package Text::Tradition::Collation;
+use feature 'say';
use Encode qw( decode_utf8 );
use File::Temp;
+use File::Which;
use Graph;
use IPC::Run qw( run binary );
-use Text::CSV_XS;
+use Text::CSV;
use Text::Tradition::Collation::Reading;
use Text::Tradition::Collation::RelationshipStore;
-use XML::LibXML;
+use Text::Tradition::Error;
+use XML::Easy::Syntax qw( $xml10_namestartchar_rx $xml10_namechar_rx );
use Moose;
has 'sequence' => (
handles => {
relationships => 'relationships',
related_readings => 'related_readings',
+ get_relationship => 'get_relationship',
+ del_relationship => 'del_relationship',
+ equivalence => 'equivalence',
+ equivalence_graph => 'equivalence_graph',
},
writer => '_set_relations',
);
has 'tradition' => (
is => 'ro',
isa => 'Text::Tradition',
+ writer => '_set_tradition',
weak_ref => 1,
);
default => 1,
);
-has 'collapse_punctuation' => (
- is => 'rw',
- isa => 'Bool',
- default => 1,
- );
-
has 'ac_label' => (
is => 'rw',
isa => 'Str',
default => ' (a.c.)',
);
+has 'wordsep' => (
+ is => 'rw',
+ isa => 'Str',
+ default => ' ',
+ );
+
has 'start' => (
is => 'ro',
isa => 'Text::Tradition::Collation::Reading',
writer => '_set_end',
weak_ref => 1,
);
+
+has 'cached_svg' => (
+ is => 'rw',
+ isa => 'Str',
+ predicate => 'has_cached_svg',
+ clearer => 'wipe_svg',
+ );
+
+has 'cached_table' => (
+ is => 'rw',
+ isa => 'HashRef',
+ predicate => 'has_cached_table',
+ clearer => 'wipe_table',
+ );
+
+has '_graphcalc_done' => (
+ is => 'rw',
+ isa => 'Bool',
+ default => undef,
+ );
=head1 NAME
transposed readings should be treated as two linked readings rather than one,
and therefore whether the collation graph is acyclic. Defaults to true.
-=item * collapse_punctuation - TODO
-
=item * baselabel - The default label for the path taken by a base text
(if any). Defaults to 'base text'.
a text has more than one possible reading due to scribal corrections or
the like. Defaults to ' (a.c.)'.
+=item * wordsep - The string used to separate words in the original text.
+Defaults to ' '.
+
=back
=head1 ACCESSORS
=head2 linear
-=head2 collapse_punctuation
-
=head2 wit_list_separator
=head2 baselabel
=head2 ac_label
+=head2 wordsep
+
Simple accessors for collation attributes.
=head2 start
Removes the given reading from the collation, implicitly removing its
paths and relationships.
-=head2 merge_readings( $main, $second )
+=head2 merge_readings( $main, $second, $concatenate, $with_str )
-Merges the $second reading into the $main one.
-The arguments may be either readings or reading IDs.
+Merges the $second reading into the $main one. If $concatenate is true, then
+the merged node will carry the text of both readings, concatenated with either
+$with_str (if specified) or a sensible default (the empty string if the
+appropriate 'join_*' flag is set on either reading, or else $self->wordsep.)
+
+The first two arguments may be either readings or reading IDs.
=head2 has_reading( $id )
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 } ) );
+ $self->_set_start( $self->add_reading(
+ { 'collation' => $self, 'is_start' => 1, 'init' => 1 } ) );
+ $self->_set_end( $self->add_reading(
+ { 'collation' => $self, 'is_end' => 1, 'init' => 1 } ) );
}
### Reading construct/destruct functions
my( $self, $reading ) = @_;
unless( ref( $reading ) eq 'Text::Tradition::Collation::Reading' ) {
my %args = %$reading;
+ if( $args{'init'} ) {
+ # If we are initializing an empty collation, don't assume that we
+ # have set a tradition.
+ delete $args{'init'};
+ } elsif( $self->tradition->has_language && !exists $args{'language'} ) {
+ $args{'language'} = $self->tradition->language;
+ }
$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;
+ throw( "Collation already has a reading with id " . $reading->id );
}
+ $self->_graphcalc_done(0);
$self->_add_reading( $reading->id => $reading );
# Once the reading has been added, put it in both graphs.
$self->sequence->add_vertex( $reading->id );
$arg = $arg->id;
}
# Remove the reading from the graphs.
+ $self->_graphcalc_done(0);
+ $self->_clear_cache; # Explicitly clear caches to GC the reading
$self->sequence->delete_vertex( $arg );
$self->relations->delete_reading( $arg );
$self->$orig( $arg );
};
-# merge_readings( $main, $to_be_deleted );
+=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;
+
+my $rno = scalar $c->readings;
+# Split n21 for testing purposes
+my $new_r = $c->add_reading( { 'id' => 'n21p0', 'text' => 'un', 'join_next' => 1 } );
+my $old_r = $c->reading( 'n21' );
+$old_r->alter_text( 'to' );
+$c->del_path( 'n20', 'n21', 'A' );
+$c->add_path( 'n20', 'n21p0', 'A' );
+$c->add_path( 'n21p0', 'n21', 'A' );
+$c->flatten_ranks();
+ok( $c->reading( 'n21p0' ), "New reading exists" );
+is( scalar $c->readings, $rno, "Reading add offset by flatten_ranks" );
+
+# Combine n3 and n4 ( with his )
+$c->merge_readings( 'n3', 'n4', 1 );
+ok( !$c->reading('n4'), "Reading n4 is gone" );
+is( $c->reading('n3')->text, 'with his', "Reading n3 has both words" );
+
+# Collapse n9 and n10 ( rood / root )
+$c->merge_readings( 'n9', 'n10' );
+ok( !$c->reading('n10'), "Reading n10 is gone" );
+is( $c->reading('n9')->text, 'rood', "Reading n9 has an unchanged word" );
+
+# Combine n21 and n21p0
+my $remaining = $c->reading('n21');
+$remaining ||= $c->reading('n22'); # one of these should still exist
+$c->merge_readings( 'n21p0', $remaining, 1 );
+ok( !$c->reading('n21'), "Reading $remaining is gone" );
+is( $c->reading('n21p0')->text, 'unto', "Reading n21p0 merged correctly" );
+
+=end testing
+
+=cut
sub merge_readings {
my $self = shift;
+ # Sanity check
+ my( $kept_obj, $del_obj, $combine, $combine_char ) = $self->_objectify_args( @_ );
+ my $mergemeta = $kept_obj->is_meta;
+ throw( "Cannot merge meta and non-meta reading" )
+ unless ( $mergemeta && $del_obj->is_meta )
+ || ( !$mergemeta && !$del_obj->is_meta );
+ if( $mergemeta ) {
+ throw( "Cannot merge with start or end node" )
+ if( $kept_obj eq $self->start || $kept_obj eq $self->end
+ || $del_obj eq $self->start || $del_obj eq $self->end );
