use vars qw/ @EXPORT_OK /;
@EXPORT_OK = qw/ run_analysis group_variants analyze_variant_location wit_stringify /;
+=head1 NAME
+
+Text::Tradition::Analysis - functions for stemma analysis of a tradition
+
+=head1 SYNOPSIS
+
+ use Text::Tradition;
+ use Text::Tradition::Analysis qw/ run_analysis analyze_variant_location /;
+ my $t = Text::Tradition->new(
+ 'name' => 'this is a text',
+ 'input' => 'TEI',
+ 'file' => '/path/to/tei_parallel_seg_file.xml' );
+ $t->add_stemma( 'dotfile' => $stemmafile );
+
+ my $variant_data = run_analysis( $tradition );
+ # Recalculate rank $n treating all orthographic variants as equivalent
+ my $reanalyze = analyze_variant_location( $tradition, $n, 0, 'orthographic' );
+
+=head1 DESCRIPTION
+
+Text::Tradition is a library for representation and analysis of collated
+texts, particularly medieval ones. The Collation is the central feature of
+a Tradition, where the text, its sequence of readings, and its relationships
+between readings are actually kept.
+
+=head1 SUBROUTINES
+
+=head2 run_analysis( $tradition, $stemma_id, @merge_relationship_types )
+
+Runs the analysis described in analyze_variant_location on every location
+in the collation of the given tradition, against the stemma specified in
+$stemma_id. If $stemma_id is not specified, it defaults to 0 (referencing
+the first stemma saved for the tradition.)
+
+The optional @merge_relationship_types contains a list of relationship types
+to treat as equivalent for the analysis.
+
+=begin testing
+
+use Text::Tradition;
+use Text::Tradition::Analysis qw/ run_analysis analyze_variant_location /;
+
+my $datafile = 't/data/florilegium_tei_ps.xml';
+my $tradition = Text::Tradition->new( 'input' => 'TEI',
+ 'name' => 'test0',
+ 'file' => $datafile );
+my $s = $tradition->add_stemma( 'dotfile' => 't/data/florilegium.dot' );
+is( ref( $s ), 'Text::Tradition::Stemma', "Added stemma to tradition" );
+
+my $data = run_analysis( $tradition );
+# TODO should be 21!
+is( $data->{'genealogical_count'}, 42, "Got right genealogical count" );
+is( $data->{'conflict_count'}, 17, "Got right conflict count" );
+is( $data->{'variant_count'}, 58, "Got right total variant number" );
+
+=end testing
+
+=cut
+
sub run_analysis {
- my( $tradition ) = @_;
- # What we will return
- my $variants = [];
- my $data = {};
+ my( $tradition, $stemma_id, @collapse ) = @_;
+ $stemma_id = 0 unless $stemma_id;
- # We need a stemma in order to run this...
- unless( $tradition->stemma_count ) {
- warn "Tradition '" . $tradition->name . "' has no stemma to analyze";
- return undef;
- }
- my $stemma = $tradition->stemma(0); # TODO allow multiple
-
- # We have the collation, so get the alignment table with witnesses in rows.
- # Also return the reading objects in the table, rather than just the words.
- my $wits = {};
- map { $wits->{$_} = 1 } $stemma->witnesses;
- # For each column in the alignment table, we want to see if the existing
- # groupings of witnesses match our stemma hypothesis. We also need to keep
- # track of the maximum number of variants at any one location.
- my $max_variants = 0;
- my ( $genealogical, $conflicts ) = ( 0, 0, 0 );
+ # Run the variant analysis on every rank in the graph that doesn't
+ # have a common reading. Return the results.
+ my @variants; # holds results from analyze_variant_location
+ my $genealogical; # counter of 'genealogical' variants
+ my $conflicts; # counter of conflicting readings
- my $variant_groups = group_variants( $tradition->collation, $wits );
- foreach my $rank ( 0 .. $#{$variant_groups} ) {
- my $groups = $variant_groups->[$rank]->{'groups'};
- my $readings = $variant_groups->[$rank]->{'readings'};
- my $lacunose = $variant_groups->[$rank]->{'lacunose'};
-
- $max_variants = scalar @$groups if scalar @$groups > $max_variants;
-
- # We can already look up witnesses for a reading; we also want to look
- # up readings for a given witness.
