot set relationship at different positions" );
+# Return a list of the witnesses in which the reading appears.
+sub reading_witnesses {
+ my( $self, $reading ) = @_;
+ # We need only check either the incoming or the outgoing edges; I have
+ # arbitrarily chosen "incoming".
+ 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;
+}
- 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 );
- if( $options->{'global'} ) {
- # Look for all readings with the source label, and if there are
- # colocated readings with the target label, join them too.
- foreach my $r ( grep { $_->label eq $source->label } $self->readings() ) {
- next if $r->name eq $source->name;
- my @colocated = grep { $_->label eq $target->label }
- $self->same_position_as( $r );
- if( @colocated ) {
- warn "Multiple readings with same label at same position!"
- if @colocated > 1;
- my $colo = $colocated[0];
- next if $colo->edges_to( $r ) || $r->edges_to( $colo );
- $options->{'primary_relation'} = $options->{'this_relation'};
- $options->{'this_relation'} = [ $r, $colocated[0] ];
- my $dup_rel = Text::Tradition::Collation::Relationship->new( %$options );
- $self->graph->add_edge( $r, $colocated[0], $dup_rel );
- push( @joined, [ $r->name, $colocated[0]->name ] );
- }
+sub related_readings {
+ my( $self, $reading, $colocated ) = @_;
+ my $return_object;
+ if( ref( $reading ) eq 'Text::Tradition::Collation::Reading' ) {
+ $reading = $reading->id;
+ $return_object = 1;
+# print STDERR "Returning related objects\n";
+# } else {
+# print STDERR "Returning related object names\n";
}
- }
- return( 1, @joined );
+ my @related = $self->relations->all_reachable( $reading );
+ if( $colocated ) {
+ my @colo = grep { $self->relations->has_edge_attribute( $reading, $_, 'colocated' ) } @related;
+ @related = @colo;
+ }
+ return $return_object ? map { $self->reading( $_ ) } @related : @related;
}
=head2 Output method(s)
=cut
sub as_svg {
- my( $self, $recalc ) = @_;
- return $self->svg if $self->has_svg;
-
- $self->collapse_graph_paths();
-
+ my( $self ) = @_;
+
my @cmd = qw/dot -Tsvg/;
my( $svg, $err );
- my $in = $self->as_dot();
- run( \@cmd, \$in, ">", binary(), \$svg );
- $self->_save_svg( $svg );
- $self->expand_graph_paths();
+ 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;
}
sub as_dot {
my( $self, $view ) = @_;
- $view = 'path' unless $view;
+ $view = 'sequence' unless $view;
# TODO consider making some of these things configurable
- my $dot = sprintf( "digraph %s {\n", $self->tradition->name );
+ 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 .= sprintf( "\tnode [ fontsize=%d, fillcolor=%s, style=%s, shape=%s ];\n",
- 11, "white", "filled", $self->graph->get_attribute( 'node', 'shape' ) );
+ 11, "white", "filled", "ellipse" );
foreach my $reading ( $self->readings ) {
- # Need not output nodes without separate labels
- next if $reading->name eq $reading->label;
- # TODO output readings or segments, but not both
- next if $reading->class eq 'node.segment';
- $dot .= sprintf( "\t\"%s\" [ label=\"%s\" ]\n", $reading->name, $reading->label );
+ # 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 );
}
+
+ # TODO do something sensible for relationships
- my @edges = $view eq 'relationship' ? $self->relationships : $self->paths;
+ my @edges = $self->paths;
foreach my $edge ( @edges ) {
- my %variables = ( 'color' => '#000000',
- 'fontcolor' => '#000000',
- 'label' => $edge->label,
- );
- my $varopts = join( ', ', map { $_.'="'.$variables{$_}.'"' } sort keys %variables );
- $dot .= sprintf( "\t\"%s\" -> \"%s\" [ %s ]\n",
- $edge->from->name, $edge->to->name, $varopts );
+ my %variables = ( 'color' => '#000000',
+ 'fontcolor' => '#000000',
+ 'label' => join( ', ', $self->path_display_label( $edge ) ),
+ );
+ my $varopts = join( ', ', map { $_.'="'.$variables{$_}.'"' } sort keys %variables );
+ $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 )
=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 );
- # TODO Add some global graph data
+ # 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_keys;
my $ndi = 0;
- foreach my $datum ( qw/ name reading identical position class / ) {
- $node_data_keys{$datum} = 'dn'.$ndi++;
- my $key = $root->addNewChild( $graphml_ns, 'key' );
- $key->setAttribute( 'attr.name', $datum );
- $key->setAttribute( 'attr.type', 'string' );
- $key->setAttribute( 'for', 'node' );
- $key->setAttribute( 'id', $node_data_keys{$datum} );
+ 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, i.e. witnesses
my $edi = 0;
my %edge_data_keys;
- foreach my $edge_key( qw/ witness_main witness_ante_corr relationship class / ) {
- $edge_data_keys{$edge_key} = '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} );
+ my %edge_data = (
+ class => 'string', # Path or relationship?