+ }
# We only need the IDs for adding paths to the graph, not the reading
# objects themselves.
- my( $kept, $deleted, $combine_char ) = $self->_stringify_args( @_ );
-
+ my $kept = $kept_obj->id;
+ my $deleted = $del_obj->id;
+ $self->_graphcalc_done(0);
+
# The kept reading should inherit the paths and the relationships
# of the deleted reading.
foreach my $path ( $self->sequence->edges_at( $deleted ) ) {
@wits{keys %$fwits} = values %$fwits;
$self->sequence->set_edge_attributes( @vector, \%wits );
}
- $self->relations->merge_readings( $kept, $deleted, $combine_char );
+ $self->relations->merge_readings( $kept, $deleted, $combine );
# 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 );
+ if( $combine ) {
+ # Combine the text of the readings
+ my $joinstr = $combine_char;
+ unless( defined $joinstr ) {
+ $joinstr = '' if $kept_obj->join_next || $del_obj->join_prior;
+ $joinstr = $self->wordsep unless defined $joinstr;
+ }
+ $kept_obj->alter_text( join( $joinstr, $kept_obj->text, $del_obj->text ) );
+ # Change this reading to a joining one if necessary
+ $kept_obj->_set_join_next( $del_obj->join_next );
+ $kept_obj->normal_form(
+ join( $joinstr, $kept_obj->normal_form, $del_obj->normal_form ) );
+ # Combine the lexemes present in the readings
+ if( $kept_obj->has_lexemes && $del_obj->has_lexemes ) {
+ $kept_obj->add_lexeme( $del_obj->lexemes );
+ }
}
$self->del_reading( $deleted );
}
+=head2 compress_readings
+
+Where possible in the graph, compresses plain sequences of readings into a
+single reading. The sequences must consist of readings with no
+relationships to other readings, with only a single witness path between
+them and no other witness paths from either that would skip the other. The
+readings must also not be marked as nonsense or bad grammar.
+
+WARNING: This operation cannot be undone.
+
+=cut
+
+sub compress_readings {
+ my $self = shift;
+ # Anywhere in the graph that there is a reading that joins only to a single
+ # successor, and neither of these have any relationships, just join the two
+ # readings.
+ my %gobbled;
+ foreach my $rdg ( sort { $a->rank <=> $b->rank } $self->readings ) {
+ # While we are here, get rid of any extra wordforms from a disambiguated
+ # reading.
+ if( $rdg->disambiguated ) {
+ foreach my $lex ( $rdg->lexemes ) {
+ $lex->clear_matching_forms();
+ $lex->add_matching_form( $lex->form );
+ }
+ }
+ # Now look for readings that can be joined to their successors.
+ next if $rdg->is_meta;
+ next if $gobbled{$rdg->id};
+ next if $rdg->grammar_invalid || $rdg->is_nonsense;
+ next if $rdg->related_readings();
+ my %seen;
+ while( $self->sequence->successors( $rdg ) == 1 ) {
+ my( $next ) = $self->reading( $self->sequence->successors( $rdg ) );
+ throw( "Infinite loop" ) if $seen{$next->id};
+ $seen{$next->id} = 1;
+ last if $self->sequence->predecessors( $next ) > 1;
+ last if $next->is_meta;
+ last if $next->grammar_invalid || $next->is_nonsense;
+ last if $next->related_readings();
+ say "Joining readings $rdg and $next";
+ $self->merge_readings( $rdg, $next, 1 );
+ }
+ }
+ # Make sure we haven't screwed anything up
+ foreach my $wit ( $self->tradition->witnesses ) {
+ my $pathtext = $self->path_text( $wit->sigil );
+ my $origtext = join( ' ', @{$wit->text} );
+ throw( "Text differs for witness " . $wit->sigil )
+ unless $pathtext eq $origtext;
+ if( $wit->is_layered ) {
+ $pathtext = $self->path_text( $wit->sigil.$self->ac_label );
+ $origtext = join( ' ', @{$wit->layertext} );
+ throw( "Ante-corr text differs for witness " . $wit->sigil )
+ unless $pathtext eq $origtext;
+ }
+ }
+
+ $self->relations->rebuild_equivalence();
+ $self->calculate_ranks();
+}
# Helper function for manipulating the graph.
sub _stringify_args {
- my( $self, $first, $second, $arg ) = @_;
+ my( $self, $first, $second, @args ) = @_;
$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 );
+ return( $first, $second, @args );
}
# Helper function for manipulating the graph.
# objects themselves.
my( $source, $target, $wit ) = $self->_stringify_args( @_ );
+ $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;
# objects themselves.
my( $source, $target, $wit ) = $self->_stringify_args( @args );
+ $self->_graphcalc_done(0);
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 );
+ $self->relations->delete_equivalence_edge( $source, $target );
}
}
sub clear_witness {
my( $self, @sigils ) = @_;
+ $self->_graphcalc_done(0);
# Clear the witness(es) out of the paths
foreach my $e ( $self->paths ) {
foreach my $sig ( @sigils ) {
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 );
+ my( @vectors ) = $self->relations->add_relationship( $source, $target, $opts );
+ $self->_graphcalc_done(0);
+ return @vectors;
}
+around qw/ get_relationship del_relationship / => sub {
+ my $orig = shift;
+ my $self = shift;
+ my @args = @_;
+ if( @args == 1 && ref( $args[0] ) eq 'ARRAY' ) {
+ @args = @{$_[0]};
+ }
+ my( $source, $target ) = $self->_stringify_args( @args );
+ $self->$orig( $source, $target );
+};
+
=head2 reading_witnesses( $reading )
Return a list of sigils corresponding to the witnesses in which the reading appears.
my $wits = $self->sequence->get_edge_attributes( @$e );
@all_witnesses{ keys %$wits } = 1;
}
+ my $acstr = $self->ac_label;
+ foreach my $acwit ( grep { $_ =~ s/^(.*)\Q$acstr\E$/$1/ } keys %all_witnesses ) {
+ delete $all_witnesses{$acwit.$acstr} if exists $all_witnesses{$acwit};
+ }
return keys %all_witnesses;
}
=head1 OUTPUT METHODS
-=head2 as_svg
+=head2 as_svg( \%options )
Returns an SVG string that represents the graph, via as_dot and graphviz.
+See as_dot for a list of options. Must have GraphViz (dot) installed to run.
=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;
+ my( $self, $opts ) = @_;
+ throw( "Need GraphViz installed to output SVG" )
+ unless File::Which::which( 'dot' );
+ my $want_subgraph = exists $opts->{'from'} || exists $opts->{'to'};
+ $self->calculate_ranks()
+ unless( $self->_graphcalc_done || $opts->{'nocalc'} || !$self->linear );
+ if( !$self->has_cached_svg || $opts->{'recalc'} || $want_subgraph ) {
+ my @cmd = qw/dot -Tsvg/;
+ my( $svg, $err );
+ my $dotfile = File::Temp->new();
+ ## USE FOR DEBUGGING
+ # $dotfile->unlink_on_destroy(0);
+ binmode $dotfile, ':utf8';
+ print $dotfile $self->as_dot( $opts );
+ push( @cmd, $dotfile->filename );
+ run( \@cmd, ">", binary(), \$svg );
+ $svg = decode_utf8( $svg );
+ $self->cached_svg( $svg ) unless $want_subgraph;
+ return $svg;
+ } else {
+ return $self->cached_svg;
+ }
}
-=head2 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.
