[scpubgit/stemmatology.git] / lib / Text / Tradition / Analysis.pm

package Text::Tradition::Analysis;

use strict;
use warnings;
use Text::Tradition;
use Text::Tradition::Stemma;

sub new {
	my( $class, $args ) = @_;
	my $self = {};
	bless( $self, $class );	
	$self->{'data'} = [];
	foreach my $t ( @{$args->{'traditions'}} ) {
	    $self->run_analysis( $t->{'file'}, $t->{'stemmadot'} );
	}
	return $self;
}

sub run_analysis {
	my( $self, $file, $stemmadot ) = @_;
	# 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,
		);
	$data->{'title'} = $tradition->name;
	
	my $stemma = Text::Tradition::Stemma->new(
		'collation' => $tradition->collation,
		'dot' => $stemmadot,
		);
	# We will return the stemma picture
	$svg = $stemma->as_svg( { size => "8,7.5" } );;
	$data->{'svg'} = $svg;
	
	# 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;
	my $all_wits_table = $tradition->collation->make_alignment_table( 'refs', $wits );
	
	# 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 ( $total, $genealogical, $conflicts ) = ( 0, 0, 0 );
	
	# 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 ) {
		# 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 $rdg_text = '(omitted)';  # Initialize in case of empty reading
			if( $rdg ) {
			    if( $rdg->is_lacuna ) {
			        $rdg_text = undef;   # Don't count lacunae
			        push( @$lacunose, $col_wits->[$j] );
			    } else {
    				$rdg_text = $rdg->text; 
				    # Get the rank from any real reading; they should be identical.
				    $rank = $rdg->rank;
				}
			}
			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 );
			}
		}
		
		# 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;  
		
		# 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
		$DB::single = 1 if $rank == 25;
		my $variant_row = analyze_variant_location( $group_readings, $groups, 
		    $stemma->graph, $lacunose );
		$variant_row->{'id'} = $rank;
		$genealogical++ if $variant_row->{'genealogical'};
		$conflicts += grep { $_->{'conflict'} } @{$variant_row->{'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 );
#                 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_row );
	}
	
	# Go through our variant rows, after we have seen all of them once,
	# and add the number of empty columns needed by each.
	foreach my $row ( @$variants ) {
		my $empty = $html_columns - scalar @{$row->{'readings'}};
		$row->{'empty'} = $empty;
	}
	
	# Populate self with our analysis data.
	$data->{'variants'} = $variants;
	$data->{'variant_count'} = $total;
	$data->{'conflict_count'} = $conflicts;
	$data->{'genealogical_count'} = $genealogical;
	push( @{$self->{'data'}}, $data );
}

# variant_row -> genealogical
#             -> readings [ { text, group, conflict, missing } ]

sub analyze_variant_location {
    my( $group_readings, $groups, $graph, $lacunose ) = @_;
    my %contig;
    my $conflict = {};
    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;
    }
    foreach my $g ( sort { scalar @$b <=> scalar @$a } @$groups ) {
        my $gst = wit_stringify( $g );
        # Copy the graph, and delete all non-members from the new graph.
        my $part = $graph->undirected_copy;
        map { $part->delete_vertex( $_ ) 
                if $contig{$_} && $contig{$_} ne $gst } $graph->vertices;
        # Now all the members of the group should still be reachable 
        # from the first member. 
        my %reachable = ( $g->[0] => 1 );       
        map { $reachable{$_} = 1 } $part->all_reachable( $g->[0] );

        # ...and none of these nodes should be marked as being in another 
        # group.
        foreach ( keys %reachable ) {
            if( $contig{$_} && $contig{$_} ne $gst ) {
                $conflict->{$group_readings->{$gst}} = $group_readings->{$contig{$_}};
            } else {
                $contig{$_} = $gst;
            }
        }
        # None of the unreachable nodes should be in our group either.
        foreach ( $part->vertices ) {
            next if $reachable{$_};
            $conflict->{$group_readings->{$gst}} = $group_readings->{$gst}
                if $contig{$_} && $contig{$_} eq $gst;
        }
        