- my $group_readings = {};
- foreach my $x ( 0 .. $#$groups ) {
- $group_readings->{wit_stringify( $groups->[$x] )} = $readings->[$x];
- }
-
- # For all the groups with more than one member, collect the list of all
- # contiguous vertices needed to connect them.
- my $variant_loc = analyze_variant_location( $group_readings, $groups,
- $stemma->graph, $lacunose );
- $variant_loc->{'id'} = $rank;
- $genealogical++ if $variant_loc->{'genealogical'};
- $conflicts += grep { $_->{'conflict'} } @{$variant_loc->{'readings'}};
-
- # Now run the same analysis given the calculated distance tree(s).
-# my @trees = @{$stemma->distance_trees};
-# if( @trees ) {
-# foreach my $tree ( 0 .. $#trees ) {
-# my $dc = analyze_variant_location( $group_readings, $groups, $tree, $lacunose, 'undirected' );
-# foreach my $rdg ( keys %$dc ) {
-# my $var = $dc->{$rdg};
-# # TODO Do something with this
-# }
-# }
-# }
-
- # Record that we used this variant in an analysis
- push( @$variants, $variant_loc );
+ # Find and mark 'common' ranks for exclusion.
+ my %common_rank;
+ foreach my $rdg ( $tradition->collation->common_readings ) {
+ $common_rank{$rdg->rank} = 1;
}
-
- # Go through our variant locations, after we have seen all of them once,
- # and add the number of empty columns needed by each.
- foreach my $row ( @$variants ) {
- my $empty = $max_variants - scalar @{$row->{'readings'}};
- $row->{'empty'} = $empty;
+
+ foreach my $rank ( 1 .. $tradition->collation->end->rank-1 ) {
+ next if $common_rank{$rank};
+ my $variant_row = analyze_variant_location(
+ $tradition, $rank, $stemma_id, @collapse );
+ push( @variants, $variant_row );
+ $genealogical++ if $variant_row->{'genealogical'};
+ $conflicts += grep { $_->{'conflict'} } @{$variant_row->{'readings'}};
}
- $data->{'variants'} = $variants;
- $data->{'variant_count'} = $tradition->collation->end->rank - 1;
- $data->{'conflict_count'} = $conflicts;
- $data->{'genealogical_count'} = $genealogical;
- return $data;
+ return {
+ 'variants' => \@variants,
+ 'variant_count' => scalar @variants, # TODO redundant
+ 'conflict_count' => $conflicts,
+ 'genealogical_count' => $genealogical,
+ };
}
+=head2 group_variants( $tradition, $rank, $lacunose, @merge_relationship_types )
+
+Groups the variants at the given $rank of the collation, treating any
+relationships in @merge_relationship_types as equivalent. $lacunose should
+be a reference to an array, to which the sigla of lacunose witnesses at this
+rank will be appended.
+
+Returns two ordered lists $readings, $groups, where $readings->[$n] is attested
+by the witnesses listed in $groups->[$n].
+
+=cut
+
+# Return group_readings, groups, lacunose
sub group_variants {
- my( $c, $wits ) = @_;
- my $variant_groups = [];
+ my( $tradition, $rank, $lacunose, $collapse ) = @_;
+ my $c = $tradition->collation;
+ # Get the alignment table readings
+ my %readings_at_rank;
+ my @gap_wits;
+ foreach my $tablewit ( @{$tradition->collation->alignment_table->{'alignment'}} ) {
+ my $rdg = $tablewit->{'tokens'}->[$rank-1];
+ if( $rdg && $rdg->{'t'}->is_lacuna ) {
+ push( @$lacunose, $tablewit->{'witness'} );
+ } elsif( $rdg ) {
+ $readings_at_rank{$rdg->{'t'}->text} = $rdg->{'t'};
+ } else {
+ push( @gap_wits, $tablewit->{'witness'} );
+ }
+ }
- # We have the collation, so get the alignment table with witnesses in rows.
- # Also return the reading objects in the table, rather than just the words.
- my $all_wits_table = $c->make_alignment_table( 'refs', $wits );
- # Strip the list of sigla and save it for correlation to the readings.
- my @table_wits = map { $_->{'witness'} } @{$all_wits_table->{'alignment'}};
- # Any witness in the stemma that has no row should be noted.
- foreach ( @table_wits ) {
- $wits->{$_}++; # Witnesses present in table and stemma now have value 2.