+ 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
+
+ # Add the collation graph itself
my $graph = $root->addNewChild( $graphml_ns, 'graph' );
$graph->setAttribute( 'edgedefault', 'directed' );
- $graph->setAttribute( 'id', 'g0' ); # TODO make this meaningful
+ $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' );
+
+ # Collation attribute data
+ foreach my $datum ( @graph_attributes ) {
+ my $value = $datum eq 'version' ? '2.0' : $self->$datum;
+ _add_graphml_data( $graph, $graph_data_keys{$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' );
- my $node_xmlid = 'n' . $node_ctr++;
- $node_hash{ $n->name } = $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{'position'}, $n->position->reference )
- if $n->has_position;
- _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;
- }
-
- # Add any segments we have
- foreach my $n ( sort { $a->name cmp $b->name } $self->segments ) {
- 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 );
- _add_graphml_data( $node_el, $node_data_keys{'class'}, $n->sub_class );
- _add_graphml_data( $node_el, $node_data_keys{'name'}, $n->name );
+ foreach my $n ( sort { $a->id cmp $b->id } $self->readings ) {
+ my $node_el = $graph->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;
+ }
}
- # Add the path, relationship, and segment edges
+ # Add the path edges
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 );
- 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'};
- # TODO kind of hacky
- if( $e->label =~ /^(.*?)\s+(\(a\.c\.\))$/ ) {
- $base = $1;
- $key = $edge_data_keys{'witness_ante_corr'};
- }
- _add_graphml_data( $edge_el, $key, $base );
- } elsif( $e->sub_class eq 'relationship' ) {
- # It's a relationship
- _add_graphml_data( $edge_el, $edge_data_keys{'relationship'}, $e->label );
- } # else a segment, nothing to record but source, target, class
+ 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 = $graph->addNewChild( $graphml_ns, 'edge' );
+ $edge_el->setAttribute( 'source', $from );
+ $edge_el->setAttribute( 'target', $to );
+ $edge_el->setAttribute( 'id', $id );
+ # Add the edge class
+ _add_graphml_data( $edge_el, $edge_data_keys{'class'}, 'path' );
+
+ # 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 the relationship edges
+ foreach my $e ( sort { $a->[0] cmp $b->[0] } $self->relationships ) {
+ my( $id, $from, $to ) = ( 'e'.$edge_ctr++,
+ $node_hash{ $e->[0] },
+ $node_hash{ $e->[1] } );
+ my $edge_el = $graph->addNewChild( $graphml_ns, 'edge' );
+ $edge_el->setAttribute( 'source', $from );
+ $edge_el->setAttribute( 'target', $to );
+ $edge_el->setAttribute( 'id', $id );
+ # Add the edge class
+ _add_graphml_data( $edge_el, $edge_data_keys{'class'}, 'relationship' );
+
+ my $data = $self->relations->get_edge_attributes( @$e );
+ # It's a relationship, so save the relationship data
+ _add_graphml_data( $edge_el, $edge_data_keys{'relationship'}, $data->{type} );
+ _add_graphml_data( $edge_el, $edge_data_keys{'colocated'}, $data->{colocated} );
+ if( exists $data->{non_correctable} ) {
+ _add_graphml_data( $edge_el, $edge_data_keys{'non_correctable'},
+ $data->{non_correctable} );
+ }
+ if( exists $data->{non_independent} ) {
+ _add_graphml_data( $edge_el, $edge_data_keys{'non_independent'},
+ $data->{non_independent} );
+ }
}
- # Return the thing
- $self->_save_graphml( $graphml->toString(1) );
- return $graphml->toString(1);
+ # Save and return the thing
+ my $result = decode_utf8( $graphml->toString(1) );
+ return $result;
}
sub _add_graphml_data {
my( $el, $key, $value ) = @_;
- my $data_el = $el->addNewChild( $el->namespaceURI, 'data' );
return unless defined $value;
+ my $data_el = $el->addNewChild( $el->namespaceURI, 'data' );
$data_el->setAttribute( 'key', $key );
$data_el->appendText( $value );
}
-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 );
- }
+=item B<as_csv>
- foreach my $newdest ( keys %$newlabels ) {
- my $label;
- my @compressed_wits = ();
- if( @{$newlabels->{$newdest}} < $majority ) {
- $label = join( ', ', sort( @{$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', sort( @aclabels ) );
- }
-
- my $newpath =
- $self->add_path( $node, $self->reading( $newdest ), $label );
- if( @compressed_wits ) {
- $newpath->hidden_witnesses( \@compressed_wits );
- }
- }
+print $graph->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.
