Commit | Line | Data |
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1 | package Text::Tradition::Collation; |
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2 | |
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3 | use Encode qw( decode_utf8 ); |
4 | use File::Temp; |
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5 | use Graph; |
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6 | use Graph::Easy; |
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7 | use IPC::Run qw( run binary ); |
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8 | use Text::CSV_XS; |
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9 | use Text::Tradition::Collation::Path; |
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10 | use Text::Tradition::Collation::Reading; |
11 | use Text::Tradition::Collation::Relationship; |
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12 | use XML::LibXML; |
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13 | use Moose; |
14 | |
15 | has 'graph' => ( |
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16 | is => 'ro', |
17 | isa => 'Graph::Easy', |
18 | handles => { |
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19 | add_reading => 'add_node', |
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20 | add_lacuna => 'add_node', |
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21 | del_reading => 'del_node', |
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22 | add_path => 'add_edge', |
23 | del_path => 'del_edge', |
24 | reading => 'node', |
25 | path => 'edge', |
26 | readings => 'nodes', |
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27 | paths => 'edges', |
28 | relationships => 'edges', |
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29 | }, |
30 | default => sub { Graph::Easy->new( undirected => 0 ) }, |
31 | ); |
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32 | |
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33 | |
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34 | has 'tradition' => ( # TODO should this not be ro? |
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35 | is => 'rw', |
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36 | isa => 'Text::Tradition', |
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37 | weak_ref => 1, |
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38 | ); |
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39 | |
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40 | has 'svg' => ( |
41 | is => 'ro', |
42 | isa => 'Str', |
43 | writer => '_save_svg', |
44 | predicate => 'has_svg', |
45 | ); |
46 | |
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47 | has 'graphml' => ( |
48 | is => 'ro', |
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49 | isa => 'Str', |
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50 | writer => '_save_graphml', |
51 | predicate => 'has_graphml', |
52 | ); |
53 | |
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54 | has 'csv' => ( |
55 | is => 'ro', |
56 | isa => 'Str', |
57 | writer => '_save_csv', |
58 | predicate => 'has_csv', |
59 | ); |
60 | |
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61 | has 'wit_list_separator' => ( |
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62 | is => 'rw', |
63 | isa => 'Str', |
64 | default => ', ', |
65 | ); |
66 | |
67 | has 'baselabel' => ( |
68 | is => 'rw', |
69 | isa => 'Str', |
70 | default => 'base text', |
71 | ); |
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72 | |
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73 | has 'collapsed' => ( |
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74 | is => 'rw', |
75 | isa => 'Bool', |
76 | ); |
77 | |
78 | has 'linear' => ( |
79 | is => 'rw', |
80 | isa => 'Bool', |
81 | default => 1, |
82 | ); |
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83 | |
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84 | has 'ac_label' => ( |
85 | is => 'rw', |
86 | isa => 'Str', |
87 | default => ' (a.c.)', |
88 | ); |
89 | |
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90 | |
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91 | # The collation can be created two ways: |