        # Write the reading.
        my $reading = { 'text' => $group_readings->{$gst},
                        'missing' => wit_stringify( $lacunose ),
                        'conflict' => exists( $conflict->{$group_readings->{$gst}} ) };
        if( $reading->{'conflict'} ) {
            $reading->{'group'} = $gst;
        } else {
            my @all_vertices = grep { !$missing{$_} } keys %reachable;
            $reading->{'group'} = wit_stringify( \@all_vertices );
        }
        push( @{$variant_row->{'readings'}}, $reading );
    }
    $variant_row->{'genealogical'} = !( keys %$conflict );
    return $variant_row;
}

# 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 {
    my( $arr, $wit, $acstr ) = @_;
    my $skip;
    if( $wit =~ /^(.*)\Q$acstr\E$/ ) {
        my $real = $1;
        $skip = grep { $_ =~ /^\Q$real\E$/ } @$arr;
    } 
    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 );
}

# Take an array of witness groupings and produce a string like
# ['A','B'] / ['C','D','E'] / ['F']

sub wit_stringify {
    my $groups = shift;
    my @gst;
    # If we were passed an array of witnesses instead of an array of 
    # groupings, then "group" the witnesses first.
    unless( ref( $groups->[0] ) ) {
        my $mkgrp = [ $groups ];
        $groups = $mkgrp;
    }
    foreach my $g ( @$groups ) {
        push( @gst, '[' . join( ',', map { "'$_'" } @$g ) . ']' );
    }
    return join( ' / ', @gst );
}
    
