-#!/usr/bin/env perl
-
package Text::Tradition::Collation;
+
+use Encode qw( decode_utf8 );
+use File::Temp;
+use Graph;
+use IPC::Run qw( run binary );
+use Text::CSV_XS;
+use Text::Tradition::Collation::Reading;
+use Text::Tradition::Collation::RelationshipStore;
+use XML::LibXML;
use Moose;
-has 'graph' => (
- is => 'ro',
- isa => 'Text::Tradition::Graph',
- );
+has 'sequence' => (
+ is => 'ro',
+ isa => 'Graph',
+ default => sub { Graph->new() },
+ handles => {
+ paths => 'edges',
+ },
+ );
+
+has 'relations' => (
+ is => 'ro',
+ isa => 'Text::Tradition::Collation::RelationshipStore',
+ handles => {
+ relationships => 'relationships',
+ related_readings => 'related_readings',
+ },
+ writer => '_set_relations',
+ );
-# The graph is full of nodes, which have positions and equivalences.
-# These have to be stored externally to the graph itself.
-has 'positions' => (
- is => 'ro';
- isa => 'Text::Tradition::Graph::Position',
- );
+has 'tradition' => (
+ is => 'ro',
+ isa => 'Text::Tradition',
+ weak_ref => 1,
+ );
-has 'equivalences' => (
- is => 'rw';
- isa => 'Text::Tradition::Graph::Equivalence',
- );
+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 { {} },
+ );
-# We need a way to access the parent object.
-has 'tradition' => (
- is => 'ro',
- isa => 'Text::Tradition',
- );
+has 'wit_list_separator' => (
+ is => 'rw',
+ isa => 'Str',
+ default => ', ',
+ );
+
+has 'baselabel' => (
+ is => 'rw',
+ isa => 'Str',
+ default => 'base text',
+ );
+
+has 'linear' => (
+ is => 'rw',
+ isa => 'Bool',
+ default => 1,
+ );
+
+has 'ac_label' => (
+ is => 'rw',
+ isa => 'Str',
+ default => ' (a.c.)',
+ );
+
+has 'start' => (
+ is => 'ro',
+ isa => 'Text::Tradition::Collation::Reading',
+ writer => '_set_start',
+ weak_ref => 1,
+ );
+
+has 'end' => (
+ is => 'ro',
+ isa => 'Text::Tradition::Collation::Reading',
+ writer => '_set_end',
+ weak_ref => 1,
+ );
# The collation can be created two ways:
# 1. Collate a set of witnesses (with CollateX I guess) and process
# constructor will also need to make the witness objects, if we didn't
# come through option 1.
+sub BUILD {
+ my $self = shift;
+ $self->_set_relations( Text::Tradition::Collation::RelationshipStore->new( 'collation' => $self ) );
+ $self->_set_start( $self->add_reading( { 'collation' => $self, 'is_start' => 1 } ) );
+ $self->_set_end( $self->add_reading( { 'collation' => $self, 'is_end' => 1 } ) );
+}
+
+### Reading construct/destruct functions
+
+sub add_reading {
+ my( $self, $reading ) = @_;
+ unless( ref( $reading ) eq 'Text::Tradition::Collation::Reading' ) {
+ my %args = %$reading;
+ $reading = Text::Tradition::Collation::Reading->new(
+ 'collation' => $self,
+ %args );
+ }
+ # First check to see if a reading with this ID exists.
+ if( $self->reading( $reading->id ) ) {
+ warn "Collation already has a reading with id " . $reading->id;
+ return undef;
+ }
+ $self->_add_reading( $reading->id => $reading );
+ # Once the reading has been added, put it in both graphs.
+ $self->sequence->add_vertex( $reading->id );
+ $self->relations->add_reading( $reading->id );
+ return $reading;
+};
+
+around del_reading => sub {
+ my $orig = shift;
+ my $self = shift;
+ my $arg = shift;
+
+ if( ref( $arg ) eq 'Text::Tradition::Collation::Reading' ) {
+ $arg = $arg->id;
+ }
+ # Remove the reading from the graphs.
+ $self->sequence->delete_vertex( $arg );
+ $self->relations->delete_reading( $arg );
+
+ # Carry on.
+ $self->$orig( $arg );
+};
+
+# merge_readings( $main, $to_be_deleted );
+
+sub merge_readings {
+ my $self = shift;
+
+ # We only need the IDs for adding paths to the graph, not the reading
+ # objects themselves.