92 | # 1. Collate a set of witnesses (with CollateX I guess) and process |
93 | # the results as in 2. |
94 | # 2. Read a pre-prepared collation in one of a variety of formats, |
95 | # and make the graph from that. |
96 | |
97 | # The graph itself will (for now) be immutable, and the positions |
98 | # within the graph will also be immutable. We need to calculate those |
99 | # positions upon graph construction. The equivalences between graph |
100 | # nodes will be mutable, entirely determined by the user (or possibly |
101 | # by some semantic pre-processing provided by the user.) So the |
102 | # constructor should just make an empty equivalences object. The |
103 | # constructor will also need to make the witness objects, if we didn't |
104 | # come through option 1. |
105 | |
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106 | sub BUILD { |
107 | my( $self, $args ) = @_; |
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108 | $self->graph->use_class('node', 'Text::Tradition::Collation::Reading'); |
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109 | $self->graph->use_class('edge', 'Text::Tradition::Collation::Path'); |
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110 | |
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111 | # Pass through any graph-specific options. |
112 | my $shape = exists( $args->{'shape'} ) ? $args->{'shape'} : 'ellipse'; |
113 | $self->graph->set_attribute( 'node', 'shape', $shape ); |
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114 | |
115 | # Start and end points for all texts |
116 | $self->start( 'INIT' ); |
117 | $self->end( 'INIT' ); |
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118 | } |
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119 | |
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120 | around add_lacuna => sub { |
121 | my $orig = shift; |
122 | my $self = shift; |
123 | my $id = shift @_; |
124 | my $l = $self->$orig( '#LACUNA_' . $id . '#' ); |
125 | $l->is_lacuna( 1 ); |
126 | return $l; |
127 | }; |
128 | |
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129 | # Wrapper around add_path |
130 | |
131 | around add_path => sub { |
132 | my $orig = shift; |
133 | my $self = shift; |
134 | |
135 | # Make sure there are three arguments |
136 | unless( @_ == 3 ) { |
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137 | warn "Call add_path with args source, target, witness"; |
138 | return; |
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139 | } |
140 | # Make sure the proposed path does not yet exist |
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141 | # NOTE 'reading' will currently return readings and segments |
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142 | my( $source, $target, $wit ) = @_; |
143 | $source = $self->reading( $source ) |
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144 | unless ref( $source ) eq 'Text::Tradition::Collation::Reading'; |
7854e12e |
145 | $target = $self->reading( $target ) |
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146 | unless ref( $target ) eq 'Text::Tradition::Collation::Reading'; |
7854e12e |
147 | foreach my $path ( $source->edges_to( $target ) ) { |
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148 | if( $path->label eq $wit && $path->class eq 'edge.path' ) { |
149 | return; |
150 | } |
7854e12e |
151 | } |
152 | # Do the deed |
153 | $self->$orig( @_ ); |
154 | }; |
155 | |
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156 | # Wrapper around paths |
157 | around paths => sub { |
158 | my $orig = shift; |
159 | my $self = shift; |
160 | |
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161 | my @result = grep { $_->sub_class eq 'path' } $self->$orig( @_ ); |
df6d9812 |
162 | return @result; |
163 | }; |
164 | |
165 | around relationships => sub { |
166 | my $orig = shift; |
167 | my $self = shift; |
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168 | my @result = grep { $_->sub_class eq 'relationship' } $self->$orig( @_ ); |
169 | return @result; |
170 | }; |
171 | |
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172 | # Wrapper around merge_nodes |
