package Text::Tradition::Collation;
+
+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' => (
- is => 'ro',
- isa => 'Graph::Easy',
- writer => '_init_graph',
- handles => {
- add_node => 'add_reading',
- del_node => 'del_reading',
- add_edge => 'add_path',
- del_edge => 'del_path',
- nodes => 'readings',
- edges => 'paths',
- );
-
-
-# TODO do we not have a way to access the parent object?
-has 'tradition' => (
- is => 'ro',
- isa => 'Text::Tradition',
- );
+ is => 'ro',
+ isa => 'Graph::Easy',
+ 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',
+ },
+ default => sub { Graph::Easy->new( undirected => 0 ) },
+ );
+
+
+has 'tradition' => ( # TODO should this not be ro?
+ is => 'rw',
+ isa => 'Text::Tradition',
+ );
+
+has 'svg' => (
+ is => 'ro',
+ isa => 'Str',
+ writer => '_save_svg',
+ predicate => 'has_svg',
+ );
+
+has 'graphml' => (
+ is => 'ro',
+ isa => 'Str',
+ writer => '_save_graphml',
+ predicate => 'has_graphml',
+ );
+
+has 'csv' => (
+ is => 'ro',
+ isa => 'Str',
+ writer => '_save_csv',
+ predicate => 'has_csv',
+ );
+
+# 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]]',
+ default => sub { {} },
+ );
+
+has 'wit_list_separator' => (
+ is => 'rw',
+ isa => 'Str',
+ default => ', ',
+ );
+
+has 'baselabel' => (
+ is => 'rw',
+ isa => 'Str',
+ default => 'base text',
+ );
+
+has 'collapsed' => (
+ is => 'rw',
+ isa => 'Bool',
+ );
+
+has 'linear' => (
+ is => 'rw',
+ isa => 'Bool',
+ default => 1,
+ );
+
+has 'ac_label' => (
+ is => 'rw',
+ isa => 'Str',
+ default => ' (a.c.)',
+ );
+
# 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.
-# TODO BUILDARGS
+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' );
+}
+
+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;
+};
+
+# Wrapper around add_path
+
+around add_path => sub {
+ my $orig = shift;
+ my $self = shift;
+
+ # 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( @_ );
+};
+
+# Wrapper around paths
+around paths => sub {
+ my $orig = shift;
+ my $self = shift;
+
+ my @result = grep { $_->sub_class eq 'path' } $self->$orig( @_ );
+ return @result;
+};
-# Wrappers around some methods
+around relationships => sub {
+ my $orig = shift;
+ my $self = shift;
+ my @result = grep { $_->sub_class eq 'relationship' } $self->$orig( @_ );
+ return @result;
+};
+# Wrapper around merge_nodes
sub merge_readings {
my $self = shift;
my $first_node = shift;
return $self->graph->merge_nodes( @_ );
}
+# 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;
+}
+
+## 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.
+
+sub add_relationship {
+ my( $self, $source, $target, $options ) = @_;
+
+ # Make sure there is not another relationship between these two
+ # readings already
+ $source = $self->reading( $source )
+ unless ref( $source ) && $source->isa( 'Graph::Easy::Node' );
+ $target = $self->reading( $target )
+ unless ref( $target ) && $target->isa( 'Graph::Easy::Node' );
+ foreach my $rel ( $source->edges_to( $target ), $target->edges_to( $source ) ) {
+ if( $rel->class eq 'edge.relationship' ) {
+ return ( undef, "Relationship already exists between these readings" );
+ }
+ }
+ if( $options->{'equal_rank'} && !relationship_valid( $source, $target ) ) {
+ return ( undef, 'Relationship creates witness loop' );
+ }
+
+ # TODO Think about positional hilarity if relationships are added after positions
+ # are assigned.
+
+ my @joined = ( [ $source->name, $target->name ] ); # Keep track of the nodes we join.
+
+ $options->{'this_relation'} = [ $source, $target ];
+ my $rel;
+ eval { $rel = Text::Tradition::Collation::Relationship->new( %$options ) };
+ if( $@ ) {
+ return ( undef, $@ );
+ }
+ $self->graph->add_edge( $source, $target, $rel );
+
+ # TODO Handle global relationship setting
+
+ return( 1, @joined );
+}
+
+sub relationship_valid {
+ my( $source, $target ) = @_;
+ # Check that linking the source and target in a relationship won't lead
+ # to a path loop for any witness.