+=head2 as_dot( \%options )
-=cut
+Returns a string that is the collation graph expressed in dot
+(i.e. GraphViz) format. Options include:
-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;
-}
+=over 4
+=item * from
-=head2 as_dot( $from, $to )
+=item * to
-Returns a string that is the collation graph expressed in dot
-(i.e. GraphViz) format. If $from or $to is passed, as_dot creates
-a subgraph rather than the entire graph.
+=item * color_common
+
+=back
=cut
sub as_dot {
- my( $self, $startrank, $endrank ) = @_;
-
+ my( $self, $opts ) = @_;
+ my $startrank = $opts->{'from'} if $opts;
+ my $endrank = $opts->{'to'} if $opts;
+ my $color_common = $opts->{'color_common'} if $opts;
+ my $STRAIGHTENHACK = !$startrank && !$endrank && $self->end->rank
+ && $self->end->rank > 100;
+ $STRAIGHTENHACK = 1 if $opts->{'straight'}; # even for subgraphs or small graphs
+
# Check the arguments
if( $startrank ) {
return if $endrank && $startrank > $endrank;
$endrank = undef if $endrank == $self->end->rank;
}
- # 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 %graph_attrs = (
+ 'rankdir' => 'LR',
+ 'bgcolor' => 'none',
+ );
+ my %node_attrs = (
+ 'fontsize' => 14,
+ 'fillcolor' => 'white',
+ 'style' => 'filled',
+ 'shape' => 'ellipse'
+ );
+ my %edge_attrs = (
+ 'arrowhead' => 'open',
+ 'color' => '#000000',
+ 'fontcolor' => '#000000',
+ );
+
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" );
+ $dot .= "\tgraph " . _dot_attr_string( \%graph_attrs ) . ";\n";
+ $dot .= "\tnode " . _dot_attr_string( \%node_attrs ) . ";\n";
# Output substitute start/end readings if necessary
if( $startrank ) {
- $dot .= "\t\"#SUBSTART#\" [ label=\"...\" ];\n";
+ $dot .= "\t\"__SUBSTART__\" [ label=\"...\",id=\"__START__\" ];\n";
}
if( $endrank ) {
- $dot .= "\t\"#SUBEND#\" [ label=\"...\" ];\n";
+ $dot .= "\t\"__SUBEND__\" [ label=\"...\",id=\"__END__\" ];\n";
+ }
+ if( $STRAIGHTENHACK ) {
+ ## HACK part 1
+ my $startlabel = $startrank ? '__SUBSTART__' : '__START__';
+ $dot .= "\tsubgraph { rank=same \"$startlabel\" \"#SILENT#\" }\n";
+ $dot .= "\t\"#SILENT#\" [ shape=diamond,color=white,penwidth=0,label=\"\" ];"
}
my %used; # Keep track of the readings that actually appear in the graph
- foreach my $reading ( $self->readings ) {
+ # Sort the readings by rank if we have ranks; this speeds layout.
+ my @all_readings = $self->end->has_rank
+ ? sort { $a->rank <=> $b->rank } $self->readings
+ : $self->readings;
+ # TODO Refrain from outputting lacuna nodes - just grey out the edges.
+ foreach my $reading ( @all_readings ) {
# Only output readings within our rank range.
next if $startrank && $reading->rank < $startrank;
next if $endrank && $reading->rank > $endrank;
$used{$reading->id} = 1;
# Need not output nodes without separate labels
next if $reading->id eq $reading->text;
- my $label = $reading->punctuated_form;
+ my $rattrs;
+ my $label = $reading->text;
+ $label .= '-' if $reading->join_next;
+ $label = "-$label" if $reading->join_prior;
$label =~ s/\"/\\\"/g;
- $dot .= sprintf( "\t\"%s\" [ label=\"%s\" ];\n", $reading->id, $label );
+ $rattrs->{'label'} = $label;
+ $rattrs->{'id'} = $reading->id;
+ $rattrs->{'fillcolor'} = '#b3f36d' if $reading->is_common && $color_common;
+ $dot .= sprintf( "\t\"%s\" %s;\n", $reading->id, _dot_attr_string( $rattrs ) );
}
- # Add the real edges
+ # Add the real edges. Need to weight one edge per rank jump, in a
+ # continuous line.
+ # my $weighted = $self->_add_edge_weights;
my @edges = $self->paths;
my( %substart, %subend );
foreach my $edge ( @edges ) {
# Do we need to output this edge?
- $DB::single = 1 if $edge->[0] =~ /n(8|13)/;
- if( $used{$edge->[0]} && $used{$edge->[1]} ) {;
- my %variables = ( 'color' => '#000000',
- 'fontcolor' => '#000000',
- 'label' => join( ', ', $self->path_display_label( $self->path_witnesses( $edge ) ) ),
- );
- my $varopts = join( ', ', map { $_.'="'.$variables{$_}.'"' } sort keys %variables );
+ if( $used{$edge->[0]} && $used{$edge->[1]} ) {
+ my $label = $self->_path_display_label( $self->path_witnesses( $edge ) );
+ my $variables = { %edge_attrs, 'label' => $label };
+
# 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 );
+ my $rank0 = $self->reading( $edge->[0] )->rank
+ if $self->reading( $edge->[0] )->has_rank;
+ my $rank1 = $self->reading( $edge->[1] )->rank
+ if $self->reading( $edge->[1] )->has_rank;
+ if( defined $rank0 && defined $rank1 && $rank1 - $rank0 > 1 ) {
+ $variables->{'minlen'} = $rank1 - $rank0;
+ }
+
+ # Add the calculated edge weights
+ # if( exists $weighted->{$edge->[0]}
+ # && $weighted->{$edge->[0]} eq $edge->[1] ) {
+ # # $variables->{'color'} = 'red';
+ # $variables->{'weight'} = 3.0;
+ # }
+
+ # EXPERIMENTAL: make edge width reflect no. of witnesses
+ my $extrawidth = scalar( $self->path_witnesses( $edge ) ) * 0.2;
+ $variables->{'penwidth'} = $extrawidth + 0.8; # gives 1 for a single wit
+
+ my $varopts = _dot_attr_string( $variables );
+ $dot .= sprintf( "\t\"%s\" -> \"%s\" %s;\n",
+ $edge->[0], $edge->[1], $varopts );
} elsif( $used{$edge->[0]} ) {
- $subend{$edge->[0]} = 1;
+ $subend{$edge->[0]} = $edge->[1];
} elsif( $used{$edge->[1]} ) {
- $substart{$edge->[1]} = 1;
+ $substart{$edge->[1]} = $edge->[0];
}
}
# Add substitute start and end edges if necessary
foreach my $node ( keys %substart ) {
- my $witstr = $self->path_display_label ( $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\"#SUBSTART#\" -> \"%s\" [ %s ];\n", $node, $varopts );
+ my $witstr = $self->_path_display_label ( $self->path_witnesses( $substart{$node}, $node ) );
+ my $variables = { %edge_attrs, 'label' => $witstr };
+ my $nrdg = $self->reading( $node );
+ if( $nrdg->has_rank && $nrdg->rank > $startrank ) {
+ # Substart is actually one lower than $startrank
+ $variables->{'minlen'} = $nrdg->rank - ( $startrank - 1 );
+ }
+ my $varopts = _dot_attr_string( $variables );
+ $dot .= "\t\"__SUBSTART__\" -> \"$node\" $varopts;\n";
}
foreach my $node ( keys %subend ) {
- my $witstr = $self->path_display_label ( $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\" -> \"#SUBEND#\" [ %s ];\n", $node, $varopts );
+ my $witstr = $self->_path_display_label ( $self->path_witnesses( $node, $subend{$node} ) );
+ my $variables = { %edge_attrs, 'label' => $witstr };
+ my $varopts = _dot_attr_string( $variables );
+ $dot .= "\t\"$node\" -> \"__SUBEND__\" $varopts;\n";
}
-
+ # HACK part 2
+ if( $STRAIGHTENHACK ) {
+ my $endlabel = $endrank ? '__SUBEND__' : '__END__';
+ $dot .= "\t\"$endlabel\" -> \"#SILENT#\" [ color=white,penwidth=0 ];\n";
+ }
+
$dot .= "}\n";
return $dot;
}
+sub _dot_attr_string {
+ my( $hash ) = @_;
+ my @attrs;
+ foreach my $k ( sort keys %$hash ) {
+ my $v = $hash->{$k};
+ push( @attrs, $k.'="'.$v.'"' );
+ }
+ return( '[ ' . join( ', ', @attrs ) . ' ]' );
+}
+
+sub _add_edge_weights {
+ my $self = shift;
+ # Walk the graph from START to END, choosing the successor node with
+ # the largest number of witness paths each time.