+ my( $kept, $deleted, $combine_char ) = $self->_stringify_args( @_ );
+
+ # The kept reading should inherit the paths and the relationships
+ # of the deleted reading.
+ foreach my $path ( $self->sequence->edges_at( $deleted ) ) {
+ my @vector = ( $kept );
+ push( @vector, $path->[1] ) if $path->[0] eq $deleted;
+ unshift( @vector, $path->[0] ) if $path->[1] eq $deleted;
+ next if $vector[0] eq $vector[1]; # Don't add a self loop
+ my %wits = %{$self->sequence->get_edge_attributes( @$path )};
+ $self->sequence->add_edge( @vector );
+ my $fwits = $self->sequence->get_edge_attributes( @vector );
+ @wits{keys %$fwits} = values %$fwits;
+ $self->sequence->set_edge_attributes( @vector, \%wits );
+ }
+ $self->relations->merge_readings( $kept, $deleted, $combine_char );
+
+ # Do the deletion deed.
+ if( $combine_char ) {
+ my $kept_obj = $self->reading( $kept );
+ my $new_text = join( $combine_char, $kept_obj->text,
+ $self->reading( $deleted )->text );
+ $kept_obj->alter_text( $new_text );
+ }
+ $self->del_reading( $deleted );
+}
+
+
+# Helper function for manipulating the graph.
+sub _stringify_args {
+ my( $self, $first, $second, $arg ) = @_;
+ $first = $first->id
+ if ref( $first ) eq 'Text::Tradition::Collation::Reading';
+ $second = $second->id
+ if ref( $second ) eq 'Text::Tradition::Collation::Reading';
+ return( $first, $second, $arg );
+}
+
+### Path logic
+
+sub add_path {
+ my $self = shift;
+
+ # We only need the IDs for adding paths to the graph, not the reading
+ # objects themselves.
+ my( $source, $target, $wit ) = $self->_stringify_args( @_ );
+
+ # Connect the readings
+ $self->sequence->add_edge( $source, $target );
+ # Note the witness in question
+ $self->sequence->set_edge_attribute( $source, $target, $wit, 1 );
+};
+
+sub del_path {
+ my $self = shift;
+ my @args;
+ if( ref( $_[0] ) eq 'ARRAY' ) {
+ my $e = shift @_;
+ @args = ( @$e, @_ );
+ } else {
+ @args = @_;
+ }
+
+ # We only need the IDs for adding paths to the graph, not the reading
+ # objects themselves.
+ my( $source, $target, $wit ) = $self->_stringify_args( @args );
+
+ if( $self->sequence->has_edge_attribute( $source, $target, $wit ) ) {
+ $self->sequence->delete_edge_attribute( $source, $target, $wit );
+ }
+ unless( keys %{$self->sequence->get_edge_attributes( $source, $target )} ) {
+ $self->sequence->delete_edge( $source, $target );
+ }
+}
+
+
+# Extra graph-alike utility
+sub has_path {
+ my $self = shift;
+ my( $source, $target, $wit ) = $self->_stringify_args( @_ );
+ return undef unless $self->sequence->has_edge( $source, $target );
+ return $self->sequence->has_edge_attribute( $source, $target, $wit );
+}
+
+=head2 add_relationship( $reading1, $reading2, $definition )
+
+Adds the specified relationship between the two readings. A relationship
+is transitive (i.e. undirected); the options for its definition may be found
+in Text::Tradition::Collation::Relationship.
+
+=cut
+
+# Wouldn't it be lovely if edges could be objects, and all this type checking
+# and attribute management could be done via Moose?
+
+sub add_relationship {
+ my $self = shift;
+ my( $source, $target, $opts ) = $self->_stringify_args( @_ );
+ my( $ret, @vectors ) = $self->relations->add_relationship( $source,
+ $self->reading( $source ), $target, $self->reading( $target ), $opts );
+ # Force a full rank recalculation every time. Yuck.
+ $self->calculate_ranks() if $ret && $self->end->has_rank;
+ return( $ret, @vectors );
+}
+
+=head2 reading_witnesses( $reading )
+
+Return a list of sigils corresponding to the witnesses in which the reading appears.
+
+=cut
+
+sub reading_witnesses {
+ my( $self, $reading ) = @_;
+ # We need only check either the incoming or the outgoing edges; I have
+ # arbitrarily chosen "incoming". Thus, special-case the start node.