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173 | sub merge_readings { |
174 | my $self = shift; |
175 | my $first_node = shift; |
176 | my $second_node = shift; |
177 | $first_node->merge_from( $second_node ); |
178 | unshift( @_, $first_node, $second_node ); |
179 | return $self->graph->merge_nodes( @_ ); |
180 | } |
181 | |
15d2d3df |
182 | # Extra graph-alike utility |
183 | sub has_path { |
184 | my( $self, $source, $target, $label ) = @_; |
185 | my @paths = $source->edges_to( $target ); |
186 | my @relevant = grep { $_->label eq $label } @paths; |
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187 | return scalar @relevant; |
188 | } |
189 | |
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190 | ## Dealing with relationships between readings. This is a different |
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191 | ## sort of graph edge. Return a success/failure value and a list of |
192 | ## node pairs that have been linked. |
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193 | |
194 | sub add_relationship { |
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195 | my( $self, $source, $target, $options ) = @_; |
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196 | |
197 | # Make sure there is not another relationship between these two |
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198 | # readings already |
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199 | $source = $self->reading( $source ) |
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200 | unless ref( $source ) && $source->isa( 'Graph::Easy::Node' ); |
ef9d481f |
201 | $target = $self->reading( $target ) |
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202 | unless ref( $target ) && $target->isa( 'Graph::Easy::Node' ); |
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203 | foreach my $rel ( $source->edges_to( $target ), $target->edges_to( $source ) ) { |
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204 | if( $rel->class eq 'edge.relationship' ) { |
205 | return ( undef, "Relationship already exists between these readings" ); |
206 | } |
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207 | } |
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208 | if( $options->{'equal_rank'} && !relationship_valid( $source, $target ) ) { |
209 | return ( undef, 'Relationship creates witness loop' ); |
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210 | } |
211 | |
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212 | # TODO Think about positional hilarity if relationships are added after positions |
213 | # are assigned. |
214 | |
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215 | my @joined = ( [ $source->name, $target->name ] ); # Keep track of the nodes we join. |
216 | |
217 | $options->{'this_relation'} = [ $source, $target ]; |
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218 | my $rel; |
219 | eval { $rel = Text::Tradition::Collation::Relationship->new( %$options ) }; |
220 | if( $@ ) { |
221 | return ( undef, $@ ); |
222 | } |
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223 | $self->graph->add_edge( $source, $target, $rel ); |
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224 | |
225 | # TODO Handle global relationship setting |
226 | |
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227 | return( 1, @joined ); |
3265b0ce |
228 | } |
229 | |
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230 | sub relationship_valid { |
231 | my( $source, $target ) = @_; |
232 | # Check that linking the source and target in a relationship won't lead |
233 | # to a path loop for any witness. |
234 | my @proposed_related = ( $source, $target ); |
235 | push( @proposed_related, $source->related_readings ); |
236 | push( @proposed_related, $target->related_readings ); |
237 | my %pr_ids; |
238 | map { $pr_ids{ $_->name } = 1 } @proposed_related; |
239 | # The lists of 'in' and 'out' should not have any element that appears |
240 | # in 'proposed_related'. |
241 | foreach my $pr ( @proposed_related ) { |
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242 | foreach my $e ( grep { $_->sub_class eq 'path' } $pr->incoming ) { |