+ my $weighted = {};
+ my $curr = $self->start->id;
+ my $ranked = $self->end->has_rank;
+ while( $curr ne $self->end->id ) {
+ my $rank = $ranked ? $self->reading( $curr )->rank : 0;
+ my @succ = sort { $self->path_witnesses( $curr, $a )
+ <=> $self->path_witnesses( $curr, $b ) }
+ $self->sequence->successors( $curr );
+ my $next = pop @succ;
+ my $nextrank = $ranked ? $self->reading( $next )->rank : 0;
+ # Try to avoid lacunae in the weighted path.
+ while( @succ &&
+ ( $self->reading( $next )->is_lacuna ||
+ $nextrank - $rank > 1 ) ){
+ $next = pop @succ;
+ }
+ $weighted->{$curr} = $next;
+ $curr = $next;
+ }
+ return $weighted;
+}
+
+=head2 path_witnesses( $edge )
+
+Returns the list of sigils whose witnesses are associated with the given edge.
+The edge can be passed as either an array or an arrayref of ( $source, $target ).
+
+=cut
+
sub path_witnesses {
my( $self, @edge ) = @_;
# If edge is an arrayref, cope.
@edge = @$e;
}
my @wits = keys %{$self->sequence->get_edge_attributes( @edge )};
- return sort @wits;
+ return @wits;
}
-sub path_display_label {
- my( $self, @wits ) = @_;
+# Helper function. Make a display label for the given witnesses, showing a.c.
+# witnesses only where the main witness is not also in the list.
+sub _path_display_label {
+ my $self = shift;
+ my %wits;
+ map { $wits{$_} = 1 } @_;
+
+ # If an a.c. wit is listed, remove it if the main wit is also listed.
+ # Otherwise keep it for explicit listing.
+ my $aclabel = $self->ac_label;
+ my @disp_ac;
+ foreach my $w ( sort keys %wits ) {
+ if( $w =~ /^(.*)\Q$aclabel\E$/ ) {
+ if( exists $wits{$1} ) {
+ delete $wits{$w};
+ } else {
+ push( @disp_ac, $w );
+ }
+ }
+ }
+
+ # See if we are in a majority situation.
my $maj = scalar( $self->tradition->witnesses ) * 0.6;
- if( scalar @wits > $maj ) {
- return 'majority';
+ $maj = $maj > 5 ? $maj : 5;
+ if( scalar keys %wits > $maj ) {
+ unshift( @disp_ac, 'majority' );
+ return join( ', ', @disp_ac );
} else {
- return join( ', ', @wits );
+ return join( ', ', sort keys %wits );
}
}
-
+
+=head2 readings_at_rank( $rank )
+
+Returns a list of readings at a given rank, taken from the alignment table.
+
+=cut
+
+sub readings_at_rank {
+ my( $self, $rank ) = @_;
+ my $table = $self->alignment_table;
+ # Table rank is real rank - 1.
+ my @elements = map { $_->{'tokens'}->[$rank-1] } @{$table->{'alignment'}};
+ my %readings;
+ foreach my $e ( @elements ) {
+ next unless ref( $e ) eq 'HASH';
+ next unless exists $e->{'t'};
+ $readings{$e->{'t'}->id} = $e->{'t'};
+ }
+ return values %readings;
+}
=head2 as_graphml
is( scalar $st->collation->paths, $PATHS, "Reparsed collation has all paths" );
is( scalar $st->collation->relationships, 3, "Reparsed collation has new relationships" );
+# Now add a stemma, write to GraphML, and look at the output.
+my $stemma = $tradition->add_stemma( 'dotfile' => 't/data/florilegium.dot' );
+is( ref( $stemma ), 'Text::Tradition::Stemma', "Parsed dotfile into stemma" );
+is( $tradition->stemmata, 1, "Tradition now has the stemma" );
+$graphml = $c->as_graphml;
+like( $graphml, qr/digraph/, "Digraph declaration exists in GraphML" );
+
+# Now add a user, write to GraphML, and look at the output.
+unlike( $graphml, qr/testuser/, "Test user name does not exist in GraphML yet" );
+my $testuser = Text::Tradition::User->new(
+ id => 'testuser', password => 'testpass' );
+is( ref( $testuser ), 'Text::Tradition::User', "Created test user object" );
+$testuser->add_tradition( $tradition );
+is( $tradition->user->id, $testuser->id, "Tradition assigned to test user" );
+$graphml = $c->as_graphml;
+like( $graphml, qr/testuser/, "Test user name now exists in GraphML" );
+
=end testing
=cut
sub as_graphml {
- my( $self ) = @_;
-
+ my( $self, $options ) = @_;
+ $self->calculate_ranks unless $self->_graphcalc_done;
+
+ my $start = $options->{'from'}
+ ? $self->reading( $options->{'from'} ) : $self->start;
+ my $end = $options->{'to'}
+ ? $self->reading( $options->{'to'} ) : $self->end;
+ if( $start->has_rank && $end->has_rank && $end->rank < $start->rank ) {
+ throw( 'Start node must be before end node' );
+ }
+ # The readings need to be ranked for this to work.