+ if( $reading eq $self->start ) {
+ return map { $_->sigil } $self->tradition->witnesses;
+ }
+ my %all_witnesses;
+ foreach my $e ( $self->sequence->edges_to( $reading ) ) {
+ my $wits = $self->sequence->get_edge_attributes( @$e );
+ @all_witnesses{ keys %$wits } = 1;
+ }
+ return keys %all_witnesses;
+}
+
+=head2 Output method(s)
+
+=over
+
+=item B<as_svg>
+
+print $collation->as_svg();
+
+Returns an SVG string that represents the graph, via as_dot and graphviz.
+
+=cut
+
+sub as_svg {
+ my( $self ) = @_;
+
+ my @cmd = qw/dot -Tsvg/;
+ my( $svg, $err );
+ my $dotfile = File::Temp->new();
+ ## TODO REMOVE
+ # $dotfile->unlink_on_destroy(0);
+ binmode $dotfile, ':utf8';
+ print $dotfile $self->as_dot();
+ push( @cmd, $dotfile->filename );
+ run( \@cmd, ">", binary(), \$svg );
+ $svg = decode_utf8( $svg );
+ return $svg;
+}
+
+=item B<svg_subgraph>
+
+print $collation->svg_subgraph( $from, $to )
+
+Returns an SVG string that represents the portion of the graph given by the
+specified range. The $from and $to variables refer to ranks within the graph.
+
+=cut
+
+sub svg_subgraph {
+ my( $self, $from, $to ) = @_;
+
+ my $dot = $self->as_dot( $from, $to );
+ unless( $dot ) {
+ warn "Could not output a graph with range $from - $to";
+ return;
+ }
+
+ my @cmd = qw/dot -Tsvg/;
+ my( $svg, $err );
+ my $dotfile = File::Temp->new();
+ ## TODO REMOVE
+ # $dotfile->unlink_on_destroy(0);
+ binmode $dotfile, ':utf8';
+ print $dotfile $dot;
+ push( @cmd, $dotfile->filename );
+ run( \@cmd, ">", binary(), \$svg );
+ $svg = decode_utf8( $svg );
+ return $svg;
+}
+
+
+=item B<as_dot>
+
+print $collation->as_dot();
+
+Returns a string that is the collation graph expressed in dot
+(i.e. GraphViz) format. The 'view' argument determines what kind of
+graph is produced.
+ * 'path': a graph of witness paths through the collation (DEFAULT)
+ * 'relationship': a graph of how collation readings relate to
+ each other
+
+=cut
+
+sub as_dot {
+ my( $self, $startrank, $endrank ) = @_;
+
+ # Check the arguments
+ if( $startrank ) {
+ return if $endrank && $startrank > $endrank;
+ return if $startrank > $self->end->rank;
+ }
+ if( defined $endrank ) {
+ return if $endrank < 0;
+ }
+
+ # TODO consider making some of these things configurable
+ my $graph_name = $self->tradition->name;
+ $graph_name =~ s/[^\w\s]//g;
+ $graph_name = join( '_', split( /\s+/, $graph_name ) );
+ my $dot = sprintf( "digraph %s {\n", $graph_name );
+ $dot .= "\tedge [ arrowhead=open ];\n";
+ $dot .= "\tgraph [ rankdir=LR,bgcolor=none ];\n";
+ $dot .= sprintf( "\tnode [ fontsize=%d, fillcolor=%s, style=%s, shape=%s ];\n",
+ 11, "white", "filled", "ellipse" );
+
+ # Output substitute start/end readings if necessary
+ if( $startrank ) {
+ $dot .= "\t\"#SUBSTART#\" [ label=\"...\" ];\n";
+ }
+ if( $endrank ) {
+ $dot .= "\t\"#SUBEND#\" [ label=\"...\" ];\n";
+ }
+ my %used; # Keep track of the readings that actually appear in the graph
+ my %subedges;
+ my %subend;
+ foreach my $reading ( $self->readings ) {
+ # Only output readings within our rank range.