+ my @proposed_related = ( $source, $target );
+ push( @proposed_related, $source->related_readings );
+ push( @proposed_related, $target->related_readings );
+ my %pr_ids;
+ map { $pr_ids{ $_->name } = 1 } @proposed_related;
+ # The lists of 'in' and 'out' should not have any element that appears
+ # in 'proposed_related'.
+ foreach my $pr ( @proposed_related ) {
+ foreach my $e ( grep { $_->sub_class eq 'path' } $pr->incoming ) {
+ if( exists $pr_ids{ $e->from->name } ) {
+ return 0;
+ }
+ }
+ foreach my $e ( grep { $_->sub_class eq 'path' } $pr->outgoing ) {
+ if( exists $pr_ids{ $e->to->name } ) {
+ return 0;
+ }
+ }
+ }
+ return 1;
+}
+
+=head2 Output method(s)
+
+=over
+
+=item B<as_svg>
+
+print $graph->as_svg( $recalculate );
+
+Returns an SVG string that represents the graph. Uses GraphViz to do
+this, because Graph::Easy doesn\'t cope well with long graphs. Unless
+$recalculate is passed (and is a true value), the method will return a
+cached copy of the SVG after the first call to the method.
+
+=cut
+
+sub as_svg {
+ my( $self, $recalc ) = @_;
+ return $self->svg if $self->has_svg;
+
+ $self->collapse_graph_paths();
+
+ 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 );
+ $self->_save_svg( $svg );
+ $self->expand_graph_paths();
+ return $svg;
+}
+
+=item B<as_dot>
+
+print $graph->as_dot( $view, $recalculate );
+
+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, $view ) = @_;
+ $view = 'path' unless $view;
+ # TODO consider making some of these things configurable
+ my $graph_name = $self->tradition->name;
+ $graph_name =~ s/[^\w\s]//g;
+ $graph_name = join( '_', split( /\s+/, $graph_name ) );
+ my $dot = sprintf( "digraph %s {\n", $graph_name );
+ $dot .= "\tedge [ arrowhead=open ];\n";
+ $dot .= "\tgraph [ rankdir=LR ];\n";
+ $dot .= sprintf( "\tnode [ fontsize=%d, fillcolor=%s, style=%s, shape=%s ];\n",
+ 11, "white", "filled", $self->graph->get_attribute( 'node', 'shape' ) );
+
+ 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 );
+ }
+
+ my @edges = $view eq 'relationship' ? $self->relationships : $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 );
+ }
+ $dot .= "}\n";
+ return $dot;
+}
+
+=item B<as_graphml>
+
+print $graph->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, $recalc ) = @_;
+ return $self->graphml if $self->has_graphml;
+
+ # 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/ 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 rank 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} );
+ }
+
+ # 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 $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( 'for', 'edge' );
+ $key->setAttribute( 'id', $edge_data_keys{$edge_key} );
+ }
+
+ # Add the graph, its nodes, and its edges
+ my $graph = $root->addNewChild( $graphml_ns, 'graph' );
+ $graph->setAttribute( 'edgedefault', 'directed' );
+ $graph->setAttribute( 'id', $self->tradition->name );
+ $graph->setAttribute( 'parse.edgeids', 'canonical' );
+ $graph->setAttribute( 'parse.edges', scalar($self->paths) );
+ $graph->setAttribute( 'parse.nodeids', 'canonical' );
+ $graph->setAttribute( 'parse.nodes', scalar($self->readings) );
+ $graph->setAttribute( 'parse.order', 'nodesfirst' );
+
+ # Collation attribute data
+ foreach my $datum ( @graph_attributes ) {
+ _add_graphml_data( $graph, $graph_data_keys{$datum}, $self->$datum );
+ }
+
+ 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{'rank'}, $n->rank )
+ if $n->has_rank;
+ _add_graphml_data( $node_el, $node_data_keys{'class'}, $n->sub_class );
+ _add_graphml_data( $node_el, $node_data_keys{'identical'}, $n->primary->name )
+ if $n->has_primary && $n->primary ne $n;
+ }
+
+ # Add the path and relationship 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 );
+ }
+ }
+
+ # Save and return the thing