1;
Commit	Line	Data
d71100ed	1	package Text::Tradition::Analysis;
	2
	3	use strict;
	4	use warnings;
	5	use Text::Tradition;
	6	use Text::Tradition::Stemma;
	7
	8	sub new {
	9	my( $class, $args ) = @_;
	10	my $self = {};
d71100ed	11	bless( $self, $class );
e367f5c0	12	$self->{'data'} = [];
	13	foreach my $t ( @{$args->{'traditions'}} ) {
	14	$self->run_analysis( $t->{'file'}, $t->{'stemmadot'} );
	15	}
d71100ed	16	return $self;
	17	}
	18
	19	sub run_analysis {
732152b1	20	my( $self, $file, $stemmadot ) = @_;
d71100ed	21	# What we will return
	22	my $svg;
	23	my $variants = [];
e367f5c0	24	my $data = {};
d71100ed	25
3d79e248	26	# Read in the file and stemma
d71100ed	27	my $tradition = Text::Tradition->new(
3d79e248	28	'input' => 'Self',
3d79e248	29	'file' => $file,
d71100ed	30	'linear' => 1,
d71100ed	31	);
e367f5c0	32	$data->{'title'} = $tradition->name;
732152b1	33
d71100ed	34	my $stemma = Text::Tradition::Stemma->new(
	35	'collation' => $tradition->collation,
	36	'dot' => $stemmadot,
	37	);
	38	# We will return the stemma picture
e367f5c0	39	$svg = $stemma->as_svg( { size => "8,7.5" } );;
e367f5c0	40	$data->{'svg'} = $svg;
d71100ed	41
	42	# We have the collation, so get the alignment table with witnesses in rows.
	43	# Also return the reading objects in the table, rather than just the words.
08e0fb85	44	my $wits = {};
	45	map { $wits->{$_} = 1 } $stemma->witnesses;
	46	my $all_wits_table = $tradition->collation->make_alignment_table( 'refs', $wits );
d71100ed	47
	48	# For each column in the alignment table, we want to see if the existing
	49	# groupings of witnesses match our stemma hypothesis. We also want, at the
	50	# end, to produce an HTML table with all the variants.
	51	my $html_columns = 0;
732152b1	52	my ( $total, $genealogical, $conflicts ) = ( 0, 0, 0 );
d71100ed	53
	54	# Strip the list of sigla and save it for correlation to the readings.
	55	my $col_wits = shift @$all_wits_table;
	56
	57	# We will return a data structure, an array for each row that looks like:
	58	# { id = X, genealogical = Y, readings = [ text = X, group = Y], empty = N }
	59	foreach my $i ( 0 .. $#$all_wits_table ) {
	60	# For each column in the table, group the readings by witness.
	61	my $rdg_wits = {};
	62	my $col_rdgs = shift @$all_wits_table;
	63	my $rank;
c4e11e3f	64	my $lacunose = [];
d71100ed	65	foreach my $j ( 0 .. $#{$col_rdgs} ) {
d71100ed	66	my $rdg = $col_rdgs->[$j];
d71100ed	67	my $rdg_text = '(omitted)'; # Initialize in case of empty reading
d71100ed	68	if( $rdg ) {
c4e11e3f	69	if( $rdg->is_lacuna ) {
	70	$rdg_text = undef; # Don't count lacunae
	71	push( @$lacunose, $col_wits->[$j] );
	72	} else {
	73	$rdg_text = $rdg->text;
	74	# Get the rank from any real reading; they should be identical.
	75	$rank = $rdg->rank;
	76	}
d71100ed	77	}
	78	if( defined $rdg_text ) {
	79	# Initialize the witness array if we haven't got one yet
	80	$rdg_wits->{$rdg_text} = [] unless $rdg_wits->{$rdg_text};
	81	# Add the relevant witness, subject to a.c. logic
	82	add_variant_wit( $rdg_wits->{$rdg_text}, $col_wits->[$j],
	83	$tradition->collation->ac_label );
	84	}
	85	}
	86
	87	# See if this column has any potentially genealogical variants.
	88	# If not, skip to the next.
	89	$total++ unless scalar keys %$rdg_wits == 1;
	90	my( $groups, $readings ) = useful_variant( $rdg_wits );
	91	next unless $groups && $readings;
	92
d71100ed	93	# Keep track of our widest row
	94	$html_columns = scalar @$groups if scalar @$groups > $html_columns;
	95
	96	# We can already look up witnesses for a reading; we also want to look
	97	# up readings for a given witness.
	98	my $group_readings = {};
	99	foreach my $x ( 0 .. $#$groups ) {
	100	$group_readings->{wit_stringify( $groups->[$x] )} = $readings->[$x];
	101	}
	102
	103	# For all the groups with more than one member, collect the list of all
	104	# contiguous vertices needed to connect them.
	105	# TODO: deal with a.c. reading logic
94a077d6	106	$DB::single = 1 if $rank == 25;
732152b1	107	my $variant_row = analyze_variant_location( $group_readings, $groups,
08e0fb85	108	$stemma->graph, $lacunose );
732152b1	109	$variant_row->{'id'} = $rank;
	110	$genealogical++ if $variant_row->{'genealogical'};
	111	$conflicts += grep { $_->{'conflict'} } @{$variant_row->{'readings'}};
	112
d71100ed	113	# Now run the same analysis given the calculated distance tree(s).
732152b1	114	# my @trees = @{$stemma->distance_trees};
	115	# if( @trees ) {
	116	# foreach my $tree ( 0 .. $#trees ) {
08e0fb85	117	# my $dc = analyze_variant_location( $group_readings, $groups, $tree );
732152b1	118	# foreach my $rdg ( keys %$dc ) {