+ next if $startrank && $reading->rank < $startrank;
+ next if $endrank && $reading->rank > $endrank;
+ $used{$reading->id} = 1;
+ $subedges{$reading->id} = '#SUBSTART#'
+ if $startrank && $startrank == $reading->rank;
+ $subedges{$reading->id} = '#SUBEND#'
+ if $endrank && $endrank == $reading->rank;
+ # Need not output nodes without separate labels
+ next if $reading->id eq $reading->text;
+ my $label = $reading->text;
+ $label =~ s/\"/\\\"/g;
+ $dot .= sprintf( "\t\"%s\" [ label=\"%s\" ];\n", $reading->id, $label );
+ }
+
+ # Add substitute start and end edges if necessary
+ foreach my $node ( keys %subedges ) {
+ my @vector = ( $subedges{$node}, $node );
+ @vector = reverse( @vector ) if $vector[0] =~ /END/;
+ my $witstr = join( ', ', sort $self->reading_witnesses( $self->reading( $node ) ) );
+ my %variables = ( 'color' => '#000000',
+ 'fontcolor' => '#000000',
+ 'label' => $witstr,
+ );
+ my $varopts = join( ', ', map { $_.'="'.$variables{$_}.'"' } sort keys %variables );
+ $dot .= sprintf( "\t\"%s\" -> \"%s\" [ %s ];\n", @vector, $varopts );
+ }
+
+ # Add the real edges
+ my @edges = $self->paths;
+ foreach my $edge ( @edges ) {
+ # Do we need to output this edge?
+ if( $used{$edge->[0]} && $used{$edge->[1]} ) {;
+ my %variables = ( 'color' => '#000000',
+ 'fontcolor' => '#000000',
+ 'label' => join( ', ', $self->path_display_label( $edge ) ),
+ );
+ my $varopts = join( ', ', map { $_.'="'.$variables{$_}.'"' } sort keys %variables );
+ # Account for the rank gap if necessary
+ my $rankgap = $self->reading( $edge->[1] )->rank
+ - $self->reading( $edge->[0] )->rank;
+ $varopts .= ", minlen=$rankgap" if $rankgap > 1;
+ $dot .= sprintf( "\t\"%s\" -> \"%s\" [ %s ];\n",
+ $edge->[0], $edge->[1], $varopts );
+ }
+ }
+
+ $dot .= "}\n";
+ return $dot;
+}
+
+sub path_witnesses {
+ my( $self, @edge ) = @_;
+ # If edge is an arrayref, cope.
+ if( @edge == 1 && ref( $edge[0] ) eq 'ARRAY' ) {
+ my $e = shift @edge;
+ @edge = @$e;
+ }
+ my @wits = keys %{$self->sequence->get_edge_attributes( @edge )};
+ return sort @wits;
+}
+
+sub path_display_label {
+ my( $self, $edge ) = @_;
+ my @wits = $self->path_witnesses( $edge );
+ my $maj = scalar( $self->tradition->witnesses ) * 0.6;
+ if( scalar @wits > $maj ) {
+ return 'majority';
+ } else {
+ return join( ', ', @wits );
+ }
+}
+
+
+=item B<as_graphml>
+
+print $collation->as_graphml( $recalculate )
+
+Returns a GraphML representation of the collation graph, with
+transposition information and position information. Unless
+$recalculate is passed (and is a true value), the method will return a
+cached copy of the SVG after the first call to the method.
+
+=cut
+
+sub as_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';
+
+ # Create the document and root node
+ my $graphml = XML::LibXML->createDocument( "1.0", "UTF-8" );
+ my $root = $graphml->createElementNS( $graphml_ns, 'graphml' );
+ $graphml->setDocumentElement( $root );
+ $root->setNamespace( $xsi_ns, 'xsi', 0 );
+ $root->setAttributeNS( $xsi_ns, 'schemaLocation', $graphml_schema );
+
+ # Add the data keys for the graph
+ my %graph_data_keys;
+ my $gdi = 0;
+ my @graph_attributes = qw/ version wit_list_separator baselabel linear ac_label /;
+ foreach my $datum ( @graph_attributes ) {
+ $graph_data_keys{$datum} = 'dg'.$gdi++;
+ my $key = $root->addNewChild( $graphml_ns, 'key' );
+ $key->setAttribute( 'attr.name', $datum );