+ my $result = decode_utf8( $graphml->toString(1) );
+ $self->_save_graphml( $result );
+ 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 $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, $recalc ) = @_;
+ return $self->csv if $self->has_csv;
+ 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 ) );
+ }
+ $self->_save_csv( join( "\n", @result ) );
+ return $self->csv;
+}
+
+# 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 ) = @_;
+ unless( $self->linear ) {
+ warn "Need a linear graph in order to make an alignment table";
+ return;
+ }
+ my $table;
+ my @all_pos = sort { $a <=> $b } $self->possible_positions;
+ foreach my $wit ( $self->tradition->witnesses ) {
+ # print STDERR "Making witness row(s) for " . $wit->sigil . "\n";
+ my @row = _make_witness_row( $wit->path, \@all_pos, $noderefs );
+ unshift( @row, $wit->sigil );
+ push( @$table, \@row );
+ if( $wit->has_ante_corr ) {
+ my @ac_row = _make_witness_row( $wit->uncorrected_path, \@all_pos, $noderefs );
+ unshift( @ac_row, $wit->sigil . $self->ac_label );
+ push( @$table, \@ac_row );
+ }
+ }
+
+ # Return a table where the witnesses read in columns rather than rows.
+ my $turned = _turn_table( $table );
+ return $turned;
+}
+
+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->name . "\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];
+ }
+ }
+ 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
+
+=over
+
+=item B<start>
+
+my $beginning = $collation->start();
+
+Returns the beginning of the collation, a meta-reading with label '#START#'.
+
+=cut
+
+sub start {
+ # Return the beginning reading of the graph.
+ my( $self, $new_start ) = @_;
+ my $start = $self->reading( '#START#' );
+ if( ref( $new_start ) eq 'Text::Tradition::Collation::Reading' ) {
+ # Replace the existing start node.
+ $self->del_reading( '#START#' );
+ $self->graph->rename_node( $new_start, '#START#' );
+ $start = $new_start;
+ } elsif ( $new_start && $new_start eq 'INIT' ) {
+ # Make a new start node.
+ $start = $self->add_reading( '#START#' );
+ }
+ # Make sure the start node is a meta node
+ $start->is_meta( 1 );
+ # Make sure the start node has a start position.
+ unless( $start->has_rank ) {
+ $start->rank( '0' );
+ }
+ return $start;
+}
+
+=item B<end>
+
+my $end = $collation->end();
+
+Returns the end of the collation, a meta-reading with label '#END#'.
+
+=cut
+
+sub end {
+ my $self = shift;
+ my( $new_end ) = @_;
+ my $end = $self->reading( '#END#' );
+ if( ref( $new_end ) eq 'Text::Tradition::Collation::Reading' ) {
+ $self->del_reading( '#END#' );
+ $self->graph->rename_node( $new_end, '#END#' );
+ $end = $new_end
+ } elsif ( $new_end && $new_end eq 'INIT' ) {
+ # Make a new start node.
+ $end = $self->add_reading( '#END#' );
+ }
+ # Make sure the start node is a meta node
+ $end->is_meta( 1 );
+ return $end;
+}
+
+=item B<reading_sequence>
+
+my @readings = $graph->reading_sequence( $first, $last, $path[, $alt_path] );
+
+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 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;
+ }
+ # 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;
+
+ return @readings;
+}
+
+=item B<next_reading>
+
+my $next_reading = $graph->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;
+ return $self->_find_linked_reading( 'next', @_ );
+}
+
+=item B<prior_reading>
+
+my $prior_reading = $graph->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;
+ return $self->_find_linked_reading( 'prior', @_ );
+}
+
+sub _find_linked_reading {
+ my( $self, $direction, $node, $path, $alt_path ) = @_;
+ my @linked_paths = $direction eq 'next'
+ ? $node->outgoing() : $node->incoming();
+ 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;
+ 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;
+ }
+ }
+ }
+ # Got this far? Return the alternate path if it exists.