- }
- my @not_collated = grep { $wits->{$_} == 1 } keys %$wits;
- foreach my $i ( 0 .. $all_wits_table->{'length'} - 1 ) {
- # For each column in the table, group the readings by witness.
- my $rdg_wits = {};
- my @col_rdgs = map { $_->{tokens}->[$i] } @{$all_wits_table->{'alignment'}};
- my $lacunose = [ @not_collated ];
- foreach my $j ( 0 .. $#col_rdgs ) {
- my $rdg = $col_rdgs[$j];
- my $rdg_text = '(omitted)'; # Initialize in case of empty reading
- if( $rdg ) {
- if( $rdg->{'t'}->is_lacuna ) {
- $rdg_text = undef; # Don't count lacunae
- push( @$lacunose, $table_wits[$j] );
- } else {
- $rdg_text = $rdg->{'t'}->text;
- }
- }
- if( defined $rdg_text ) {
- # Initialize the witness array if we haven't got one yet
- $rdg_wits->{$rdg_text} = [] unless $rdg_wits->{$rdg_text};
- # Add the relevant witness, subject to a.c. logic
- add_variant_wit( $rdg_wits->{$rdg_text}, $table_wits[$j],
- $c->ac_label );
+ # Group the readings, collapsing groups by relationship if needed
+ my %grouped_readings;
+ foreach my $rdg ( sort { $b->witnesses <=> $a->witnesses } values %readings_at_rank ) {
+ # Skip readings that have been collapsed into others.
+ next if exists $grouped_readings{$rdg->text} && !$grouped_readings{$rdg->text};
+ my @wits = $rdg->witnesses;
+ if( $collapse ) {
+ my $filter = sub { my $r = $_[0]; grep { $_ eq $r->type } @$collapse; };
+ foreach my $other ( $rdg->related_readings( $filter ) ) {
+ push( @wits, $other->witnesses );
+ $grouped_readings{$other->text} = 0;
}
}
-
- # See if this column has any potentially genealogical variants.
- # If not, skip to the next.
- my( $groups, $readings ) = useful_variant( $rdg_wits );
- next unless $groups && $readings;
-
- push( @$variant_groups,
- { 'groups' => $groups, 'readings' => $readings, 'lacunose' => $lacunose } );
+ $grouped_readings{$rdg->text} = \@wits;
+ }
+ $grouped_readings{'(omitted)'} = \@gap_wits if @gap_wits;
+ # Get rid of our collapsed readings
+ map { delete $grouped_readings{$_} unless $grouped_readings{$_} }
+ keys %grouped_readings
+ if $collapse;
+
+ # Return the readings and groups, sorted by size
+ my( @readings, @groups );
+ foreach my $r ( sort { @{$grouped_readings{$b}} <=> @{$grouped_readings{$a}} }
+ keys %grouped_readings ) {
+ push( @readings, $r );
+ push( @groups, $grouped_readings{$r} );
}
- return $variant_groups;
+ return( \@readings, \@groups );
}
+=head2 analyze_variant_location( $tradition, $rank, $stemma_id, @merge_relationship_types )
+Runs an analysis of the given tradition, at the location given in $rank,
+against the graph of the stemma specified in $stemma_id. The argument
+@merge_relationship_types is an optional list of relationship types for
+which readings so related should be treated as equivalent.
-# variant_row -> genealogical
-# -> readings [ { text, group, conflict, missing } ]
+Returns a data structure as follows:
+
+ { 'id' => $rank,
+ 'genealogical' => boolean,
+ 'readings => [ { text => $reading_text,
+ group => [ witnesses ],
+ conflict => [ conflicting ],
+ missing => [ excluded ] }, ... ]
+ }
+where 'conflicting' is the list of witnesses whose readings conflict with
+this group, and 'excluded' is the list of witnesses either not present in
+the stemma or lacunose at this location.