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243 | if( exists $pr_ids{ $e->from->name } ) { |
244 | return 0; |
245 | } |
246 | } |
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247 | foreach my $e ( grep { $_->sub_class eq 'path' } $pr->outgoing ) { |
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248 | if( exists $pr_ids{ $e->to->name } ) { |
249 | return 0; |
250 | } |
251 | } |
252 | } |
253 | return 1; |
254 | } |
255 | |
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256 | =head2 Output method(s) |
257 | |
258 | =over |
259 | |
260 | =item B<as_svg> |
261 | |
262 | print $graph->as_svg( $recalculate ); |
263 | |
264 | Returns an SVG string that represents the graph. Uses GraphViz to do |
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265 | this, because Graph::Easy doesn\'t cope well with long graphs. Unless |
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266 | $recalculate is passed (and is a true value), the method will return a |
267 | cached copy of the SVG after the first call to the method. |
268 | |
269 | =cut |
270 | |
271 | sub as_svg { |
272 | my( $self, $recalc ) = @_; |
273 | return $self->svg if $self->has_svg; |
274 | |
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275 | $self->collapse_graph_paths(); |
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276 | |
277 | my @cmd = qw/dot -Tsvg/; |
278 | my( $svg, $err ); |
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279 | my $dotfile = File::Temp->new(); |
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280 | ## TODO REMOVE |
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281 | # $dotfile->unlink_on_destroy(0); |
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282 | binmode $dotfile, ':utf8'; |
283 | print $dotfile $self->as_dot(); |
284 | push( @cmd, $dotfile->filename ); |
285 | run( \@cmd, ">", binary(), \$svg ); |
286 | $svg = decode_utf8( $svg ); |
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287 | $self->_save_svg( $svg ); |
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288 | $self->expand_graph_paths(); |
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289 | return $svg; |
290 | } |
291 | |
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292 | =item B<as_dot> |
293 | |
294 | print $graph->as_dot( $view, $recalculate ); |
295 | |
296 | Returns a string that is the collation graph expressed in dot |
297 | (i.e. GraphViz) format. The 'view' argument determines what kind of |
298 | graph is produced. |
299 | * 'path': a graph of witness paths through the collation (DEFAULT) |
300 | * 'relationship': a graph of how collation readings relate to |
301 | each other |
302 | |
303 | =cut |
304 | |
305 | sub as_dot { |
306 | my( $self, $view ) = @_; |
307 | $view = 'path' unless $view; |
308 | # TODO consider making some of these things configurable |
67da8d6c |
309 | my $graph_name = $self->tradition->name; |
310 | $graph_name =~ s/[^\w\s]//g; |
311 | $graph_name = join( '_', split( /\s+/, $graph_name ) ); |
312 | my $dot = sprintf( "digraph %s {\n", $graph_name ); |
df6d9812 |
313 | $dot .= "\tedge [ arrowhead=open ];\n"; |
314 | $dot .= "\tgraph [ rankdir=LR ];\n"; |
315 | $dot .= sprintf( "\tnode [ fontsize=%d, fillcolor=%s, style=%s, shape=%s ];\n", |
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316 | 11, "white", "filled", $self->graph->get_attribute( 'node', 'shape' ) ); |
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317 | |
318 | foreach my $reading ( $self->readings ) { |
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319 | # Need not output nodes without separate labels |
320 | next if $reading->name eq $reading->label; |
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321 | $dot .= sprintf( "\t\"%s\" [ label=\"%s\" ];\n", $reading->name, $reading->label ); |
df6d9812 |
322 | } |
323 | |
324 | my @edges = $view eq 'relationship' ? $self->relationships : $self->paths; |
325 | foreach my $edge ( @edges ) { |
910a0a6d |
326 | my %variables = ( 'color' => '#000000', |
327 | 'fontcolor' => '#000000', |
328 | 'label' => $edge->label, |
329 | ); |
330 | my $varopts = join( ', ', map { $_.'="'.$variables{$_}.'"' } sort keys %variables ); |