+ $start = $self->start unless $start->has_rank;
+ $end = $self->end unless $end->has_rank;
+ my $rankoffset = 0;
+ unless( $start eq $self->start ) {
+ $rankoffset = $start->rank - 1;
+ }
+ my %use_readings;
+
# Some namespaces
my $graphml_ns = 'http://graphml.graphdrawing.org/xmlns';
my $xsi_ns = 'http://www.w3.org/2001/XMLSchema-instance';
'http://graphml.graphdrawing.org/xmlns/1.0/graphml.xsd';
# Create the document and root node
+ require XML::LibXML;
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 );
+
+ # List of attribute types to save on our objects and their corresponding
+ # GraphML types
+ my %save_types = (
+ 'Str' => 'string',
+ 'Int' => 'int',
+ 'Bool' => 'boolean',
+ 'ReadingID' => 'string',
+ 'RelationshipType' => 'string',
+ 'RelationshipScope' => 'string',
+ );
+
+ # List of attribute names *not* to save on our objects.
+ # We will also not save any attribute beginning with _.
+ my %skipsave;
+ map { $skipsave{$_} = 1 } qw/ cached_svg /;
- # Add the data keys for the graph
+ # Add the data keys for the graph. Include an extra key 'version' for the
+ # GraphML output version.
my %graph_data_keys;
my $gdi = 0;
- my @graph_attributes = qw/ version wit_list_separator baselabel linear ac_label /;
- foreach my $datum ( @graph_attributes ) {
+ my %graph_attributes = ( 'version' => 'string' );
+ # Graph attributes include those of Tradition and those of Collation.
+ my %gattr_from;
+ my $tmeta = $self->tradition->meta;
+ my $cmeta = $self->meta;
+ map { $gattr_from{$_->name} = 'Tradition' } $tmeta->get_all_attributes;
+ map { $gattr_from{$_->name} = 'Collation' } $cmeta->get_all_attributes;
+ foreach my $attr ( ( $tmeta->get_all_attributes, $cmeta->get_all_attributes ) ) {
+ next if $attr->name =~ /^_/;
+ next if $skipsave{$attr->name};
+ next unless $save_types{$attr->type_constraint->name};
+ $graph_attributes{$attr->name} = $save_types{$attr->type_constraint->name};
+ }
+ # Extra custom keys for complex objects that should be saved in some form.
+ # The subroutine should return a string, or undef/empty.
+ $graph_attributes{'stemmata'} = sub {
+ my @stemstrs;
+ map { push( @stemstrs, $_->editable( {linesep => ''} ) ) }
+ $self->tradition->stemmata;
+ join( "\n", @stemstrs );
+ };
+ $graph_attributes{'user'} = sub {
+ $self->tradition->user ? $self->tradition->user->id : undef
+ };
+
+ foreach my $datum ( sort keys %graph_attributes ) {
$graph_data_keys{$datum} = 'dg'.$gdi++;
my $key = $root->addNewChild( $graphml_ns, 'key' );
+ my $dtype = ref( $graph_attributes{$datum} ) ? 'string'
+ : $graph_attributes{$datum};
$key->setAttribute( 'attr.name', $datum );
- $key->setAttribute( 'attr.type', $key eq 'linear' ? 'boolean' : 'string' );
+ $key->setAttribute( 'attr.type', $dtype );
$key->setAttribute( 'for', 'graph' );
$key->setAttribute( 'id', $graph_data_keys{$datum} );
}
- # Add the data keys for nodes
+ # Add the data keys for reading nodes
+ my %reading_attributes;
+ my $rmeta = Text::Tradition::Collation::Reading->meta;
+ foreach my $attr( $rmeta->get_all_attributes ) {
+ next if $attr->name =~ /^_/;
+ next if $skipsave{$attr->name};
+ next unless $save_types{$attr->type_constraint->name};
+ $reading_attributes{$attr->name} = $save_types{$attr->type_constraint->name};
+ }
+ # Extra custom key for the reading morphology
+ $reading_attributes{'lexemes'} = 'string';
+
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 ) {
+ foreach my $datum ( sort keys %reading_attributes ) {
$node_data_keys{$datum} = 'dn'.$ndi++;
my $key = $root->addNewChild( $graphml_ns, 'key' );
$key->setAttribute( 'attr.name', $datum );
- $key->setAttribute( 'attr.type', $node_data{$datum} );
+ $key->setAttribute( 'attr.type', $reading_attributes{$datum} );
$key->setAttribute( 'for', 'node' );
$key->setAttribute( 'id', $node_data_keys{$datum} );
}
- # Add the data keys for edges, i.e. witnesses
+ # Add the data keys for edges, that is, paths and relationships. Path
+ # data does not come from a Moose class so is here manually.
my $edi = 0;
my %edge_data_keys;
- my %edge_data = (
- class => 'string', # Class, deprecated soon
+ my %edge_attributes = (
witness => 'string', # ID/label for a path
- relationship => 'string', # ID/label for a relationship
extra => 'boolean', # Path key
- scope => 'string', # Relationship key
- non_correctable => 'boolean', # Relationship key
- non_independent => 'boolean', # Relationship key
);
- foreach my $datum ( keys %edge_data ) {
+ my @path_attributes = keys %edge_attributes; # track our manual additions
+ my $pmeta = Text::Tradition::Collation::Relationship->meta;
+ foreach my $attr( $pmeta->get_all_attributes ) {
+ next if $attr->name =~ /^_/;
+ next if $skipsave{$attr->name};
+ next unless $save_types{$attr->type_constraint->name};
+ $edge_attributes{$attr->name} = $save_types{$attr->type_constraint->name};
+ }
+ foreach my $datum ( sort keys %edge_attributes ) {
$edge_data_keys{$datum} = 'de'.$edi++;
my $key = $root->addNewChild( $graphml_ns, 'key' );
$key->setAttribute( 'attr.name', $datum );
- $key->setAttribute( 'attr.type', $edge_data{$datum} );
+ $key->setAttribute( 'attr.type', $edge_attributes{$datum} );
$key->setAttribute( 'for', 'edge' );
$key->setAttribute( 'id', $edge_data_keys{$datum} );
}
- # Add the collation graph itself
+ # Add the collation graph itself. First, sanitize the name to a valid XML ID.