+
+=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;
+ foreach my $row ( @$table ) {
+ $csv->combine( @$row );
+ push( @result, decode_utf8( $csv->string ) );
+ }
+ return join( "\n", @result );
+}
+
+# Make an alignment table - $noderefs controls whether the objects
+# in the table are the nodes or simply their readings.
+
+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;
+ $DB::single = 1;
+ my @all_pos = ( 1 .. $self->end->rank - 1 );
+ foreach my $wit ( $self->tradition->witnesses ) {
+ # 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 );
+ unshift( @row, $wit->sigil );
+ push( @$table, \@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 );
+ unshift( @ac_row, $wit->sigil . $self->ac_label );
+ push( @$table, \@ac_row );
+ }
}
- $self->collapsed( 1 );
+ 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;
}
-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;
- my @wits = split( /, /, $path->label );
- if( $path->has_hidden_witnesses ) {
- push( @wits, @{$path->hidden_witnesses} );
- }
- $self->del_path( $path );
- foreach ( @wits ) {
- $self->add_path( $from, $to, $_ );
- }
+sub _make_witness_row {
+ my( $path, $positions, $noderefs ) = @_;
+ my %char_hash;
+ map { $char_hash{$_} = undef } @$positions;
+ foreach my $rdg ( @$path ) {
+ my $rtext = $rdg->text;
+ $rtext = '#LACUNA#' if $rdg->is_lacuna;
+ # print STDERR "No rank for " . $rdg->id . "\n" unless defined $rdg->rank;
+ $char_hash{$rdg->rank} = $noderefs ? $rdg : $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 : '#LACUNA#';
+ }
+ push( @filled_row, $el );
+ $last_el = $el;
+ }
+ return @filled_row;
+}
+
+# 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 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>
=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;
}
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 $self->reading( $answer );
}
=item B<prior_reading>
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";
+ . " 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} ) {
- print STDERR "Making path for " . $wit->sigil . "\n";
- $self->make_witness_path( $wit );
- @common_readings = _find_common( \@common_readings, $wit->path );
- @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 );
}
- map { $_->make_common } @common_readings;
- return @common_readings;
}
sub make_witness_path {
my @chain = @{$wit->path};
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], $sig );
}
- @chain = @{$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 );
+ 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 { $a->position->cmp_with( $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 ) = @_;
-
- # First assign positions to all the common nodes.
- my $l = 1;
- foreach my $oc ( @ordered_common ) {
- $oc->position( $l++, 1 );
- }
-
- if( $self->linear ) {
- # For the space between each common node, we have to find all the chains
- # from all the witnesses. The longest chain gives us our max, and the
- # others get min/max ranges to fit.
- my $first = shift @ordered_common;
- while( @ordered_common ) {
- my %paths;
- my $next = shift @ordered_common;
- my $longest = 0;
- foreach my $wit ( @{$self->tradition->witnesses} ) {
- # Key to the path is not important; we just have to get
- # all unique paths.