331 | $dot .= sprintf( "\t\"%s\" -> \"%s\" [ %s ];\n", |
332 | $edge->from->name, $edge->to->name, $varopts ); |
df6d9812 |
333 | } |
df6d9812 |
334 | $dot .= "}\n"; |
335 | return $dot; |
336 | } |
337 | |
8e1394aa |
338 | =item B<as_graphml> |
339 | |
340 | print $graph->as_graphml( $recalculate ) |
341 | |
342 | Returns a GraphML representation of the collation graph, with |
343 | transposition information and position information. Unless |
344 | $recalculate is passed (and is a true value), the method will return a |
345 | cached copy of the SVG after the first call to the method. |
346 | |
347 | =cut |
348 | |
349 | sub as_graphml { |
350 | my( $self, $recalc ) = @_; |
351 | return $self->graphml if $self->has_graphml; |
352 | |
353 | # Some namespaces |
354 | my $graphml_ns = 'http://graphml.graphdrawing.org/xmlns'; |
355 | my $xsi_ns = 'http://www.w3.org/2001/XMLSchema-instance'; |
356 | my $graphml_schema = 'http://graphml.graphdrawing.org/xmlns ' . |
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357 | 'http://graphml.graphdrawing.org/xmlns/1.0/graphml.xsd'; |
8e1394aa |
358 | |
359 | # Create the document and root node |
360 | my $graphml = XML::LibXML->createDocument( "1.0", "UTF-8" ); |
361 | my $root = $graphml->createElementNS( $graphml_ns, 'graphml' ); |
362 | $graphml->setDocumentElement( $root ); |
363 | $root->setNamespace( $xsi_ns, 'xsi', 0 ); |
364 | $root->setAttributeNS( $xsi_ns, 'schemaLocation', $graphml_schema ); |
365 | |
e309421a |
366 | # Add the data keys for the graph |
367 | my %graph_data_keys; |
368 | my $gdi = 0; |
369 | my @graph_attributes = qw/ wit_list_separator baselabel linear ac_label /; |
370 | foreach my $datum ( @graph_attributes ) { |
371 | $graph_data_keys{$datum} = 'dg'.$gdi++; |
372 | my $key = $root->addNewChild( $graphml_ns, 'key' ); |
373 | $key->setAttribute( 'attr.name', $datum ); |
374 | $key->setAttribute( 'attr.type', $key eq 'linear' ? 'boolean' : 'string' ); |
375 | $key->setAttribute( 'for', 'graph' ); |
376 | $key->setAttribute( 'id', $graph_data_keys{$datum} ); |
377 | } |
f6066bac |
378 | |
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379 | # Add the data keys for nodes |
ef9d481f |
380 | my %node_data_keys; |
381 | my $ndi = 0; |
d9e873d0 |
382 | foreach my $datum ( qw/ name reading identical rank class / ) { |
910a0a6d |
383 | $node_data_keys{$datum} = 'dn'.$ndi++; |
384 | my $key = $root->addNewChild( $graphml_ns, 'key' ); |
385 | $key->setAttribute( 'attr.name', $datum ); |
386 | $key->setAttribute( 'attr.type', 'string' ); |
387 | $key->setAttribute( 'for', 'node' ); |
388 | $key->setAttribute( 'id', $node_data_keys{$datum} ); |
8e1394aa |
389 | } |
390 | |
df6d9812 |
391 | # Add the data keys for edges, i.e. witnesses |
ef9d481f |
392 | my $edi = 0; |
393 | my %edge_data_keys; |
c9bf3dbf |
394 | my @string_keys = qw/ class witness relationship /; |
395 | my @bool_keys = qw/ extra equal_rank non_correctable non_independent /; |
396 | foreach my $edge_key( @string_keys ) { |
910a0a6d |
397 | $edge_data_keys{$edge_key} = 'de'.$edi++; |
398 | my $key = $root->addNewChild( $graphml_ns, 'key' ); |
399 | $key->setAttribute( 'attr.name', $edge_key ); |
c9bf3dbf |
400 | $key->setAttribute( 'attr.type', 'string' ); |
401 | $key->setAttribute( 'for', 'edge' ); |
402 | $key->setAttribute( 'id', $edge_data_keys{$edge_key} ); |
403 | } |
404 | foreach my $edge_key( @bool_keys ) { |
405 | $edge_data_keys{$edge_key} = 'de'.$edi++; |
406 | my $key = $root->addNewChild( $graphml_ns, 'key' ); |
407 | $key->setAttribute( 'attr.name', $edge_key ); |
408 | $key->setAttribute( 'attr.type', 'boolean' ); |
910a0a6d |
409 | $key->setAttribute( 'for', 'edge' ); |
410 | $key->setAttribute( 'id', $edge_data_keys{$edge_key} ); |
8e1394aa |
411 | } |
ef9d481f |
412 | |
8e1394aa |
413 | # Add the graph, its nodes, and its edges |
414 | my $graph = $root->addNewChild( $graphml_ns, 'graph' ); |
415 | $graph->setAttribute( 'edgedefault', 'directed' ); |
94c00c71 |
416 | $graph->setAttribute( 'id', $self->tradition->name ); |
8e1394aa |
417 | $graph->setAttribute( 'parse.edgeids', 'canonical' ); |
df6d9812 |
418 | $graph->setAttribute( 'parse.edges', scalar($self->paths) ); |