+ return $direction eq 'next' ? $alt_le->to() : $alt_le->from()
+ 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;
+
+ # Got this far? We have no appropriate path.
+ warn "Could not find $direction node from " . $node->label
+ . " 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
+# Walk the paths for each witness in the graph, and return the nodes
+# that the graph has in common. If $using_base is true, some
+# different logic is needed.
+# NOTE This does not create paths; it merely finds common readings.
+
+sub walk_witness_paths {
+ my( $self ) = @_;
+ # For each witness, walk the path through the graph.
+ # Then we need to find the common nodes.
+ # TODO This method is going to fall down if we have a very gappy
+ # text in the collation.
+ my $paths = {};
+ my @common_readings;
+ foreach my $wit ( $self->tradition->witnesses ) {
+ my $curr_reading = $self->start;
+ my @wit_path = $self->reading_sequence( $self->start, $self->end,
+ $wit->sigil );
+ $wit->path( \@wit_path );
+
+ # Detect the common readings.
+ @common_readings = _find_common( \@common_readings, \@wit_path );
+ }
+
+ # Mark all the nodes as either common or not.
+ foreach my $cn ( @common_readings ) {
+ print STDERR "Setting " . $cn->name . " / " . $cn->label
+ . " as common node\n";
+ $cn->make_common;
+ }
+ foreach my $n ( $self->readings() ) {
+ $n->make_variant unless $n->is_common;
+ }
+ # Return an array of the common nodes in order.
+ return @common_readings;
+}
+
+sub _find_common {
+ my( $common_readings, $new_path ) = @_;
+ my @cr;
+ if( @$common_readings ) {
+ foreach my $n ( @$new_path ) {
+ push( @cr, $n ) if grep { $_ eq $n } @$common_readings;
+ }
+ } else {
+ push( @cr, @$new_path );
+ }
+ return @cr;
+}
+
+sub _remove_common {
+ my( $common_readings, $divergence ) = @_;
+ my @cr;
+ my %diverged;
+ map { $diverged{$_->name} = 1 } @$divergence;
+ foreach( @$common_readings ) {
+ push( @cr, $_ ) unless $diverged{$_->name};
+ }
+ return @cr;
+}
+
+
+# For use when a collation is constructed from a base text and an apparatus.
+# We have the sequences of readings and just need to add path edges.
+
+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( $wit->has_ante_corr ) {
+ @chain = @{$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 );
+ }
+ }
+}
+
+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->name};
+ 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 ) {
+ $rel_containers{$_->name} = $rn;
+ }
+ } else {
+ # Add a new node to mirror the old node.
+ $rel_containers{$r->name} = $r->name;
+ $topo_graph->add_vertex( $r->name );
+ }
+ }
+
+ # Add the edges. Need only one edge between any pair of nodes.
+ 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 );
+ }
+ }
+
+ # Now do the rankings, starting with the start node.
+ my $topo_start = $rel_containers{$self->start->name};
+ 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->name}} ) {
+ $r->rank( $node_ranks->{$rel_containers{$r->name}} );
+ } else {
+ $DB::single = 1;
+ die "No rank calculated for node " . $r->name
+ . " - 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;
+ }
+ }
+}
+
+
+sub possible_positions {
+ my $self = shift;
+ my %all_pos;
+ map { $all_pos{ $_->rank } = 1 } $self->readings;
+ return keys %all_pos;
+}
+
+# TODO think about indexing this.
+sub readings_at_position {
+ my( $self, $position, $strict ) = @_;
+ my @answer;
+ foreach my $r ( $self->readings ) {
+ push( @answer, $r ) if $r->is_at_position( $position, $strict );
+ }
+ 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 common_readings {
+ my $self = shift;
+ my @common = grep { $_->is_common } $self->readings();
+ return sort { $a->rank <=> $b->rank } @common;
+}
+
+=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};
+ }
+ }
+
+ 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 ) = @_;
+
+ 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 = $self->wit_list_separator;
+ my @answer = split( /\Q$regex\E/, $label );
+ 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
projects / scpubgit/stemmatology.git / blobdiff