+
+=cut
sub analyze_variant_location {
- my( $group_readings, $groups, $graph, $lacunose, $undirected ) = @_;
+ my( $tradition, $rank, $sid, @collapse ) = @_;
+ $DB::single = 1 if @collapse;
+ # Get the readings in this tradition at this rank
+ my @rank_rdgs = grep { $_->rank == $rank } $tradition->collation->readings;
+ # Get the applicable stemma
+ my $undirected; # TODO Allow undirected distance tree analysis too
+ my $stemma = $tradition->stemma( $sid );
+ my $graph = $stemma->graph;
+ # Figure out which witnesses we are working with
+ my @lacunose = _set( 'symmdiff', [ $stemma->witnesses ],
+ [ map { $_->sigil } $tradition->witnesses ] );
+
+ # Now group the readings
+ my( $readings, $groups ) =
+ group_variants( $tradition, $rank, \@lacunose, \@collapse );
+ my $group_readings = {};
+ # Lookup table group string -> readings
+ foreach my $x ( 0 .. $#$groups ) {
+ $group_readings->{wit_stringify( $groups->[$x] )} = $readings->[$x];
+ }
+
+ # Now do the work.
my $contig = {};
my $subgraph = {};
my $is_conflicted;
my $conflict = {};
- my $missing = {};
- map { $missing->{$_} = 1 } @$lacunose;
- my $variant_row = { 'readings' => [] };
+ my $variant_row = { 'id' => $rank, 'readings' => [] };
# Mark each ms as in its own group, first.
foreach my $g ( @$groups ) {
my $gst = wit_stringify( $g );
my $nodes_in_subtree = 0;
foreach my $root ( @roots ) {
# Prune the tree to get rid of extraneous hypotheticals.
- $root = prune_subtree( $part, $root, $contig );
+ $root = _prune_subtree( $part, $root, $contig );
# Get all the successor nodes of our root.
my $tmp_reach = { $root => 1 };
map { $tmp_reach->{$_} = 1 } $part->all_successors( $root );
# Write the reading.
my $reading = { 'text' => $group_readings->{$gst},
- 'missing' => wit_stringify( $lacunose ),
+ 'missing' => wit_stringify( \@lacunose ),
'group' => $gst }; # This will change if we find no conflict
if( $is_conflicted ) {
$reading->{'conflict'} = $conflict->{$group_readings->{$gst}}
}
# Now write the group and conflict information into the respective rows.
+ my %missing;
+ map { $missing{$_} = 1 } @lacunose; # quick lookup table
foreach my $rdg ( @{$variant_row->{'readings'}} ) {
$rdg->{'conflict'} = $conflict->{$rdg->{'text'}};
next if $rdg->{'conflict'};
- my @members = grep { $contig->{$_} eq $rdg->{'group'} && !$missing->{$_} }
+ my @members = grep { $contig->{$_} eq $rdg->{'group'} && !$missing{$_} }
keys %$contig;
$rdg->{'group'} = wit_stringify( \@members );
}
return $variant_row;
}
-sub prune_subtree {
+sub _prune_subtree {
my( $tree, $root, $contighash ) = @_;
# First, delete hypothetical leaves / orphans until there are none left.
my @orphan_hypotheticals = grep { ref( $contighash->{$_} ) }
push( @$arr, $wit ) unless $skip;
}
-# Return an answer if the variant is useful, i.e. if there are at least 2 variants
-# with at least 2 witnesses each.
-sub useful_variant {
- my( $readings ) = @_;
- my $total = keys %$readings;
- foreach my $var ( keys %$readings ) {
- $total-- if @{$readings->{$var}} == 1;
- }
- return( undef, undef ) if $total <= 1;
- my( $groups, $text );
- foreach my $var ( keys %$readings ) {
- push( @$groups, $readings->{$var} );
- push( @$text, $var );
- }
- return( $groups, $text );
-}
+=head2 wit_stringify( $groups )
+
+Takes an array of witness groupings and produces a string like
+['A','B'] / ['C','D','E'] / ['F']
-# Take an array of witness groupings and produce a string like
-# ['A','B'] / ['C','D','E'] / ['F']
+=cut
sub wit_stringify {
my $groups = shift;
}
return join( ' / ', @gst );
}
-
-1;
\ No newline at end of file
+
+sub _set {
+ my( $op, $lista, $listb ) = @_;
+ my %union;
+ my %scalars;
+ map { $union{$_} = 1; $scalars{$_} = $_ } @$lista;
+ map { $union{$_} += 1; $scalars{$_} = $_ } @$listb;
+ my @set;
+ if( $op eq 'intersection' ) {
+ @set = grep { $union{$_} == 2 } keys %union;
+ } elsif( $op eq 'symmdiff' ) {
+ @set = grep { $union{$_} == 1 } keys %union;
+ } elsif( $op eq 'union' ) {
+ @set = keys %union;
+ }
+ return map { $scalars{$_} } @set;
+}
+
+1;
+
+=head1 LICENSE
+
+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.