8e1394aa |
419 | $graph->setAttribute( 'parse.nodeids', 'canonical' ); |
df6d9812 |
420 | $graph->setAttribute( 'parse.nodes', scalar($self->readings) ); |
8e1394aa |
421 | $graph->setAttribute( 'parse.order', 'nodesfirst' ); |
e309421a |
422 | |
423 | # Collation attribute data |
424 | foreach my $datum ( @graph_attributes ) { |
425 | _add_graphml_data( $graph, $graph_data_keys{$datum}, $self->$datum ); |
426 | } |
8e1394aa |
427 | |
428 | my $node_ctr = 0; |
429 | my %node_hash; |
b15511bf |
430 | # Add our readings to the graph |
b5054ca9 |
431 | foreach my $n ( sort { $a->name cmp $b->name } $self->readings ) { |
910a0a6d |
432 | my $node_el = $graph->addNewChild( $graphml_ns, 'node' ); |
433 | my $node_xmlid = 'n' . $node_ctr++; |
434 | $node_hash{ $n->name } = $node_xmlid; |
435 | $node_el->setAttribute( 'id', $node_xmlid ); |
436 | _add_graphml_data( $node_el, $node_data_keys{'name'}, $n->name ); |
437 | _add_graphml_data( $node_el, $node_data_keys{'reading'}, $n->label ); |
d9e873d0 |
438 | _add_graphml_data( $node_el, $node_data_keys{'rank'}, $n->rank ) |
439 | if $n->has_rank; |
910a0a6d |
440 | _add_graphml_data( $node_el, $node_data_keys{'class'}, $n->sub_class ); |
1f7aa795 |
441 | $DB::single = 1 if $n->has_primary && $n->primary ne $n; |
910a0a6d |
442 | _add_graphml_data( $node_el, $node_data_keys{'identical'}, $n->primary->name ) |
94c00c71 |
443 | if $n->has_primary && $n->primary ne $n; |
b15511bf |
444 | } |
445 | |
94c00c71 |
446 | # Add the path and relationship edges |
df6d9812 |
447 | my $edge_ctr = 0; |
ef9d481f |
448 | foreach my $e ( sort { $a->from->name cmp $b->from->name } $self->graph->edges() ) { |
910a0a6d |
449 | my( $name, $from, $to ) = ( 'e'.$edge_ctr++, |
450 | $node_hash{ $e->from->name() }, |
451 | $node_hash{ $e->to->name() } ); |
452 | my $edge_el = $graph->addNewChild( $graphml_ns, 'edge' ); |
453 | $edge_el->setAttribute( 'source', $from ); |
454 | $edge_el->setAttribute( 'target', $to ); |
455 | $edge_el->setAttribute( 'id', $name ); |
456 | # Add the edge class |
457 | _add_graphml_data( $edge_el, $edge_data_keys{'class'}, $e->sub_class ); |
94c00c71 |
458 | |
459 | # For some classes we have extra information to save. |
910a0a6d |
460 | if( $e->sub_class eq 'path' ) { |
461 | # It's a witness path, so add the witness |
462 | my $base = $e->label; |
463 | my $key = $edge_data_keys{'witness_main'}; |
94c00c71 |
464 | # Is this an ante-corr witness? |
465 | my $aclabel = $self->ac_label; |
466 | if( $e->label =~ /^(.*)\Q$aclabel\E$/ ) { |
467 | # Keep the base witness |
910a0a6d |
468 | $base = $1; |
94c00c71 |
469 | # ...and record that this is an 'extra' reading path |
470 | _add_graphml_data( $edge_el, $edge_data_keys{'extra'}, 'true' ); |
910a0a6d |
471 | } |
94c00c71 |
472 | _add_graphml_data( $edge_el, $edge_data_keys{'witness'}, $base ); |
910a0a6d |
473 | } elsif( $e->sub_class eq 'relationship' ) { |
c9bf3dbf |
474 | # It's a relationship, so save the relationship data |
910a0a6d |
475 | _add_graphml_data( $edge_el, $edge_data_keys{'relationship'}, $e->label ); |
c9bf3dbf |
476 | _add_graphml_data( $edge_el, $edge_data_keys{'equal_rank'}, $e->equal_rank ); |
477 | _add_graphml_data( $edge_el, $edge_data_keys{'non_correctable'}, $e->non_correctable ); |
478 | _add_graphml_data( $edge_el, $edge_data_keys{'non_independent'}, $e->non_independent ); |
94c00c71 |
479 | } |
8e1394aa |
480 | } |
481 | |
94c00c71 |
482 | # Save and return the thing |
483 | my $result = decode_utf8( $graphml->toString(1) ); |
484 | $self->_save_graphml( $result ); |
485 | return $result; |
df6d9812 |
486 | } |
487 | |
b15511bf |
488 | sub _add_graphml_data { |
489 | my( $el, $key, $value ) = @_; |
b15511bf |
490 | return unless defined $value; |
c9bf3dbf |
491 | my $data_el = $el->addNewChild( $el->namespaceURI, 'data' ); |
b15511bf |
492 | $data_el->setAttribute( 'key', $key ); |
493 | $data_el->appendText( $value ); |
8e1394aa |
494 | } |
495 | |
910a0a6d |
496 | =item B<as_csv> |
497 | |
498 | print $graph->as_csv( $recalculate ) |
499 | |
500 | Returns a CSV alignment table representation of the collation graph, one |
501 | row per witness (or witness uncorrected.) Unless $recalculate is passed |
