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 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 'relations' => (
+ is => 'ro',
+ isa => 'Graph',
+ default => sub { Graph->new( undirected => 1 ) },
+ handles => {
+ relationships => 'edges',
+ },
+ );
-has 'tradition' => ( # TODO should this not be ro?
- is => 'rw',
+has 'tradition' => (
+ is => 'ro',
isa => 'Text::Tradition',
weak_ref => 1,
);
-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' => (
- is => 'ro',
- isa => 'Str',
- writer => '_save_csv',
- predicate => 'has_csv',
- );
+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_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_vertex( $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_vertex( $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 ) = $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 $deleted;
+ my %wits = %{$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] );
+ # 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.
+ $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;
+
+ # We only need the IDs for adding paths to the graph, not the reading
+ # objects themselves.
+ my( $source, $target, $wit ) = $self->_stringify_args( @_ );
+
+ if( $self->sequence->has_edge_attribute( $source, $target, $wit ) ) {
+ $self->sequence->del_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.
+### Relationship logic
-sub add_relationship {
- my( $self, $source, $target, $options ) = @_;
+=head2 add_relationship( $reading1, $reading2, $definition )
+
+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:
+
+=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'} ||
+ $options->{'type'} !~ /^(spelling|orthographic|grammatical|meaning|repetition|transposition)$/i ) {
+ my $t = $options->{'type'} ? $options->{'type'} : '';
+ return( undef, "Invalid or missing type" . $options->{'type'} );
+ }
+ if( $options->{'type'} =~ /^(spelling|orthographic|grammatical|meaning)$/ ) {
+ $options->{'colocated'} = 1;
+ }
+
# 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( $self->relations->has_edge( $source, $target ) ) {
+ return ( undef, "Relationship already exists between these readings" );
}
- if( $options->{'equal_rank'} && !relationship_valid( $source, $target ) ) {
+ if( $options->{'colocated'} && !$self->relationship_valid( $source, $target ) ) {
return ( undef, 'Relationship creates witness loop' );
}
- # 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 );
+ my @vector = ( $source, $target );
+ $self->relations->add_edge( @vector );
+ $self->relations->set_edge_attributes( @vector, $options );
# TODO Handle global relationship setting
- return( 1, @joined );
+ return( 1, @vector );
}
sub relationship_valid {
- my( $source, $target ) = @_;
+ my( $self, $source, $target ) = @_;
# Check that linking the source and target in a relationship won't lead
- # to a path loop for any witness.
+ # 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, $source->related_readings );
- push( @proposed_related, $target->related_readings );
+ push( @proposed_related, $source->related_readings( 'colocated' ) );
+ push( @proposed_related, $target->related_readings( 'colocated' ) );
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;
- }
- }
+ map { $pr_ids{ $_->id } = 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;
}
+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";
+ }
+ 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)
=over
=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 $dotfile = File::Temp->new();
push( @cmd, $dotfile->filename );
run( \@cmd, ">", binary(), \$svg );
$svg = decode_utf8( $svg );
- $self->_save_svg( $svg );
- $self->expand_graph_paths();
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 $graph_name = $self->tradition->name;
$graph_name =~ s/[^\w\s]//g;
$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;
- $dot .= sprintf( "\t\"%s\" [ label=\"%s\" ];\n", $reading->name, $reading->label );
+ next if $reading->id eq $reading->text;
+ $dot .= sprintf( "\t\"%s\" [ label=\"%s\" ];\n", $reading->id, $reading->text );
}
+
+ # 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,
+ 'label' => join( ', ', $self->path_witnesses( $edge ) ),
);
my $varopts = join( ', ', map { $_.'="'.$variables{$_}.'"' } sort keys %variables );
$dot .= sprintf( "\t\"%s\" -> \"%s\" [ %s ];\n",
- $edge->from->name, $edge->to->name, $varopts );
+ $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;
+}
+
=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';
# 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',
+ reading => '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', # 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', $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
+
+ # Add the collation graph itself
my $graph = $root->addNewChild( $graphml_ns, 'graph' );
$graph->setAttribute( 'edgedefault', 'directed' );
$graph->setAttribute( 'id', $self->tradition->name );
my $node_ctr = 0;
my %node_hash;
# Add our readings to the graph
- foreach my $n ( sort { $a->name cmp $b->name } $self->readings ) {
+ 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->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{'id'}, $n->id );
+ _add_graphml_data( $node_el, $node_data_keys{'reading'}, $n->text );
_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 );
- $DB::single = 1 if $n->has_primary && $n->primary ne $n;
- _add_graphml_data( $node_el, $node_data_keys{'identical'}, $n->primary->name )
- if $n->has_primary && $n->primary ne $n;
}
- # Add the path and relationship 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 );
-
- # 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 = $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} );
+ }
}
# Save and return the thing
my $result = decode_utf8( $graphml->toString(1) );
- $self->_save_graphml( $result );
return $result;
}
=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;
$csv->combine( @$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
return;
}
my $table;
- my @all_pos = ( 0 .. $self->end->rank - 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 );
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;
+ # 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;
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 = ( $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 );
+ $DB::single = 1 if $next->id eq $end->id;
unless( $next ) {
- warn "Did not find any path for $witness from reading " . $n->name;
+ warn "Did not find any path for $witness from reading " . $n->id;
last;
}
push( @readings, $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;
}
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 ) {
+ 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.
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} );
+ $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?";
}
}
# 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 ];
- }
-}
-
no Moose;
__PACKAGE__->meta->make_immutable;
projects / scpubgit/stemmatology.git / blobdiff