use strict;
use warnings;
+use Benchmark;
+use Exporter 'import';
use Text::Tradition;
use Text::Tradition::Stemma;
-sub new {
- my( $class, $args ) = @_;
- my $self = {};
- # Our object needs to have a stemma graph and a variant table.
- my( $svg, $variants ) = run_analysis( $args->{'file'}, $args->{'stemmadot'} );
- $self->{'svg'} = $svg;
- $self->{'variants'} = $variants;
-
- bless( $self, $class );
- return $self;
-}
+use vars qw/ @EXPORT_OK /;
+@EXPORT_OK = qw/ run_analysis group_variants analyze_variant_location wit_stringify /;
sub run_analysis {
- my( $file, $stemmadot ) = @_;
+ my( $tradition ) = @_;
# What we will return
- my $svg;
my $variants = [];
+ my $data = {};
- # Read in the file and stemma
- my $tradition = Text::Tradition->new(
- 'input' => 'Self',
- 'file' => $file,
- 'linear' => 1,
- );
- my $stemma = Text::Tradition::Stemma->new(
- 'collation' => $tradition->collation,
- 'dot' => $stemmadot,
- );
- # We will return the stemma picture
- $svg = $stemma->as_svg;
- ### DIRTY HACK
- $svg =~ s/transform=\"scale\(1 1\)/transform=\"scale\(0.7 0.7\)/;
-
+ # 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 );
- my $all_wits_table = $tradition->collation->make_alignment_table( 'refs' );
+ 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 );
+ }
+
+ # 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;
+ }
- # For each column in the alignment table, we want to see if the existing
- # groupings of witnesses match our stemma hypothesis. We also want, at the
- # end, to produce an HTML table with all the variants.
- my $html_columns = 0;
- my $html_data = [];
- my $total = 0; # Keep track of the total number of variant locations
+ $data->{'variants'} = $variants;
+ $data->{'variant_count'} = $tradition->collation->end->rank - 1;
+ $data->{'conflict_count'} = $conflicts;
+ $data->{'genealogical_count'} = $genealogical;
+ return $data;
+}
+
+sub group_variants {
+ my( $c, $wits ) = @_;
+ my $variant_groups = [];
+ # 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 $col_wits = shift @$all_wits_table;
-
- # We will return a data structure, an array for each row that looks like:
- # { id = X, genealogical = Y, readings = [ text = X, group = Y], empty = N }
- foreach my $i ( 0 .. $#$all_wits_table ) {
+ 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 $col_rdgs = shift @$all_wits_table;
- my $rank;
- my $lacunose = [];
- foreach my $j ( 0 .. $#{$col_rdgs} ) {
- my $rdg = $col_rdgs->[$j];
+ 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->is_lacuna ) {
+ if( $rdg->{'t'}->is_lacuna ) {
$rdg_text = undef; # Don't count lacunae
- push( @$lacunose, $col_wits->[$j] );
+ push( @$lacunose, $table_wits[$j] );
} else {
- $rdg_text = $rdg->text;
- # Get the rank from any real reading; they should be identical.
- $rank = $rdg->rank;
+ $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}, $col_wits->[$j],
- $tradition->collation->ac_label );
+ add_variant_wit( $rdg_wits->{$rdg_text}, $table_wits[$j],
+ $c->ac_label );
}
}
# See if this column has any potentially genealogical variants.
# If not, skip to the next.
- $total++ unless scalar keys %$rdg_wits == 1;
my( $groups, $readings ) = useful_variant( $rdg_wits );
next unless $groups && $readings;
-
- # Initialize the data structure for the row that we will return
- my $variant_row = {'id' => $rank, 'readings' => [] };
- # Keep track of our widest row
- $html_columns = scalar @$groups if scalar @$groups > $html_columns;
-
- # 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.
- # TODO: deal with a.c. reading logic
- my $conflict = analyze_variant_location(
- $group_readings, $groups, $stemma->apsp );
- $variant_row->{'genealogical'} = keys %$conflict ? undef : 1;
- foreach my $grp ( sort keys %$group_readings ) {
- my $rdg = $group_readings->{$grp};
- my $in_conflict = exists $conflict->{$grp};
- push( @{$variant_row->{'readings'}},
- { 'text' => $rdg, 'group' => $grp, 'conflict' => $in_conflict,
- 'missing' => wit_stringify( $lacunose ) } );
- }
-
- # Now run the same analysis given the calculated distance tree(s).
-# foreach my $tree ( 0 .. $#{$stemma->distance_trees} ) {
-# my $dc = analyze_variant_location( $group_readings, $groups,
-# $stemma->distance_apsps->[$tree] );
-# foreach my $rdg ( keys %$dc ) {
-# my $var = $dc->{$rdg};
-# }
-# }
-
- # Record that we used this variant in an analysis
- push( @$variants, $variant_row );
- }
-
- # Go through our variant rows and add the number of empty columns we need.