502 | (and is a true value), the method will return a cached copy of the CSV |
503 | after the first call to the method. |
504 | |
505 | =cut |
506 | |
507 | sub as_csv { |
508 | my( $self, $recalc ) = @_; |
509 | return $self->csv if $self->has_csv; |
510 | my $table = $self->make_alignment_table; |
511 | my $csv = Text::CSV_XS->new( { binary => 1, quote_null => 0 } ); |
512 | my @result; |
513 | foreach my $row ( @$table ) { |
514 | $csv->combine( @$row ); |
515 | push( @result, decode_utf8( $csv->string ) ); |
516 | } |
517 | $self->_save_csv( join( "\n", @result ) ); |
518 | return $self->csv; |
519 | } |
520 | |
0e476982 |
521 | # Make an alignment table - $noderefs controls whether the objects |
522 | # in the table are the nodes or simply their readings. |
9f3ba6f7 |
523 | |
910a0a6d |
524 | sub make_alignment_table { |
08e0fb85 |
525 | my( $self, $noderefs, $include ) = @_; |
910a0a6d |
526 | unless( $self->linear ) { |
527 | warn "Need a linear graph in order to make an alignment table"; |
528 | return; |
529 | } |
530 | my $table; |
fa954f4c |
531 | my @all_pos = ( 0 .. $self->end->rank - 1 ); |
910a0a6d |
532 | foreach my $wit ( $self->tradition->witnesses ) { |
eca16057 |
533 | # print STDERR "Making witness row(s) for " . $wit->sigil . "\n"; |
1f7aa795 |
534 | my @wit_path = $self->reading_sequence( $self->start, $self->end, $wit->sigil ); |
535 | my @row = _make_witness_row( \@wit_path, \@all_pos, $noderefs ); |
910a0a6d |
536 | unshift( @row, $wit->sigil ); |
537 | push( @$table, \@row ); |
1f7aa795 |
538 | if( $wit->is_layered ) { |
539 | my @wit_ac_path = $self->reading_sequence( $self->start, $self->end, |
540 | $wit->sigil.$self->ac_label, $wit->sigil ); |
541 | my @ac_row = _make_witness_row( \@wit_ac_path, \@all_pos, $noderefs ); |
910a0a6d |
542 | unshift( @ac_row, $wit->sigil . $self->ac_label ); |
543 | push( @$table, \@ac_row ); |
544 | } |
545 | } |
0e476982 |
546 | |
08e0fb85 |
547 | if( $include ) { |
548 | my $winnowed = []; |
549 | # Winnow out the rows for any witness not included. |
550 | foreach my $row ( @$table ) { |
551 | next unless $include->{$row->[0]}; |
552 | push( @$winnowed, $row ); |
553 | } |
554 | $table = $winnowed; |
555 | } |
556 | |
910a0a6d |
557 | # Return a table where the witnesses read in columns rather than rows. |
558 | my $turned = _turn_table( $table ); |
08e0fb85 |
559 | # TODO We should really go through and delete empty rows. |
910a0a6d |
560 | return $turned; |
561 | } |
562 | |
563 | sub _make_witness_row { |
0e476982 |
564 | my( $path, $positions, $noderefs ) = @_; |
910a0a6d |
565 | my %char_hash; |
566 | map { $char_hash{$_} = undef } @$positions; |
567 | foreach my $rdg ( @$path ) { |
eca16057 |
568 | my $rtext = $rdg->text; |
569 | $rtext = '#LACUNA#' if $rdg->is_lacuna; |
67da8d6c |
570 | # print STDERR "No rank for " . $rdg->name . "\n" unless defined $rdg->rank; |
0e476982 |
571 | $char_hash{$rdg->rank} = $noderefs ? $rdg : $rtext; |
910a0a6d |
572 | } |
573 | my @row = map { $char_hash{$_} } @$positions; |
eca16057 |
574 | # Fill in lacuna markers for undef spots in the row |
575 | my $last_el = shift @row; |
576 | my @filled_row = ( $last_el ); |
577 | foreach my $el ( @row ) { |
0e476982 |
578 | # If we are using node reference, make the lacuna node appear many times |
579 | # in the table. If not, use the lacuna tag. |
580 | if( $last_el && _el_is_lacuna( $last_el ) && !defined $el ) { |
581 | $el = $noderefs ? $last_el : '#LACUNA#'; |
eca16057 |
582 | } |
583 | push( @filled_row, $el ); |
584 | $last_el = $el; |
585 | } |
586 | return @filled_row; |
910a0a6d |
587 | } |
588 | |
0e476982 |
589 | # Tiny utility function to say if a table element is a lacuna |
590 | sub _el_is_lacuna { |
591 | my $el = shift; |
592 | return 1 if $el eq '#LACUNA#'; |
593 | return 1 if ref( $el ) eq 'Text::Tradition::Collation::Reading' |
594 | && $el->is_lacuna; |
595 | return 0; |
596 | } |
597 | |
910a0a6d |
598 | # Helper to turn the witnesses along columns rather than rows. Assumes |
599 | # equal-sized rows. |
600 | sub _turn_table { |
601 | my( $table ) = @_; |
602 | my $result = []; |
603 | return $result unless scalar @$table; |