	119	# my $var = $dc->{$rdg};
	120	# # TODO Do something with this
	121	# }
	122	# }
	123	# }
	124
d71100ed	125	# Record that we used this variant in an analysis
	126	push( @$variants, $variant_row );
	127	}
	128
732152b1	129	# Go through our variant rows, after we have seen all of them once,
732152b1	130	# and add the number of empty columns needed by each.
d71100ed	131	foreach my $row ( @$variants ) {
	132	my $empty = $html_columns - scalar @{$row->{'readings'}};
	133	$row->{'empty'} = $empty;
	134	}
	135
732152b1	136	# Populate self with our analysis data.
e367f5c0	137	$data->{'variants'} = $variants;
	138	$data->{'variant_count'} = $total;
	139	$data->{'conflict_count'} = $conflicts;
	140	$data->{'genealogical_count'} = $genealogical;
	141	push( @{$self->{'data'}}, $data );
d71100ed	142	}
d71100ed	143
732152b1	144	# variant_row -> genealogical
	145	# -> readings [ { text, group, conflict, missing } ]
	146
d71100ed	147	sub analyze_variant_location {
08e0fb85	148	my( $group_readings, $groups, $graph, $lacunose ) = @_;
d71100ed	149	my %contig;
d71100ed	150	my $conflict = {};
732152b1	151	my %missing;
	152	map { $missing{$_} = 1 } @$lacunose;
	153	my $variant_row = { 'readings' => [] };
94a077d6	154	# Mark each ms as in its own group, first.
	155	foreach my $g ( @$groups ) {
	156	my $gst = wit_stringify( $g );
	157	map { $contig{$_} = $gst } @$g;
	158	}
d71100ed	159	foreach my $g ( sort { scalar @$b <=> scalar @$a } @$groups ) {
08e0fb85	160	my $gst = wit_stringify( $g );
	161	# Copy the graph, and delete all non-members from the new graph.
	162	my $part = $graph->undirected_copy;
	163	map { $part->delete_vertex( $_ )
	164	if $contig{$_} && $contig{$_} ne $gst } $graph->vertices;
	165	# Now all the members of the group should still be reachable
	166	# from the first member.
	167	my %reachable = ( $g->[0] => 1 );
	168	map { $reachable{$_} = 1 } $part->all_reachable( $g->[0] );
	169
	170	# ...and none of these nodes should be marked as being in another
	171	# group.
	172	foreach ( keys %reachable ) {
	173	if( $contig{$_} && $contig{$_} ne $gst ) {
	174	$conflict->{$group_readings->{$gst}} = $group_readings->{$contig{$_}};
	175	} else {
	176	$contig{$_} = $gst;
d71100ed	177	}
d71100ed	178	}
08e0fb85	179	# None of the unreachable nodes should be in our group either.
	180	foreach ( $part->vertices ) {
	181	next if $reachable{$_};
	182	$conflict->{$group_readings->{$gst}} = $group_readings->{$gst}
	183	if $contig{$_} && $contig{$_} eq $gst;
	184	}
	185
732152b1	186	# Write the reading.
	187	my $reading = { 'text' => $group_readings->{$gst},
	188	'missing' => wit_stringify( $lacunose ),
	189	'conflict' => exists( $conflict->{$group_readings->{$gst}} ) };
	190	if( $reading->{'conflict'} ) {
	191	$reading->{'group'} = $gst;
	192	} else {
08e0fb85	193	my @all_vertices = grep { !$missing{$_} } keys %reachable;
732152b1	194	$reading->{'group'} = wit_stringify( \@all_vertices );
	195	}
	196	push( @{$variant_row->{'readings'}}, $reading );
d71100ed	197	}
08e0fb85	198	$variant_row->{'genealogical'} = !( keys %$conflict );
732152b1	199	return $variant_row;
d71100ed	200	}
	201
	202	# Add the variant, subject to a.c. representation logic.
	203	# This assumes that we will see the 'main' version before the a.c. version.
	204	sub add_variant_wit {
	205	my( $arr, $wit, $acstr ) = @_;
	206	my $skip;
	207	if( $wit =~ /^(.*)\Q$acstr\E$/ ) {
	208	my $real = $1;
	209	$skip = grep { $_ =~ /^\Q$real\E$/ } @$arr;
	210	}
	211	push( @$arr, $wit ) unless $skip;
	212	}
	213
	214	# Return an answer if the variant is useful, i.e. if there are at least 2 variants
	215	# with at least 2 witnesses each.
	216	sub useful_variant {
	217	my( $readings ) = @_;
	218	my $total = keys %$readings;
	219	foreach my $var ( keys %$readings ) {
	220	$total-- if @{$readings->{$var}} == 1;
	221	}
	222	return( undef, undef ) if $total <= 1;
	223	my( $groups, $text );
	224	foreach my $var ( keys %$readings ) {
	225	push( @$groups, $readings->{$var} );
	226	push( @$text, $var );
	227	}
	228	return( $groups, $text );
	229	}
	230
	231	# Take an array of witness groupings and produce a string like
	232	# ['A','B'] / ['C','D','E'] / ['F']
	233
	234	sub wit_stringify {
	235	my $groups = shift;
	236	my @gst;
	237	# If we were passed an array of witnesses instead of an array of
	238	# groupings, then "group" the witnesses first.
	239	unless( ref( $groups->[0] ) ) {
	240	my $mkgrp = [ $groups ];
	241	$groups = $mkgrp;
	242	}
	243	foreach my $g ( @$groups ) {
	244	push( @gst, '[' . join( ',', map { "'$_'" } @$g ) . ']' );
	245	}
	246	return join( ' / ', @gst );
	247	}
	248
	249	1;