related_readings => 'related_readings',
get_relationship => 'get_relationship',
del_relationship => 'del_relationship',
+ equivalence => 'equivalence',
+ equivalence_graph => 'equivalence_graph',
},
writer => '_set_relations',
);
$self->_graphcalc_done(0);
# Connect the readings
- $self->sequence->add_edge( $source, $target );
+ unless( $self->sequence->has_edge( $source, $target ) ) {
+ $self->sequence->add_edge( $source, $target );
+ $self->relations->add_equivalence_edge( $source, $target );
+ }
# Note the witness in question
$self->sequence->set_edge_attribute( $source, $target, $wit, 1 );
-};
+}
sub del_path {
my $self = shift;
}
unless( keys %{$self->sequence->get_edge_attributes( $source, $target )} ) {
$self->sequence->delete_edge( $source, $target );
+ $self->relations->delete_equivalence_edge( $source, $target );
}
}
# Add the path edges to the sequence graph
my $edge_ctr = 0;
- $DB::single = 1;
foreach my $e ( sort { $a->[0] cmp $b->[0] } $self->sequence->edges() ) {
# We add an edge in the graphml for every witness in $e.
next unless( $use_readings{$e->[0]} || $use_readings{$e->[1]} );
$wit->clear_uncorrected_path;
}
-=head2 equivalence_graph( \%readingmap, $startrank, $endrank, @testvector )
-
-Returns an equivalence graph of the collation, in which all readings
-related via a 'colocated' relationship are transformed into a single
-vertex. Can be used to determine the validity of a new relationship. The
-mapping between equivalence vertices and reading IDs will be stored in the
-hash whose reference is passed as readingmap. For a subset of the graph,
-pass in a start and/or an ending rank (this only works if L<calculate_ranks>
-has been called at least once.)
-
-It is also possible to pass in a test relationship in @testvector, and get
-the resulting equivalence graph before the relationship has been made.
-
-=cut
-
-sub equivalence_graph {
- my( $self, $map, $start, $end, @newvector ) = @_;
- $start = undef unless $self->end->has_rank;
- $end = undef unless $self->end->has_rank;
- my $eqgraph = Graph->new();
- my $rel_ctr = 0;
- # Add the nodes
- foreach my $r ( $self->readings ) {
- unless( $r eq $self->start || $r eq $self->end ) {
- next if $start && $r->rank < $start;
- next if $end && $r->rank > $end;
- }
- next if exists $map->{$r->id};
- my @rels = $self->related_readings( $r->id, 'colocated' );
- push( @rels, $r->id );
- # Make an equivalence vertex
- my $rn = 'equivalence_' . $rel_ctr++;
- $eqgraph->add_vertex( $rn );
- # Note which readings belong to this vertex.
- push( @rels, $r->id );
- foreach( @rels ) {
- $map->{$_} = $rn;
- }
- }
-
- # Add the edges.
- foreach my $p ( $self->paths ) {
- my $efrom = exists $map->{$p->[0]} ? $map->{$p->[0]}
- : $map->{$self->start->id};
- my $eto = exists $map->{$p->[1]} ? $map->{$p->[1]}
- : $map->{$self->end->id};
- $eqgraph->add_edge( $efrom, $eto );
- }
-
- # Collapse the vertices in @newvector if applicable.
- if( @newvector ) {
- my( $eqs, $eqt ) = map { $map->{$_} } @newvector;
- $DB::single = 1 unless $eqs && $eqt;
- unless( $eqs eq $eqt ) {
- # Combine the vertices.
- map { $eqgraph->add_edge( $eqs, $_ ) } $eqgraph->successors( $eqt );
- map { $eqgraph->add_edge( $_, $eqs ) } $eqgraph->predecessors( $eqt );
- $eqgraph->delete_vertex( $eqt );
- }
- }
- return $eqgraph;
-}
-
=head2 calculate_ranks
Calculate the reading ranks (that is, their aligned positions relative
# Save the existing ranks, in case we need to invalidate the cached SVG.
my %existing_ranks;
map { $existing_ranks{$_} = $_->rank } $self->readings;
- # 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 %rel_containers;
- my $topo_graph = $self->equivalence_graph( \%rel_containers );
-
- # Now do the rankings, starting with the start node.
- my $topo_start = $rel_containers{$self->start->id};
+
+ # Do the rankings based on the relationship equivalence graph, starting
+ # with the start node.
+ my $topo_start = $self->equivalence( $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 );
+ @curr_origin = _assign_rank( $self->equivalence_graph,
+ $node_ranks, @curr_origin );
}
# Transfer our rankings from the topological graph to the real one.
foreach my $r ( $self->readings ) {
- if( defined $node_ranks->{$rel_containers{$r->id}} ) {
- $r->rank( $node_ranks->{$rel_containers{$r->id}} );
+ if( defined $node_ranks->{$self->equivalence( $r->id )} ) {
+ $r->rank( $node_ranks->{$self->equivalence( $r->id )} );
} else {
# Die. Find the last rank we calculated.
- my @all_defined = sort { ( $node_ranks->{$rel_containers{$a->id}}||-1 )
- <=> ( $node_ranks->{$rel_containers{$b->id}}||-1 ) }
+ my @all_defined = sort { ( $node_ranks->{$self->equivalence( $a->id )}||-1 )
+ <=> ( $node_ranks->{$self->equivalence( $b->id )}||-1 ) }
$self->readings;
my $last = pop @all_defined;
throw( "Ranks not calculated after $last - do you have a cycle in the graph?" );
projects / scpubgit/stemmatology.git / blobdiff