+ my $xmlidname = $self->tradition->name;
+ $xmlidname =~ s/(?!$xml10_namechar_rx)./_/g;
+ if( $xmlidname !~ /^$xml10_namestartchar_rx/ ) {
+ $xmlidname = '_'.$xmlidname;
+ }
my $sgraph = $root->addNewChild( $graphml_ns, 'graph' );
$sgraph->setAttribute( 'edgedefault', 'directed' );
- $sgraph->setAttribute( 'id', $self->tradition->name );
+ $sgraph->setAttribute( 'id', $xmlidname );
$sgraph->setAttribute( 'parse.edgeids', 'canonical' );
- $sgraph->setAttribute( 'parse.edges', scalar($self->paths) );
+ $sgraph->setAttribute( 'parse.edges', 0 ); # fill in later
$sgraph->setAttribute( 'parse.nodeids', 'canonical' );
- $sgraph->setAttribute( 'parse.nodes', scalar($self->readings) );
+ $sgraph->setAttribute( 'parse.nodes', 0 ); # fill in later
$sgraph->setAttribute( 'parse.order', 'nodesfirst' );
- # Collation attribute data
- foreach my $datum ( @graph_attributes ) {
- my $value = $datum eq 'version' ? '3.0' : $self->$datum;
+ # Tradition/collation attribute data
+ foreach my $datum ( keys %graph_attributes ) {
+ my $value;
+ if( $datum eq 'version' ) {
+ $value = '3.2';
+ } elsif( ref( $graph_attributes{$datum} ) ) {
+ my $sub = $graph_attributes{$datum};
+ $value = &$sub();
+ } elsif( $gattr_from{$datum} eq 'Tradition' ) {
+ $value = $self->tradition->$datum;
+ } else {
+ $value = $self->$datum;
+ }
_add_graphml_data( $sgraph, $graph_data_keys{$datum}, $value );
}
my %node_hash;
# Add our readings to the graph
foreach my $n ( sort { $a->id cmp $b->id } $self->readings ) {
+ next if $n->has_rank && $n ne $self->start && $n ne $self->end &&
+ ( $n->rank < $start->rank || $n->rank > $end->rank );
+ $use_readings{$n->id} = 1;
# 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 ) {
+ foreach my $d ( keys %reading_attributes ) {
my $nval = $n->$d;
- $nval = $n->punctuated_form if $d eq 'text';
+ # Custom serialization
+ if( $d eq 'lexemes' ) {
+ # If nval is a true value, we have lexemes so we need to
+ # serialize them. Otherwise set nval to undef so that the
+ # key is excluded from this reading.
+ $nval = $nval ? $n->_serialize_lexemes : undef;
+ } elsif( $d eq 'normal_form' && $n->normal_form eq $n->text ) {
+ $nval = undef;
+ }
+ if( $rankoffset && $d eq 'rank' && $n ne $self->start ) {
+ # Adjust the ranks within the subgraph.
+ $nval = $n eq $self->end ? $end->rank - $rankoffset + 1
+ : $nval - $rankoffset;
+ }
_add_graphml_data( $node_el, $node_data_keys{$d}, $nval )
if defined $nval;
}
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 ) ) {
+ next unless( $use_readings{$e->[0]} || $use_readings{$e->[1]} );
+ my @edge_wits = sort $self->path_witnesses( $e );
+ $e->[0] = $self->start->id unless $use_readings{$e->[0]};
+ $e->[1] = $self->end->id unless $use_readings{$e->[1]};
+ # Skip any path from start to end; that witness is not in the subgraph.
+ next if ( $e->[0] eq $self->start->id && $e->[1] eq $self->end->id );
+ foreach my $wit ( @edge_wits ) {
my( $id, $from, $to ) = ( 'e'.$edge_ctr++,
$node_hash{ $e->[0] },
$node_hash{ $e->[1] } );
_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' );
}
}
+ # Report the actual number of nodes and edges that went in
+ $sgraph->setAttribute( 'parse.edges', $edge_ctr );
+ $sgraph->setAttribute( 'parse.nodes', $node_ctr );
+
# Add the relationship graph to the XML
- $self->relations->as_graphml( $graphml_ns, $root, \%node_hash,
+ map { delete $edge_data_keys{$_} } @path_attributes;
+ $self->relations->_as_graphml( $graphml_ns, $root, \%node_hash,
$node_data_keys{'id'}, \%edge_data_keys );
# Save and return the thing
sub as_csv {
my( $self ) = @_;
- my $table = $self->make_alignment_table;
- my $csv = Text::CSV_XS->new( { binary => 1, quote_null => 0 } );
+ my $table = $self->alignment_table;
+ my $csv = Text::CSV->new( { binary => 1, quote_null => 0 } );
my @result;
# Make the header row
$csv->combine( map { $_->{'witness'} } @{$table->{'alignment'}} );
# 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;
+ my @row = map { $_ ? $_->{'t'}->text : $_ } @rowobjs;
$csv->combine( @row );
push( @result, decode_utf8( $csv->string ) );
}
return join( "\n", @result );
}
-=head2 make_alignment_table( $use_refs, $include_witnesses )
+=head2 alignment_table( $use_refs, $include_witnesses )
Return a reference to an alignment table, in a slightly enhanced CollateX
format which looks like this:
=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;
- }
+sub alignment_table {
+ my( $self ) = @_;
+ $self->calculate_ranks() unless $self->_graphcalc_done;
+ return $self->cached_table if $self->has_cached_table;
+
+ # Make sure we can do this
+ throw( "Need a linear graph in order to make an alignment table" )
+ unless $self->linear;
+ $self->calculate_ranks unless $self->end->has_rank;
+
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";
+ # say STDERR "Making witness row(s) for " . $wit->sigil;
my @wit_path = $self->reading_sequence( $self->start, $self->end, $wit->sigil );
- my @row = _make_witness_row( \@wit_path, \@all_pos, $noderefs );
+ my @row = _make_witness_row( \@wit_path, \@all_pos );
push( @{$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 );
+ $wit->sigil.$self->ac_label );
+ my @ac_row = _make_witness_row( \@wit_ac_path, \@all_pos );
push( @{$table->{'alignment'}},
{ 'witness' => $wit->sigil.$self->ac_label, 'tokens' => \@ac_row } );
}
}
- return $table;
+ $self->cached_table( $table );
+ return $table;
}
sub _make_witness_row {
- my( $path, $positions, $noderefs ) = @_;
+ my( $path, $positions ) = @_;
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 };
+ say STDERR "rank " . $rdg->rank if $debug;
+ # say STDERR "No rank for " . $rdg->id unless defined $rdg->rank;
+ $char_hash{$rdg->rank} = { 't' => $rdg };
}
my @row = map { $char_hash{$_} } @$positions;
# Fill in lacuna markers for undef spots in the row
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#' };
+ if( $last_el && $last_el->{'t'}->is_lacuna && !defined $el ) {
+ $el = $last_el;
}
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;
-}
-
=head1 NAVIGATION METHODS
=head2 reading_sequence( $first, $last, $sigil, $backup )
=cut
# TODO Think about returning some lazy-eval iterator.
+# TODO Get rid of backup; we should know from what witness is whether we need it.
sub reading_sequence {
- my( $self, $start, $end, $witness, $backup ) = @_;
+ my( $self, $start, $end, $witness ) = @_;
$witness = $self->baselabel unless $witness;
my @readings = ( $start );
my $n = $start;
while( $n && $n->id ne $end->id ) {
if( exists( $seen{$n->id} ) ) {
- warn "Detected loop at " . $n->id;
- last;
+ throw( "Detected loop for $witness at " . $n->id );
}
$seen{$n->id} = 1;
- my $next = $self->next_reading( $n, $witness, $backup );
+ my $next = $self->next_reading( $n, $witness );
unless( $next ) {
- warn "Did not find any path for $witness from reading " . $n->id;
- last;
+ throw( "Did not find any path for $witness from reading " . $n->id );
}
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!"