+ $key->setAttribute( 'attr.type', $key eq 'linear' ? 'boolean' : 'string' );
+ $key->setAttribute( 'for', 'graph' );
+ $key->setAttribute( 'id', $graph_data_keys{$datum} );
+ }
+
+ # Add the data keys for nodes
+ my %node_data_keys;
+ my $ndi = 0;
+ my %node_data = (
+ id => 'string',
+ text => 'string',
+ rank => 'string',
+ is_start => 'boolean',
+ is_end => 'boolean',
+ is_lacuna => 'boolean',
+ );
+ foreach my $datum ( keys %node_data ) {
+ $node_data_keys{$datum} = 'dn'.$ndi++;
+ my $key = $root->addNewChild( $graphml_ns, 'key' );
+ $key->setAttribute( 'attr.name', $datum );
+ $key->setAttribute( 'attr.type', $node_data{$datum} );
+ $key->setAttribute( 'for', 'node' );
+ $key->setAttribute( 'id', $node_data_keys{$datum} );
+ }
+
+ # Add the data keys for edges, i.e. witnesses
+ my $edi = 0;
+ my %edge_data_keys;
+ my %edge_data = (
+ class => 'string', # Class, deprecated soon
+ witness => 'string', # ID/label for a path
+ relationship => 'string', # ID/label for a relationship
+ extra => 'boolean', # Path key
+ colocated => 'boolean', # Relationship key
+ non_correctable => 'boolean', # Relationship key
+ non_independent => 'boolean', # Relationship key
+ );
+ foreach my $datum ( keys %edge_data ) {
+ $edge_data_keys{$datum} = 'de'.$edi++;
+ my $key = $root->addNewChild( $graphml_ns, 'key' );
+ $key->setAttribute( 'attr.name', $datum );
+ $key->setAttribute( 'attr.type', $edge_data{$datum} );
+ $key->setAttribute( 'for', 'edge' );
+ $key->setAttribute( 'id', $edge_data_keys{$datum} );
+ }
+
+ # Add the collation graph itself
+ my $sgraph = $root->addNewChild( $graphml_ns, 'graph' );
+ $sgraph->setAttribute( 'edgedefault', 'directed' );
+ $sgraph->setAttribute( 'id', $self->tradition->name );
+ $sgraph->setAttribute( 'parse.edgeids', 'canonical' );
+ $sgraph->setAttribute( 'parse.edges', scalar($self->paths) );
+ $sgraph->setAttribute( 'parse.nodeids', 'canonical' );
+ $sgraph->setAttribute( 'parse.nodes', scalar($self->readings) );
+ $sgraph->setAttribute( 'parse.order', 'nodesfirst' );
+
+ # Collation attribute data
+ foreach my $datum ( @graph_attributes ) {
+ my $value = $datum eq 'version' ? '3.0' : $self->$datum;
+ _add_graphml_data( $sgraph, $graph_data_keys{$datum}, $value );
+ }
+
+ my $node_ctr = 0;
+ my %node_hash;
+ # Add our readings to the graph
+ foreach my $n ( sort { $a->id cmp $b->id } $self->readings ) {
+ # Add to the main graph
+ my $node_el = $sgraph->addNewChild( $graphml_ns, 'node' );
+ my $node_xmlid = 'n' . $node_ctr++;
+ $node_hash{ $n->id } = $node_xmlid;
+ $node_el->setAttribute( 'id', $node_xmlid );
+ foreach my $d ( keys %node_data ) {
+ my $nval = $n->$d;
+ _add_graphml_data( $node_el, $node_data_keys{$d}, $nval )
+ if defined $nval;
+ }
+ }
+
+ # Add the path edges to the sequence graph
+ my $edge_ctr = 0;
+ foreach my $e ( sort { $a->[0] cmp $b->[0] } $self->sequence->edges() ) {
+ # We add an edge in the graphml for every witness in $e.
+ foreach my $wit ( $self->path_witnesses( $e ) ) {
+ my( $id, $from, $to ) = ( 'e'.$edge_ctr++,
+ $node_hash{ $e->[0] },
+ $node_hash{ $e->[1] } );
+ my $edge_el = $sgraph->addNewChild( $graphml_ns, 'edge' );
+ $edge_el->setAttribute( 'source', $from );
+ $edge_el->setAttribute( 'target', $to );
+ $edge_el->setAttribute( 'id', $id );
+
+ # It's a witness path, so add the witness
+ my $base = $wit;
+ my $key = $edge_data_keys{'witness'};
+ # Is this an ante-corr witness?