- my $length = $self->_track_paths( \%paths, $first, $next, $wit->sigil );
- $longest = $length unless $longest > $length;
- if( $wit->has_ante_corr ) {
- my $length = $self->_track_paths( \%paths, $first, $next,
- $wit->sigil.$self->ac_label, $wit->sigil );
- $longest = $length unless $longest > $length;
- }
- }
-
- # Transform the path values from unique strings to arrays.
- my @all_paths;
- foreach my $k ( keys %paths ) {
- my @v = split( /\s+/, $k );
- push( @all_paths, \@v );
- }
- @all_paths = sort { scalar @$b <=> scalar @$a } @all_paths;
-
- # Now %paths has all the unique paths, and we know how long the
- # longest of these is. Assign positions, starting with the
- # longest. All non-common positions start at 2.
- foreach my $path ( @all_paths ) {
- # Initially each element has a minimum position of 2
- # plus its position in the array (1 is the common
- # node), and a max position of the longest array
- # length minus its position in the array.
- my $range = $longest - scalar @$path;
- my $min = 2;
- foreach my $i ( 0 .. $#{$path} ) {
- my $rdg = $self->reading( $path->[$i] );
- if( $rdg->has_position ) {
- # This reading has already had a more specific
- # position set, so we need to take that into
- # account when calculating the min and max for
- # the next reading.
- my $rangeminus = $rdg->position->min - $min;
- $min = $rdg->position->min + 1;
- $range = $range - $rangeminus;
- if( $range < 0 ) {
- print STDERR "Negative range for position! " . $rdg->name . "\n"; # May remove this warning
- $range = 0;
- }
- } else {
- $rdg->position( $first->position->common, $min, $min+$range );
- $min++;
- $longest = $min+$range-2 unless $longest+2 > $min+$range; # min starts at 2 but longest assumes 0 start
- }
- }
- }
- # Now go through again and make sure the positions are
- # monotonic. Do this until they are.
- my $monotonic = 0;
- my $counter = 0;
- until( $monotonic ) {
- $monotonic = 1;
- $counter++;
- foreach my $path ( @all_paths ) {
- foreach my $i ( 0 .. $#{$path} ) {
- my $rdg = $self->reading( $path->[$i] );
- my $prior = $self->reading( $path->[$i-1] ) if $i > 0;
- my $next = $self->reading( $path->[$i+1] ) if $i < $#{$path};
- if( $prior && $rdg->position->min <= $prior->position->min ) {
- $monotonic = 0;
- $rdg->position->min( $prior->position->min + 1 );
- }
- if( $next && $rdg->position->max >= $next->position->max ) {
- $monotonic = 0;
- if( $next->position->max - 1 >= $rdg->position->min ) {
- # If moving rdg/max down would not send it below
- # rdg/min, do that.
- $rdg->position->max( $next->position->max - 1 );
- } else {
- # Otherwise increase next/max.
- $next->position->max( $rdg->position->max + 1 );
- # ...min will be fixed on the next pass.
- }
- }
- }
- }
- if( $counter > $#all_paths + 1 && !$monotonic ) {
- # We risk an infinite loop. Get out of here.
- warn "Still not monotonic after $counter passes at common point "
- . $first->position->common;
- last;
- }
- }
- print STDERR "Took $counter passes for monotonicity at " . $first->position->common. "\n"
- if $counter > 1;
-
- $first = $next;
- }
-
- } else {
-
- # Non-linear positions are pretty much impossible to pin down.
- # Any reading might appear anywhere in the graph. I guess we
- # can do positions where there aren't transpositions...
-
+ # 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();
-}
-# Helper function for the guts of calculate_positions.
-sub _track_paths {
- my $self = shift;
- my $track_hash = shift;
- # Args are first, last, wit, backup
- my @path = $self->reading_sequence( @_ );
- # Top and tail the array
- shift @path;
- pop @path;
- $track_hash->{join( ' ', map { $_->name } @path )} = $_[2]
- if @path;
- return @path;
-}
-
-sub possible_positions {
- my $self = shift;
- my @answer;
- my %positions = ();
+ # Add the edges.
foreach my $r ( $self->readings ) {
- next unless $r->has_position;
- $positions{$r->position->maxref} = 1;
+ 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 );
+ }
}
- @answer = keys %positions;
- return @answer;
-}
-
-# TODO think about indexing this.