+ throw( "Last reading found from " . $start->text .
+ " for witness $witness is not the end!" ) # TODO do we get this far?
unless $last->id eq $end->id;
return @readings;
}
sub _find_linked_reading {
- my( $self, $direction, $node, $path, $alt_path ) = @_;
+ my( $self, $direction, $node, $path ) = @_;
+
+ # Get a backup if we are dealing with a layered witness
+ my $alt_path;
+ my $aclabel = $self->ac_label;
+ if( $path && $path =~ /^(.*)\Q$aclabel\E$/ ) {
+ $alt_path = $1;
+ }
+
my @linked_paths = $direction eq 'next'
? $self->sequence->edges_from( $node )
: $self->sequence->edges_to( $node );
if( $self->sequence->has_edge_attribute( @$le, $self->baselabel ) ) {
$base_le = $le;
}
- my @le_wits = $self->path_witnesses( $le );
+ my @le_wits = sort $self->path_witnesses( $le );
if( _is_within( \@path_wits, \@le_wits ) ) {
# This is the right path.
return $direction eq 'next' ? $le->[1] : $le->[0];
my $regex = $self->wit_list_separator;
my @answer = split( /\Q$regex\E/, $label );
return @answer;
-}
+}
+
+=head2 common_readings
+Returns the list of common readings in the graph (i.e. those readings that are
+shared by all non-lacunose witnesses.)
+
+=cut
+
+sub common_readings {
+ my $self = shift;
+ my @common = grep { $_->is_common } $self->readings;
+ return @common;
+}
+
+=head2 path_text( $sigil, [, $start, $end ] )
+
+Returns the text of a witness (plus its backup, if we are using a layer)
+as stored in the collation. The text is returned as a string, where the
+individual readings are joined with spaces and the meta-readings (e.g.
+lacunae) are omitted. Optional specification of $start and $end allows
+the generation of a subset of the witness text.
+
+=cut
+
+sub path_text {
+ my( $self, $wit, $start, $end ) = @_;
+ $start = $self->start unless $start;
+ $end = $self->end unless $end;
+ my @path = grep { !$_->is_meta } $self->reading_sequence( $start, $end, $wit );
+ my $pathtext = '';
+ my $last;
+ foreach my $r ( @path ) {
+ unless ( $r->join_prior || !$last || $last->join_next ) {
+ $pathtext .= ' ';
+ }
+ $pathtext .= $r->text;
+ $last = $r;
+ }
+ return $pathtext;
+}
=head1 INITIALIZATION METHODS
sub make_witness_paths {
my( $self ) = @_;
foreach my $wit ( $self->tradition->witnesses ) {
- # print STDERR "Making path for " . $wit->sigil . "\n";
+ # say STDERR "Making path for " . $wit->sigil;
$self->make_witness_path( $wit );
}
}
my( $self, $wit ) = @_;
my @chain = @{$wit->path};
my $sig = $wit->sigil;
+ # Add start and end if necessary
+ unshift( @chain, $self->start ) unless $chain[0] eq $self->start;
+ push( @chain, $self->end ) unless $chain[-1] eq $self->end;
foreach my $idx ( 0 .. $#chain-1 ) {
$self->add_path( $chain[$idx], $chain[$idx+1], $sig );
}
if( $wit->is_layered ) {
@chain = @{$wit->uncorrected_path};
+ unshift( @chain, $self->start ) unless $chain[0] eq $self->start;
+ push( @chain, $self->end ) unless $chain[-1] eq $self->end;
foreach my $idx( 0 .. $#chain-1 ) {
my $source = $chain[$idx];
my $target = $chain[$idx+1];
Calculate the reading ranks (that is, their aligned positions relative
to each other) for the graph. This can only be called on linear collations.
+=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;
+
+# Make an svg
+my $table = $c->alignment_table;
+ok( $c->has_cached_table, "Alignment table was cached" );
+is( $c->alignment_table, $table, "Cached table returned upon second call" );
+$c->calculate_ranks;
+is( $c->alignment_table, $table, "Cached table retained with no rank change" );
+$c->add_relationship( 'n24', 'n23', { 'type' => 'spelling' } );
+isnt( $c->alignment_table, $table, "Alignment table changed after relationship add" );
+
+=end testing
+
=cut
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 );
- }
- }
+ # Save the existing ranks, in case we need to invalidate the cached SVG.
+ my %existing_ranks;
+ map { $existing_ranks{$_} = $_->rank } $self->readings;
+
+ # Do the rankings based on the relationship equivalence graph, starting
+ # with the start node.
+ my ( $node_ranks, $rank_nodes ) = $self->relations->equivalence_ranks();
- # 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}} );
+ if( defined $node_ranks->{$self->equivalence( $r->id )} ) {
+ $r->rank( $node_ranks->{$self->equivalence( $r->id )} );
} else {
- die "No rank calculated for node " . $r->id
- . " - do you have a cycle in the graph?";
+ # Die. Find the last rank we calculated.
+ 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?" );
}
}
-}
-
-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 );
- }
+ # Do we need to invalidate the cached data?
+ if( $self->has_cached_svg || $self->has_cached_table ) {
+ foreach my $r ( $self->readings ) {
+ next if defined( $existing_ranks{$r} )
+ && $existing_ranks{$r} == $r->rank;
+ # Something has changed, so clear the cache
+ $self->_clear_cache;
+ # ...and recalculate the common readings.
+ $self->calculate_common_readings();
+ last;
+ }
}
- return @next_nodes;
+ # The graph calculation information is now up to date.
+ $self->_graphcalc_done(1);
}
+sub _clear_cache {
+ my $self = shift;
+ $self->wipe_svg if $self->has_cached_svg;
+ $self->wipe_table if $self->has_cached_table;
+}
+
+
=head2 flatten_ranks
A convenience method for parsing collation data. Searches the graph for readings
sub flatten_ranks {
my $self = shift;
my %unique_rank_rdg;
+ my $changed;
foreach my $rdg ( $self->readings ) {
next unless $rdg->has_rank;
my $key = $rdg->rank . "||" . $rdg->text;
if( exists $unique_rank_rdg{$key} ) {
+ # Make sure they don't have different grammatical forms
+ my $ur = $unique_rank_rdg{$key};
+ if( $rdg->disambiguated && $ur->disambiguated ) {
+ my $rform = join( '//', map { $_->form->to_string } $rdg->lexemes );
+ my $uform = join( '//', map { $_->form->to_string } $ur->lexemes );
+ next unless $rform eq $uform;
+ } elsif( $rdg->disambiguated xor $ur->disambiguated ) {
+ next;
+ }
# Combine!
- # print STDERR "Combining readings at same rank: $key\n";
+ #say STDERR "Combining readings at same rank: $key";
+ $changed = 1;
$self->merge_readings( $unique_rank_rdg{$key}, $rdg );
+ # TODO see if this now makes a common point.