+ my $aclabel = $self->ac_label;
+ if( $wit =~ /^(.*)\Q$aclabel\E$/ ) {
+ # Keep the base witness
+ $base = $1;
+ # ...and record that this is an 'extra' reading path
+ _add_graphml_data( $edge_el, $edge_data_keys{'extra'}, $aclabel );
+ }
+ _add_graphml_data( $edge_el, $edge_data_keys{'witness'}, $base );
+ _add_graphml_data( $edge_el, $edge_data_keys{'class'}, 'path' );
+ }
+ }
+
+ # Add the relationship graph to the XML
+ $self->relations->as_graphml( $root );
+
+ # Save and return the thing
+ my $result = decode_utf8( $graphml->toString(1) );
+ return $result;
+}
+
+sub _add_graphml_data {
+ my( $el, $key, $value ) = @_;
+ return unless defined $value;
+ my $data_el = $el->addNewChild( $el->namespaceURI, 'data' );
+ $data_el->setAttribute( 'key', $key );
+ $data_el->appendText( $value );
+}
+
+=item B<as_csv>
+
+print $collation->as_csv( $recalculate )
+
+Returns a CSV alignment table representation of the collation graph, one
+row per witness (or witness uncorrected.)
+
+=cut
+
+sub as_csv {
+ my( $self ) = @_;
+ my $table = $self->make_alignment_table;
+ my $csv = Text::CSV_XS->new( { binary => 1, quote_null => 0 } );
+ my @result;
+ # Make the header row
+ $csv->combine( map { $_->{'witness'} } @{$table->{'alignment'}} );
+ push( @result, decode_utf8( $csv->string ) );
+ # Make the rest of the rows
+ foreach my $idx ( 0 .. $table->{'length'} - 1 ) {
+ my @rowobjs = map { $_->{'tokens'}->[$idx] } @{$table->{'alignment'}};
+ my @row = map { $_ ? $_->{'t'} : $_ } @rowobjs;
+ $csv->combine( @row );
+ push( @result, decode_utf8( $csv->string ) );
+ }
+ return join( "\n", @result );
+}
+
+=item B<make_alignment_table>
+
+my $table = $collation->make_alignment_table( $use_refs, \@wits_to_include )
+
+Return a reference to an alignment table, in a slightly enhanced CollateX
+format which looks like this:
+
+ $table = { alignment => [ { witness => "SIGIL",
+ tokens => [ { t => "READINGTEXT" }, ... ] },
+ { witness => "SIG2",
+ tokens => [ { t => "READINGTEXT" }, ... ] },
+ ... ],
+ length => TEXTLEN };
+
+If $use_refs is set to 1, the reading object is returned in the table
+instead of READINGTEXT; if not, the text of the reading is returned.
+If $wits_to_include is set to a hashref, only the witnesses whose sigil
+keys have a true hash value will be included.
+
+=cut
+
+sub make_alignment_table {
+ my( $self, $noderefs, $include ) = @_;
+ unless( $self->linear ) {
+ warn "Need a linear graph in order to make an alignment table";
+ return;
+ }
+ my $table = { 'alignment' => [], 'length' => $self->end->rank - 1 };
+ my @all_pos = ( 1 .. $self->end->rank - 1 );
+ foreach my $wit ( sort { $a->sigil cmp $b->sigil } $self->tradition->witnesses ) {
+ if( $include ) {
+ next unless $include->{$wit->sigil};
+ }
+ # print STDERR "Making witness row(s) for " . $wit->sigil . "\n";
+ my @wit_path = $self->reading_sequence( $self->start, $self->end, $wit->sigil );
+ my @row = _make_witness_row( \@wit_path, \@all_pos, $noderefs );
+ push( @{$table->{'alignment'}},
+ { 'witness' => $wit->sigil, 'tokens' => \@row } );
+ if( $wit->is_layered ) {
+ my @wit_ac_path = $self->reading_sequence( $self->start, $self->end,
+ $wit->sigil.$self->ac_label, $wit->sigil );
+ my @ac_row = _make_witness_row( \@wit_ac_path, \@all_pos, $noderefs );
+ push( @{$table->{'alignment'}},
+ { 'witness' => $wit->sigil.$self->ac_label, 'tokens' => \@ac_row } );
+ }
+ }
+ return $table;
+}
+
+sub _make_witness_row {
+ my( $path, $positions, $noderefs ) = @_;
+ my %char_hash;
+ map { $char_hash{$_} = undef } @$positions;
+ my $debug = 0;
+ foreach my $rdg ( @$path ) {
+ my $rtext = $rdg->text;
+ $rtext = '#LACUNA#' if $rdg->is_lacuna;
+ print STDERR "rank " . $rdg->rank . "\n" if $debug;
+ # print STDERR "No rank for " . $rdg->id . "\n" unless defined $rdg->rank;
+ $char_hash{$rdg->rank} = $noderefs ? { 't' => $rdg }
+ : { 't' => $rtext };
+ }
+ my @row = map { $char_hash{$_} } @$positions;
+ # Fill in lacuna markers for undef spots in the row
+ my $last_el = shift @row;
+ my @filled_row = ( $last_el );
+ foreach my $el ( @row ) {
+ # If we are using node reference, make the lacuna node appear many times
+ # in the table. If not, use the lacuna tag.