+
+=head1 AUTHOR
+
+Tara L Andrews E<lt>aurum@cpan.orgE<gt>
predicate => 'has_cached_svg',
clearer => 'wipe_svg',
);
+
+has 'cached_table' => (
+ is => 'rw',
+ isa => 'HashRef',
+ predicate => 'has_cached_table',
+ clearer => 'wipe_table',
+ );
=head1 NAME
### Reading construct/destruct functions
+sub _clear_cache {
+ my $self = shift;
+ $self->wipe_svg if $self->has_cached_svg;
+ $self->wipe_table if $self->has_cached_table;
+}
+
sub add_reading {
my( $self, $reading ) = @_;
unless( ref( $reading ) eq 'Text::Tradition::Collation::Reading' ) {
if( $self->reading( $reading->id ) ) {
throw( "Collation already has a reading with id " . $reading->id );
}
+ $self->_clear_cache;
$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->_clear_cache;
$self->sequence->delete_vertex( $arg );
$self->relations->delete_reading( $arg );
# We only need the IDs for adding paths to the graph, not the reading
# objects themselves.
my( $kept, $deleted, $combine_char ) = $self->_stringify_args( @_ );
+ $self->_clear_cache;
# The kept reading should inherit the paths and the relationships
# of the deleted reading.
# objects themselves.
my( $source, $target, $wit ) = $self->_stringify_args( @_ );
+ $self->_clear_cache;
# Connect the readings
$self->sequence->add_edge( $source, $target );
# Note the witness in question
# objects themselves.
my( $source, $target, $wit ) = $self->_stringify_args( @args );
+ $self->_clear_cache;
if( $self->sequence->has_edge_attribute( $source, $target, $wit ) ) {
$self->sequence->delete_edge_attribute( $source, $target, $wit );
}
sub clear_witness {
my( $self, @sigils ) = @_;
+ $self->_clear_cache;
# Clear the witness(es) out of the paths
foreach my $e ( $self->paths ) {
foreach my $sig ( @sigils ) {
$self->reading( $source ), $target, $self->reading( $target ), $opts );
# Force a full rank recalculation every time. Yuck.
$self->calculate_ranks() if $self->end->has_rank;
+ $self->_clear_cache;
return @vectors;
}
return join( ', ', @wits );
}
}
-
+
+=head2 witnesses_at_rank
+
+Returns a list of witnesses that are not lacunose, for a given rank.
+
+=cut
+
+sub witnesses_at_rank {
+ my( $self, $rank ) = @_;
+}
=head2 as_graphml
sub as_csv {
my( $self ) = @_;
- my $table = $self->make_alignment_table;
+ my $table = $self->alignment_table;
my $csv = Text::CSV_XS->new( { binary => 1, quote_null => 0 } );
my @result;
# Make the header row
# 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 ) = @_;
+sub alignment_table {
+ my( $self ) = @_;
+ my $include; # see if we can ditch this
+ ## DEBUG
+ 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;
}
# print STDERR "Making witness row(s) for " . $wit->sigil . "\n";
my @wit_path = $self->reading_sequence( $self->start, $self->end, $wit->sigil );
- my @row = _make_witness_row( \@wit_path, \@all_pos, $noderefs );
+ my @row = _make_witness_row( \@wit_path, \@all_pos );
push( @{$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 );
- my @ac_row = _make_witness_row( \@wit_ac_path, \@all_pos, $noderefs );
+ my @ac_row = _make_witness_row( \@wit_ac_path, \@all_pos );
push( @{$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;
$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 };
+ $char_hash{$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 )
sub calculate_common_readings {
my $self = shift;
my @common;
- my $table = $self->make_alignment_table( 1 );
+ my $table = $self->alignment_table;
foreach my $idx ( 0 .. $table->{'length'} - 1 ) {
- my @row = map { $_->{'tokens'}->[$idx]->{'t'} } @{$table->{'alignment'}};
+ my @row = map { $_->{'tokens'}->[$idx]
+ ? $_->{'tokens'}->[$idx]->{'t'} : '' }
+ @{$table->{'alignment'}};
my %hash;
foreach my $r ( @row ) {
if( $r ) {
projects / scpubgit/stemmatology.git / commitdiff