} else {
$unique_rank_rdg{$key} = $rdg;
}
}
+ # If we merged readings, the ranks are still fine but the alignment
+ # table is wrong. Wipe it.
+ $self->wipe_table() if $changed;
}
+
+
+=head2 calculate_common_readings
+Goes through the graph identifying the readings that appear in every witness
+(apart from those with lacunae at that spot.) Marks them as common and returns
+the list.
+
+=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;
+
+my @common = $c->calculate_common_readings();
+is( scalar @common, 8, "Found correct number of common readings" );
+my @marked = sort $c->common_readings();
+is( scalar @common, 8, "All common readings got marked as such" );
+my @expected = qw/ n1 n11 n16 n19 n20 n5 n6 n7 /;
+is_deeply( \@marked, \@expected, "Found correct list of common readings" );
+
+=end testing
+
+=cut
+
+sub calculate_common_readings {
+ my $self = shift;
+ my @common;
+ map { $_->is_common( 0 ) } $self->readings;
+ # Implicitly calls calculate_ranks
+ my $table = $self->alignment_table;
+ foreach my $idx ( 0 .. $table->{'length'} - 1 ) {
+ my @row = map { $_->{'tokens'}->[$idx]
+ ? $_->{'tokens'}->[$idx]->{'t'} : '' }
+ @{$table->{'alignment'}};
+ my %hash;
+ foreach my $r ( @row ) {
+ if( $r ) {
+ $hash{$r->id} = $r unless $r->is_meta;
+ } else {
+ $hash{'UNDEF'} = $r;
+ }
+ }
+ if( keys %hash == 1 && !exists $hash{'UNDEF'} ) {
+ my( $r ) = values %hash;
+ $r->is_common( 1 );
+ push( @common, $r );
+ }
+ }
+ return @common;
+}
+
+=head2 text_from_paths
+
+Calculate the text array for all witnesses from the path, for later consistency
+checking. Only to be used if there is no non-graph-based way to know the
+original texts.
+
+=cut
+
+sub text_from_paths {
+ my $self = shift;
+ foreach my $wit ( $self->tradition->witnesses ) {
+ my @readings = $self->reading_sequence( $self->start, $self->end, $wit->sigil );
+ my @text;
+ foreach my $r ( @readings ) {
+ next if $r->is_meta;
+ push( @text, $r->text );
+ }
+ $wit->text( \@text );
+ if( $wit->is_layered ) {
+ my @ucrdgs = $self->reading_sequence( $self->start, $self->end,
+ $wit->sigil.$self->ac_label );
+ my @uctext;
+ foreach my $r ( @ucrdgs ) {
+ next if $r->is_meta;
+ push( @uctext, $r->text );
+ }
+ $wit->layertext( \@uctext );
+ }
+ }
+}
=head1 UTILITY FUNCTIONS
=head2 common_predecessor( $reading_a, $reading_b )
Find the last reading that occurs in sequence before both the given readings.
+At the very least this should be $self->start.
=head2 common_successor( $reading_a, $reading_b )
Find the first reading that occurs in sequence after both the given readings.
+At the very least this should be $self->end.
=begin testing
);
my $c = $t->collation;
-is( $c->common_predecessor( 'n9', 'n23' )->id,
+is( $c->common_predecessor( 'n24', 'n23' )->id,
'n20', "Found correct common predecessor" );
-is( $c->common_successor( 'n9', 'n23' )->id,
- '#END#', "Found correct common successor" );
+is( $c->common_successor( 'n24', 'n23' )->id,
+ '__END__', "Found correct common successor" );
is( $c->common_predecessor( 'n19', 'n17' )->id,
'n16', "Found correct common predecessor for readings on same path" );
-is( $c->common_successor( 'n21', 'n26' )->id,
- '#END#', "Found correct common successor for readings on same path" );
+is( $c->common_successor( 'n21', 'n10' )->id,
+ '__END__', "Found correct common successor for readings on same path" );
=end testing
sub common_predecessor {
my $self = shift;
my( $r1, $r2 ) = $self->_objectify_args( @_ );
- return $self->common_in_path( $r1, $r2, 'predecessors' );
+ return $self->_common_in_path( $r1, $r2, 'predecessors' );
}
sub common_successor {
my $self = shift;
my( $r1, $r2 ) = $self->_objectify_args( @_ );
- return $self->common_in_path( $r1, $r2, 'successors' );
+ return $self->_common_in_path( $r1, $r2, 'successors' );
}
-sub common_in_path {
+
+# TODO think about how to do this without ranks...
+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 $iter = $self->end->rank;
my @candidates;
- my @last_checked = ( $r1, $r2 );
+ my @last_r1 = ( $r1 );
+ my @last_r2 = ( $r2 );
+ # my %all_seen = ( $r1 => 'r1', $r2 => 'r2' );
my %all_seen;
+ # say STDERR "Finding common $dir for $r1, $r2";
while( !@candidates ) {
- my @new_lc;
- foreach my $lc ( @last_checked ) {
+ last unless $iter--; # Avoid looping infinitely
+ # Iterate separately down the graph from r1 and r2
+ my( @new_lc1, @new_lc2 );
+ foreach my $lc ( @last_r1 ) {
foreach my $p ( $lc->$dir ) {
- if( $all_seen{$p->id} ) {
+ if( $all_seen{$p->id} && $all_seen{$p->id} ne 'r1' ) {
+ # say STDERR "Path candidate $p from $lc";
push( @candidates, $p );
- } else {
- $all_seen{$p->id} = 1;
- push( @new_lc, $p );
+ } elsif( !$all_seen{$p->id} ) {
+ $all_seen{$p->id} = 'r1';
+ push( @new_lc1, $p );
}
}
}
- @last_checked = @new_lc;
+ foreach my $lc ( @last_r2 ) {
+ foreach my $p ( $lc->$dir ) {
+ if( $all_seen{$p->id} && $all_seen{$p->id} ne 'r2' ) {
+ # say STDERR "Path candidate $p from $lc";
+ push( @candidates, $p );
+ } elsif( !$all_seen{$p->id} ) {
+ $all_seen{$p->id} = 'r2';
+ push( @new_lc2, $p );
+ }
+ }
+ }
+ @last_r1 = @new_lc1;
+ @last_r2 = @new_lc2;
}
my @answer = sort { $a->rank <=> $b->rank } @candidates;
return $dir eq 'predecessors' ? pop( @answer ) : shift ( @answer );
}
+sub throw {
+ Text::Tradition::Error->throw(
+ 'ident' => 'Collation error',
+ 'message' => $_[0],
+ );
+}
+
no Moose;
__PACKAGE__->meta->make_immutable;
-=head1 BUGS / TODO
+=head1 LICENSE
-=over
+This package is free software and is provided "as is" without express
+or implied warranty. You can redistribute it and/or modify it under
+the same terms as Perl itself.
-=item * Get rid of $backup in reading_sequence
+=head1 AUTHOR
-=back
+Tara L Andrews E<lt>aurum@cpan.orgE<gt>
projects / scpubgit/stemmatology.git / blobdiff