+ if( $last_el && _el_is_lacuna( $last_el ) && !defined $el ) {
+ $el = $noderefs ? $last_el : { 't' => '#LACUNA#' };
+ }
+ push( @filled_row, $el );
+ $last_el = $el;
+ }
+ return @filled_row;
+}
+
+# Tiny utility function to say if a table element is a lacuna
+sub _el_is_lacuna {
+ my $el = shift;
+ return 1 if $el->{'t'} eq '#LACUNA#';
+ return 1 if ref( $el->{'t'} ) eq 'Text::Tradition::Collation::Reading'
+ && $el->{'t'}->is_lacuna;
+ return 0;
+}
+
+# Helper to turn the witnesses along columns rather than rows. Assumes
+# equal-sized rows.
+sub _turn_table {
+ my( $table ) = @_;
+ my $result = [];
+ return $result unless scalar @$table;
+ my $nrows = scalar @{$table->[0]};
+ foreach my $idx ( 0 .. $nrows - 1 ) {
+ foreach my $wit ( 0 .. $#{$table} ) {
+ $result->[$idx]->[$wit] = $table->[$wit]->[$idx];
+ }
+ }
+ return $result;
+}
+
+=back
+
+=head2 Navigation methods
+
+=over
+
+=item B<start>
+
+my $beginning = $collation->start();
+
+Returns the beginning of the collation, a meta-reading with label '#START#'.
+
+=item B<end>
+
+my $end = $collation->end();
+
+Returns the end of the collation, a meta-reading with label '#END#'.
+
+
+=item B<reading_sequence>
+
+my @readings = $collation->reading_sequence( $first, $last, $path[, $alt_path] );
+
+Returns the ordered list of readings, starting with $first and ending
+with $last, along the given witness path. If no path is specified,
+assume that the path is that of the base text (if any.)
+
+=cut
+
+# TODO Think about returning some lazy-eval iterator.
+
+sub reading_sequence {
+ my( $self, $start, $end, $witness, $backup ) = @_;
+
+ $witness = $self->baselabel unless $witness;
+ my @readings = ( $start );
+ my %seen;
+ my $n = $start;
+ 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->text .
+ " for witness $witness is not the end!"
+ unless $last->id eq $end->id;
+
+ return @readings;
+}
+
+=item B<next_reading>
+
+my $next_reading = $collation->next_reading( $reading, $witpath );
+
+Returns the reading that follows the given reading along the given witness
+path.
+
+=cut
+
+sub next_reading {
+ # Return the successor via the corresponding path.
+ my $self = shift;
+ my $answer = $self->_find_linked_reading( 'next', @_ );
+ return undef unless $answer;
+ return $self->reading( $answer );
+}
+
+=item B<prior_reading>
+
+my $prior_reading = $collation->prior_reading( $reading, $witpath );
+
+Returns the reading that precedes the given reading along the given witness
+path.
+
+=cut
+
+sub prior_reading {
+ # Return the predecessor via the corresponding path.
+ my $self = shift;
+ 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'
+ ? $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 = 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( $self->sequence->has_edge_attribute( @$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->[1] : $alt_le->[0]
+ if $alt_le;
+
+ # Got this far? Return the base path if it exists.
+ 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->id
+ . " along path $path";
+ return undef;
+}
+
+# Some set logic.
+sub _is_within {
+ 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;
+ }
+ return $ret;
+}
+
+
+## INITIALIZATION METHODS - for use by parsers
+
+# For use when a collation is constructed from a base text and an apparatus.
+# We have the sequences of readings and just need to add path edges.
+# When we are done, clear out the witness path attributes, as they are no
+# longer needed.
+# TODO Find a way to replace the witness path attributes with encapsulated functions?
