From: Tara L Andrews Date: Fri, 21 Oct 2011 19:54:09 +0000 (+0200) Subject: split tree pruning into its own function; s158 works now X-Git-Url: http://git.shadowcat.co.uk/gitweb/gitweb.cgi?a=commitdiff_plain;h=231d71fcb0aa140014259130d9f4ef4aafedafda;p=scpubgit%2Fstemmatology.git split tree pruning into its own function; s158 works now --- diff --git a/TreeOfTexts/lib/TreeOfTexts/Model/Analysis.pm b/TreeOfTexts/lib/TreeOfTexts/Model/Analysis.pm index 38515ec..9c64b23 100644 --- a/TreeOfTexts/lib/TreeOfTexts/Model/Analysis.pm +++ b/TreeOfTexts/lib/TreeOfTexts/Model/Analysis.pm @@ -8,16 +8,16 @@ use base 'Catalyst::Model::Adaptor'; __PACKAGE__->config( class => 'Text::Tradition::Analysis', args => { 'traditions' => [ -# { 'file' => TreeOfTexts->path_to( 't', 'data', 'florilegium.xml' ), -# 'stemmadot' => TreeOfTexts->path_to( 't', 'data', 'stemma_a.dot' ) }, - { 'file' => TreeOfTexts->path_to( 't', 'data', 'besoin.xml' ), - 'stemmadot' => TreeOfTexts->path_to( 't', 'data', 'stemma_b.dot' ) }, -# { 'file' => TreeOfTexts->path_to( 't', 'data', 'heinrichi.xml' ), -# 'stemmadot' => TreeOfTexts->path_to( 't', 'data', 'stemma_h.dot' ) }, -# { 'file' => TreeOfTexts->path_to( 't', 'data', 'parzival.xml' ), -# 'stemmadot' => TreeOfTexts->path_to( 't', 'data', 'stemma_p.dot' ) }, -# { 'file' => TreeOfTexts->path_to( 't', 'data', 's158.xml' ), -# 'stemmadot' => TreeOfTexts->path_to( 't', 'data', 'stemma_s.dot' ) }, +# { 'file' => TreeOfTexts->path_to( 't', 'data', 'florilegium.xml' ), +# 'stemmadot' => TreeOfTexts->path_to( 't', 'data', 'stemma_a.dot' ) }, + { 'file' => TreeOfTexts->path_to( 't', 'data', 'besoin.xml' ), + 'stemmadot' => TreeOfTexts->path_to( 't', 'data', 'stemma_b.dot' ) }, +# { 'file' => TreeOfTexts->path_to( 't', 'data', 'heinrichi.xml' ), +# 'stemmadot' => TreeOfTexts->path_to( 't', 'data', 'stemma_h.dot' ) }, +# { 'file' => TreeOfTexts->path_to( 't', 'data', 'parzival.xml' ), +# 'stemmadot' => TreeOfTexts->path_to( 't', 'data', 'stemma_p.dot' ) }, + { 'file' => TreeOfTexts->path_to( 't', 'data', 's158.xml' ), + 'stemmadot' => TreeOfTexts->path_to( 't', 'data', 'stemma_s.dot' ) }, ] }, ); diff --git a/lib/Text/Tradition/Analysis.pm b/lib/Text/Tradition/Analysis.pm index a64277f..7eaee51 100644 --- a/lib/Text/Tradition/Analysis.pm +++ b/lib/Text/Tradition/Analysis.pm @@ -102,7 +102,7 @@ sub run_analysis { # For all the groups with more than one member, collect the list of all # contiguous vertices needed to connect them. - $DB::single = 1 if $rank == 733; + $DB::single = 1; my $variant_row = analyze_variant_location( $group_readings, $groups, $stemma->graph, $lacunose ); $variant_row->{'id'} = $rank; @@ -145,22 +145,22 @@ sub run_analysis { sub analyze_variant_location { my( $group_readings, $groups, $graph, $lacunose, $undirected ) = @_; - my %contig; - my %subgraph; + my $contig = {}; + my $subgraph = {}; my $is_conflicted; my $conflict = {}; - my %missing; - map { $missing{$_} = 1 } @$lacunose; + 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 { $contig{$_} = $gst } @$g; + 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; + 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 }; @@ -168,7 +168,7 @@ sub analyze_variant_location { my $part = $graph->copy; my $group_root; $part->delete_vertices( - grep { !ref( $contig{$_} ) && $contig{$_} ne $gst } $graph->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. @@ -183,7 +183,7 @@ sub analyze_variant_location { # 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 } + 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 @@ -191,19 +191,14 @@ sub analyze_variant_location { # that implicitly later. my $nodes_in_subtree = 0; foreach my $root ( @roots ) { - # Prune the tree down to the first root that either is extant - # or has more than one successor. - while( $part->successors( $root ) == 1 && ref $contig{$root} ) { - my @nextroot = $part->successors( $root ); - $part->delete_vertex( $root ); - $root = $nextroot[0]; - } + # 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; + next unless grep { $contig->{$_} } keys %$tmp_reach; if( keys %$tmp_reach > $nodes_in_subtree ) { $nodes_in_subtree = keys %$tmp_reach; $reachable = $tmp_reach; @@ -217,16 +212,16 @@ sub analyze_variant_location { # group. Paint the 'hypotheticals' with our group while we are at it, # unless there is a conflict present. foreach ( keys %$reachable ) { - if( ref $contig{$_} ) { - push( @{$contig{$_}}, $gst ); - } elsif( $contig{$_} ne $gst ) { - $conflict->{$group_readings->{$gst}} = $group_readings->{$contig{$_}}; + 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 ) { + if( $contig->{$_} eq $gst ) { $conflict->{$group_readings->{$gst}} = $group_readings->{$gst}; last; } @@ -245,7 +240,7 @@ sub analyze_variant_location { $reading->{'conflict'} = $conflict->{$group_readings->{$gst}} } else { # Save the relevant subgraph. - $subgraph{$gst} = { 'graph' => $part, + $subgraph->{$gst} = { 'graph' => $part, 'root' => $group_root, 'reachable' => $reachable }; } @@ -254,18 +249,18 @@ sub analyze_variant_location { # Now that we have gone through all the rows, check the hypothetical # readings for conflict if we haven't found one yet. - if( keys %subgraph && !keys %$conflict ) { + if( keys %$subgraph && !keys %$conflict ) { my @resolve; - foreach ( keys %contig ) { - next unless ref $contig{$_}; - if( scalar @{$contig{$_}} > 1 ) { + foreach ( keys %$contig ) { + next unless ref $contig->{$_}; + if( scalar @{$contig->{$_}} > 1 ) { push( @resolve, $_ ); } else { - $contig{$_} = scalar @{$contig{$_}} ? $contig{$_}->[0] : ''; + $contig->{$_} = scalar @{$contig->{$_}} ? $contig->{$_}->[0] : ''; } } # Do we still have a possible conflict? - my %still_contig; + 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 @@ -273,28 +268,28 @@ sub analyze_variant_location { # 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'}; + 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 ); + my %still_reachable = ( $subgraph->{$gst}->{'root'} => 1 ); map { $still_reachable{$_} = 1 } - $gpart->all_successors( $subgraph{$gst}->{'root'} ); + $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 ) ) ) { + && ( $contig->{$v} eq $gst + || ( exists $still_contig->{$v} + && $still_contig->{$v} eq $gst ) ) ) { # We need $h. - if( exists $still_contig{$h} ) { + if( exists $still_contig->{$h} ) { # Conflict! $conflict->{$group_readings->{$gst}} = - $group_readings->{$still_contig{$h}}; + $group_readings->{$still_contig->{$h}}; } else { - $still_contig{$h} = $gst; + $still_contig->{$h} = $gst; } last; } # else we don't need $h in this group. @@ -306,9 +301,9 @@ sub analyze_variant_location { # $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}; + foreach my $v ( keys %$contig ) { + next unless ref $contig->{$v}; + $contig->{$v} = $still_contig->{$v}; } } } @@ -317,8 +312,8 @@ sub analyze_variant_location { 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; + my @members = grep { $contig->{$_} eq $rdg->{'group'} && !$missing->{$_} } + keys %$contig; $rdg->{'group'} = wit_stringify( \@members ); } @@ -326,6 +321,26 @@ sub analyze_variant_location { 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 {