- foreach my $row ( @$variants ) {
- my $empty = $html_columns - scalar @{$row->{'readings'}};
- $row->{'empty'} = $empty;
+
+ push( @$variant_groups,
+ { 'groups' => $groups, 'readings' => $readings, 'lacunose' => $lacunose } );
}
-
- return( $svg, $variants );
+ return $variant_groups;
}
+
+
+# variant_row -> genealogical
+# -> readings [ { text, group, conflict, missing } ]
+
sub analyze_variant_location {
- my( $group_readings, $groups, $apsp ) = @_;
- my %contig;
+ my( $group_readings, $groups, $graph, $lacunose, $undirected ) = @_;
+ my $contig = {};
+ my $subgraph = {};
+ my $is_conflicted;
my $conflict = {};
- foreach my $g ( sort { scalar @$b <=> scalar @$a } @$groups ) {
- my @members = @$g;
+ my $missing = {};
+ map { $missing->{$_} = 1 } @$lacunose;
+ my $variant_row = { 'readings' => [] };
+ # Mark each ms as in its own group, first.
+ foreach my $g ( @$groups ) {
my $gst = wit_stringify( $g );
- map { $contig{$_} = $gst } @members; # The witnesses need themselves to be
- # in their collection.
- next unless @members > 1;
- my $curr = pop @members;
- foreach my $m ( @members ) {
- foreach my $v ( $apsp->path_vertices( $curr, $m ) ) {
- $contig{$v} = $gst unless exists $contig{$v};
- next if $contig{$v} eq $gst;
- # print STDERR "Conflict at $v between group $gst and group "
- # . $contig{$v} . "\n";
- # Record what is conflicting.
- $conflict->{$group_readings->{$gst}} = $group_readings->{$contig{$v}};
+ map { $contig->{$_} = $gst } @$g;
+ }
+ # Now for each unmarked node in the graph, initialize an array
+ # for possible group memberships. We will use this later to
+ # resolve potential conflicts.
+ map { $contig->{$_} = [] unless $contig->{$_} } $graph->vertices;
+ foreach my $g ( sort { scalar @$b <=> scalar @$a } @$groups ) {
+ my $gst = wit_stringify( $g ); # This is the group name
+ my $reachable = { $g->[0] => 1 };
+ # Copy the graph, and delete all non-members from the new graph.
+ my $part = $graph->copy;
+ my $group_root;
+ $part->delete_vertices(
+ grep { !ref( $contig->{$_} ) && $contig->{$_} ne $gst } $graph->vertices );
+
+ # Now look to see if our group is connected.
+ if( $undirected ) { # For use with distance trees etc.
+ # Find all vertices reachable from the first (arbitrary) group
+ # member. If we are genealogical this should include them all.
+ map { $reachable->{$_} = 1 } $part->all_reachable( $g->[0] );
+ # TODO This is a terrible way to do distance trees, since all
+ # non-leaf nodes are included in every graph part now. We may
+ # have to go back to SPDP.
+ } else {
+ if( @$g > 1 ) {
+ # Dispense with the trivial case of one reading.
+ # We have to take directionality into account.
+ # How many root nodes do we have?
+ my @roots = grep { ref( $contig->{$_} ) || $contig->{$_} eq $gst }
+ $part->source_vertices;
+ # Assuming that @$g > 1, find the first root node that has at
+ # least one successor belonging to our group. If this reading
+ # is genealogical, there should be only one, but we will check
+ # that implicitly later.
+ my $nodes_in_subtree = 0;
+ foreach my $root ( @roots ) {
+ # Prune the tree to get rid of extraneous hypotheticals.
+ $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 );
+ # Skip this root if none of our successors are in our group
+ # (e.g. isolated 'hypothetical' witnesses with no group)
+ next unless grep { $contig->{$_} } keys %$tmp_reach;
+ if( keys %$tmp_reach > $nodes_in_subtree ) {
+ $nodes_in_subtree = keys %$tmp_reach;
+ $reachable = $tmp_reach;
+ $group_root = $root;
+ }
+ }
+ } # else it is a single-node group, nothing to calculate.
+ }
+
+ # None of the 'reachable' nodes should be marked as being in another
+ # group. Paint the 'hypotheticals' with our group while we are at it,
+ # unless there is a conflict present.
+ foreach ( keys %$reachable ) {
+ if( ref $contig->{$_} ) {
+ push( @{$contig->{$_}}, $gst );
+ } elsif( $contig->{$_} ne $gst ) {
+ $conflict->{$group_readings->{$gst}} = $group_readings->{$contig->{$_}};
+ } # else it is an 'extant' node marked with our group already.
+ }
+ # None of the unreachable nodes should be in our group either.
+ foreach ( $part->vertices ) {
+ next if $reachable->{$_};
+ if( $contig->{$_} eq $gst ) {
+ $conflict->{$group_readings->{$gst}} = $group_readings->{$gst};
+ last;
}
}
+
+ # Now, if we have a conflict, we can write the reading in full. If not,
+ # we have to save the subgraph so that we can resolve possible conflicts
+ # on hypothetical nodes.