+
+sub make_witness_paths {
+ my( $self ) = @_;
+ foreach my $wit ( $self->tradition->witnesses ) {
+ # print STDERR "Making path for " . $wit->sigil . "\n";
+ $self->make_witness_path( $wit );
+ }
+}
+
+sub make_witness_path {
+ my( $self, $wit ) = @_;
+ my @chain = @{$wit->path};
+ my $sig = $wit->sigil;
+ foreach my $idx ( 0 .. $#chain-1 ) {
+ $self->add_path( $chain[$idx], $chain[$idx+1], $sig );
+ }
+ if( $wit->is_layered ) {
+ @chain = @{$wit->uncorrected_path};
+ foreach my $idx( 0 .. $#chain-1 ) {
+ my $source = $chain[$idx];
+ my $target = $chain[$idx+1];
+ $self->add_path( $source, $target, $sig.$self->ac_label )
+ unless $self->has_path( $source, $target, $sig );
+ }
+ }
+ $wit->clear_path;
+ $wit->clear_uncorrected_path;
+}
+
+sub calculate_ranks {
+ my $self = shift;
+ # 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 );
+ }
+ }
+
+ # Add the edges.
+ foreach my $r ( $self->readings ) {
+ foreach my $n ( $self->sequence->successors( $r->id ) ) {
+ my( $tfrom, $tto ) = ( $rel_containers{$r->id},
+ $rel_containers{$n} );
+ $DB::single = 1 unless $tfrom && $tto;
+ $topo_graph->add_edge( $tfrom, $tto );
+ }
+ }
+
+ # 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 );
+ }
+ # Transfer our rankings from the topological graph to the real one.
+ foreach my $r ( $self->readings ) {
+ if( defined $node_ranks->{$rel_containers{$r->id}} ) {
+ $r->rank( $node_ranks->{$rel_containers{$r->id}} );
+ } else {
+ $DB::single = 1;
+ die "No rank calculated for node " . $r->id
+ . " - do you have a cycle in the graph?";
+ }
+ }
+}
+
+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;
+}
+
+# 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;
+ }
+ }
+}
+
+
+## Utility functions
+
+# Return the string that joins together a list of witnesses for
+# display on a single path.
+sub witnesses_of_label {
+ my( $self, $label ) = @_;
+ my $regex = $self->wit_list_separator;
+ my @answer = split( /\Q$regex\E/, $label );
+ return @answer;
+}
+
+=begin testing
+
+use Text::Tradition;
+
+my $cxfile = 't/data/Collatex-16.xml';
+my $t = Text::Tradition->new(
+ 'name' => 'inline',
+ 'input' => 'CollateX',
+ 'file' => $cxfile,
+ );
+my $c = $t->collation;
+
+is( $c->common_predecessor( $c->reading('n9'), $c->reading('n23') )->id,
+ 'n20', "Found correct common predecessor" );
+is( $c->common_successor( $c->reading('n9'), $c->reading('n23') )->id,
+ '#END#', "Found correct common successor" );
+
+is( $c->common_predecessor( $c->reading('n19'), $c->reading('n17') )->id,
+ 'n16', "Found correct common predecessor for readings on same path" );
+is( $c->common_successor( $c->reading('n21'), $c->reading('n26') )->id,
+ '#END#', "Found correct common successor for readings on same path" );
+
+=end testing
+
+=cut
+
+## Return the closest reading that is a predecessor of both the given readings.
+sub common_predecessor {
+ my $self = shift;
+ return $self->common_in_path( @_, 'predecessors' );
+}
+
+sub common_successor {
+ my $self = shift;
+ return $self->common_in_path( @_, 'successors' );
+}
+
+sub common_in_path {
+ my( $self, $r1, $r2, $dir ) = @_;
+ my $iter = $r1->rank > $r2->rank ? $r1->rank : $r2->rank;
+ $iter = $self->end->rank - $iter if $dir eq 'successors';
+ my @candidates;
+ my @last_checked = ( $r1, $r2 );
+ my %all_seen;
+ while( !@candidates ) {
+ my @new_lc;
+ foreach my $lc ( @last_checked ) {
+ foreach my $p ( $lc->$dir ) {
+ if( $all_seen{$p->id} ) {
+ push( @candidates, $p );
+ } else {
+ $all_seen{$p->id} = 1;
+ push( @new_lc, $p );
+ }
+ }
+ }
+ @last_checked = @new_lc;
+ }
+ my @answer = sort { $a->rank <=> $b->rank } @candidates;
+ return $dir eq 'predecessors' ? pop( @answer ) : shift ( @answer );
+}
+
no Moose;
__PACKAGE__->meta->make_immutable;
+
+=head1 BUGS / TODO
+
+=over
+
+=item * Think about making Relationship objects again
+
+=back