-sub readings_at_position {
- my( $self, $position, $strict ) = @_;
- unless( ref( $position ) eq 'Text::Tradition::Collation::Position' ) {
- $position = Text::Tradition::Collation::Position->new( $position );
+
+ # 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 );
}
- my @answer;
+ # Transfer our rankings from the topological graph to the real one.
foreach my $r ( $self->readings ) {
- push( @answer, $r ) if $r->is_at_position( $position, $strict );
+ 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 @answer;
}
-## Lemmatizer functions
-
-sub init_lemmata {
- my $self = shift;
-
- foreach my $position ( $self->possible_positions ) {
- $self->lemmata->{$position} = undef;
- }
-
- foreach my $cr ( $self->common_readings ) {
- $self->lemmata->{$cr->position->maxref} = $cr->name;
+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;
}
-
-=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 *
-
-A state of 1 means 'lemmatize this reading'
-
-=item *
-
-A state of 0 means 'delemmatize this reading'
-
-=item *
-
-A state of undef means 'an ellipsis belongs in the text here because
-no decision has been made / an earlier decision was backed out'
-
-=back
-
-=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->reference } = $_->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. The lemmata hash
- # should contain fixed positions, range positions whose node was
- # just turned off, and range positions whose node is on.
- my @answer;
- my %fixed_positions;
- # TODO One of these is probably redundant.
- map { $fixed_positions{$_} = 0 } keys %{$self->lemmata};
- map { $fixed_positions{$_} = 0 } keys %{$positions_off};
- map { $fixed_positions{$_} = 1 } $self->possible_positions;
- foreach my $pos ( sort { Text::Tradition::Collation::Position::str_cmp( $a, $b ) } keys %fixed_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 = undef;
- $active = $self->lemmata->{$pos} if exists $self->lemmata->{$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 {
- unless( $fixed_positions{$pos} ) {
- $active = 0;
- delete $self->lemmata->{$pos};
- }
- 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} ] );
- delete $self->lemmata->{$pos} unless $fixed_positions{$pos};
- }
+# 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;
+ 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;
+ }
}
-
- return @answer;
}
-=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 ) = @_;
+## Utility functions
- 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 $fixed = $reading->position->fixed;
- my $old_state = $self->lemmata->{$pos->reference};
-
- 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->reference} = $rname;
- # Any other 'on' readings in the same position should be off
- # if we have a fixed position.
- push( @readings_off, $self->same_position_as( $reading, 1 ) )
- if $pos->fixed;
- # 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 $npos = $n->position;
- my $state = undef;
- $state = $self->lemmata->{$npos->reference}
- if defined $self->lemmata->{$npos->reference};
- if( $state && $state eq $n->name ) {
- # this reading is still on, so turn it off
- push( @readings_delemmatized, $n );
- my $new_state = undef;
- if( $npos->fixed && $n eq $reading ) {
- # This is the reading that was clicked, so if there are no
- # other readings there and this is a fixed position, turn off
- # the position. In all other cases, restore the ellipsis.
- my @other_n = $self->same_position_as( $n ); # TODO do we need strict?
- $new_state = 0 unless @other_n;
- }
- $self->lemmata->{$npos->reference} = $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 same_position_as {
- my( $self, $reading, $strict ) = @_;
- my $pos = $reading->position;
- my %onpath = ( $reading->name => 1 );
- # TODO This might not always be sufficient. We really want to
- # exclude all readings on this one's path between its two
- # common points.
- map { $onpath{$_->name} = 1 } $reading->neighbor_readings;
- my @same = grep { !$onpath{$_->name} }
- $self->readings_at_position( $reading->position, $strict );
- return @same;
-}
-
# 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 unique_list {
- my( @list ) = @_;
- my %h;
- map { $h{$_->name} = $_ } @list;
- return values( %h );
-}
-
-sub add_hash_entry {
- my( $hash, $key, $entry ) = @_;
- if( exists $hash->{$key} ) {
- push( @{$hash->{$key}}, $entry );
- } else {
- $hash->{$key} = [ $entry ];
- }
-}
-
no Moose;
__PACKAGE__->meta->make_immutable;
+
+=head1 BUGS / TODO
+
+=over
+
+=item * Rationalize edge classes
+
+=item * Port the internal graph from Graph::Easy to Graph
+
+=back