+ $is_conflicted = 1 if exists $conflict->{$group_readings->{$gst}};
+
+ # Write the reading.
+ my $reading = { 'text' => $group_readings->{$gst},
+ 'missing' => wit_stringify( $lacunose ),
+ 'group' => $gst }; # This will change if we find no conflict
+ if( $is_conflicted ) {
+ $reading->{'conflict'} = $conflict->{$group_readings->{$gst}}
+ } else {
+ # Save the relevant subgraph.
+ $subgraph->{$gst} = { 'graph' => $part,
+ 'root' => $group_root,
+ 'reachable' => $reachable };
+ }
+ push( @{$variant_row->{'readings'}}, $reading );
}
- return $conflict;
+
+ # Now that we have gone through all the rows, check the hypothetical
+ # readings for conflict if we haven't found one yet.
+ if( keys %$subgraph && !keys %$conflict ) {
+ my @resolve;
+ foreach ( keys %$contig ) {
+ next unless ref $contig->{$_};
+ if( scalar @{$contig->{$_}} > 1 ) {
+ push( @resolve, $_ );
+ } else {
+ $contig->{$_} = scalar @{$contig->{$_}} ? $contig->{$_}->[0] : '';
+ }
+ }
+ # Do we still have a possible conflict?
+ my $still_contig = {};
+ foreach my $h ( @resolve ) {
+ # For each of the hypothetical readings with more than one possibility,
+ # try deleting it from each of its member subgraphs in turn, and see
+ # if that breaks the contiguous grouping.
+ # TODO This can still break in a corner case where group A can use
+ # either vertex 1 or 2, and group B can use either vertex 2 or 1.
+ # Revisit this if necessary; it could get brute-force nasty.
+ foreach my $gst ( @{$contig->{$h}} ) {
+ my $gpart = $subgraph->{$gst}->{'graph'}->copy;
+ my $reachable = $subgraph->{$gst}->{'reachable'};
+ $gpart->delete_vertex( $h );
+ # Is everything else still reachable from the root?
+ # TODO If $h was the root, see if we still have a single root.
+ my %still_reachable = ( $subgraph->{$gst}->{'root'} => 1 );
+ map { $still_reachable{$_} = 1 }
+ $gpart->all_successors( $subgraph->{$gst}->{'root'} );
+ foreach my $v ( keys %$reachable ) {
+ next if $v eq $h;
+ if( !$still_reachable{$v}
+ && ( $contig->{$v} eq $gst
+ || ( exists $still_contig->{$v}
+ && $still_contig->{$v} eq $gst ) ) ) {
+ # We need $h.
+ if( exists $still_contig->{$h} ) {
+ # Conflict!
+ $conflict->{$group_readings->{$gst}} =
+ $group_readings->{$still_contig->{$h}};
+ } else {
+ $still_contig->{$h} = $gst;
+ }
+ last;
+ } # else we don't need $h in this group.
+ }
+ }
+ }
+
+ # Now, assuming no conflict, we have some hypothetical vertices in
+ # $still_contig that are the "real" group memberships. Replace these
+ # in $contig.
+ unless ( keys %$conflict ) {
+ foreach my $v ( keys %$contig ) {
+ next unless ref $contig->{$v};
+ $contig->{$v} = $still_contig->{$v};
+ }
+ }
+ }
+
+ # Now write the group and conflict information into the respective rows.
+ foreach my $rdg ( @{$variant_row->{'readings'}} ) {
+ $rdg->{'conflict'} = $conflict->{$rdg->{'text'}};
+ next if $rdg->{'conflict'};
+ my @members = grep { $contig->{$_} eq $rdg->{'group'} && !$missing->{$_} }
+ keys %$contig;
+ $rdg->{'group'} = wit_stringify( \@members );
+ }
+
+ $variant_row->{'genealogical'} = !( keys %$conflict );
+ return $variant_row;
}
+sub prune_subtree {
+ my( $tree, $root, $contighash ) = @_;
+ # First, delete hypothetical leaves / orphans until there are none left.
+ my @orphan_hypotheticals = grep { ref( $contighash->{$_} ) }
+ $tree->successorless_vertices;
+ while( @orphan_hypotheticals ) {
+ $tree->delete_vertices( @orphan_hypotheticals );
+ @orphan_hypotheticals = grep { ref( $contighash->{$_} ) }
+ $tree->successorless_vertices;
+ }
+ # Then delete a hypothetical root with only one successor, moving the
+ # root to the child.
+ while( $tree->successors( $root ) == 1 && ref $contighash->{$root} ) {
+ my @nextroot = $tree->successors( $root );
+ $tree->delete_vertex( $root );
+ $root = $nextroot[0];
+ }
+ # The tree has been modified in place, but we need to know the new root.
+ return $root;
+}
# Add the variant, subject to a.c. representation logic.
# This assumes that we will see the 'main' version before the a.c. version.
sub add_variant_wit {
projects / scpubgit/stemmatology.git / blobdiff