604 | my $nrows = scalar @{$table->[0]}; |
605 | foreach my $idx ( 0 .. $nrows - 1 ) { |
606 | foreach my $wit ( 0 .. $#{$table} ) { |
607 | $result->[$idx]->[$wit] = $table->[$wit]->[$idx]; |
608 | } |
609 | } |
610 | return $result; |
611 | } |
612 | |
613 | |
3265b0ce |
614 | sub collapse_graph_paths { |
1f563ac3 |
615 | my $self = shift; |
3265b0ce |
616 | # Our collation graph has an path per witness. This is great for |
1f563ac3 |
617 | # calculation purposes, but terrible for display. Thus we want to |
3265b0ce |
618 | # display only one path between any two nodes. |
1f563ac3 |
619 | |
620 | return if $self->collapsed; |
621 | |
3265b0ce |
622 | print STDERR "Collapsing witness paths in graph...\n"; |
1f563ac3 |
623 | |
624 | # Don't list out every witness if we have more than half to list. |
910a0a6d |
625 | my $majority = int( scalar( $self->tradition->witnesses ) / 2 ) + 1; |
a0093bf2 |
626 | # But don't compress if there are only a few witnesses. |
627 | $majority = 4 if $majority < 4; |
b15511bf |
628 | foreach my $node ( $self->readings ) { |
910a0a6d |
629 | my $newlabels = {}; |
630 | # We will visit each node, so we only look ahead. |
631 | foreach my $edge ( $node->outgoing() ) { |
632 | next unless $edge->class eq 'edge.path'; |
633 | add_hash_entry( $newlabels, $edge->to->name, $edge->name ); |
634 | $self->del_path( $edge ); |
635 | } |
636 | |
637 | foreach my $newdest ( keys %$newlabels ) { |
638 | my $label; |
639 | my @compressed_wits = @{$newlabels->{$newdest}}; |
640 | if( @compressed_wits < $majority ) { |
641 | $label = join( ', ', sort( @{$newlabels->{$newdest}} ) ); |
642 | } else { |
643 | ## TODO FIX THIS HACK |
644 | my @aclabels; |
645 | foreach my $wit ( @compressed_wits ) { |
646 | push( @aclabels, $wit ) if( $wit =~ /^(.*?)(\s*\(?a\.\s*c\.\)?)$/ ); |
647 | } |
648 | $label = join( ', ', 'majority', sort( @aclabels ) ); |
649 | } |
650 | |
651 | my $newpath = $self->add_path( $node, $self->reading( $newdest ), $label ); |
652 | $newpath->hidden_witnesses( \@compressed_wits ); |
653 | } |
1f563ac3 |
654 | } |
655 | |
656 | $self->collapsed( 1 ); |
657 | } |
658 | |
3265b0ce |
659 | sub expand_graph_paths { |
1f563ac3 |
660 | my $self = shift; |
3265b0ce |
661 | # Our collation graph has only one path between any two nodes. |
1f563ac3 |
662 | # This is great for display, but not so great for analysis. |
3265b0ce |
663 | # Expand this so that each witness has its own path between any |
1f563ac3 |
664 | # two reading nodes. |
665 | return unless $self->collapsed; |
666 | |
3265b0ce |
667 | print STDERR "Expanding witness paths in graph...\n"; |
3265b0ce |
668 | foreach my $path( $self->paths ) { |
910a0a6d |
669 | my $from = $path->from; |
670 | my $to = $path->to; |
671 | warn sprintf( "No hidden witnesses on %s -> %s ?", $from->name, $to->name ) |
672 | unless $path->has_hidden_witnesses; |
673 | my @wits = @{$path->hidden_witnesses}; |
674 | $self->del_path( $path ); |
675 | foreach ( @wits ) { |
676 | $self->add_path( $from, $to, $_ ); |
677 | } |
1f563ac3 |
678 | } |
679 | $self->collapsed( 0 ); |
680 | } |
681 | |
8e1394aa |
682 | =back |
683 | |
de51424a |
684 | =head2 Navigation methods |
685 | |
686 | =over |
687 | |
8e1394aa |
688 | =item B<start> |
689 | |
690 | my $beginning = $collation->start(); |
691 | |
692 | Returns the beginning of the collation, a meta-reading with label '#START#'. |
693 | |
694 | =cut |
695 | |
696 | sub start { |
4a8828f0 |
697 | # Return the beginning reading of the graph. |
94c00c71 |
698 | my( $self, $new_start ) = @_; |
699 | my $start = $self->reading( '#START#' ); |
700 | if( ref( $new_start ) eq 'Text::Tradition::Collation::Reading' ) { |
701 | # Replace the existing start node. |
910a0a6d |
702 | $self->del_reading( '#START#' ); |
703 | $self->graph->rename_node( $new_start, '#START#' ); |
94c00c71 |
704 | $start = $new_start; |
705 | } elsif ( $new_start && $new_start eq 'INIT' ) { |
706 | # Make a new start node. |
707 | $start = $self->add_reading( '#START#' ); |
910a0a6d |
708 | } |
94c00c71 |
709 | # Make sure the start node is a meta node |
710 | $start->is_meta( 1 ); |
910a0a6d |
711 | # Make sure the start node has a start position. |
94c00c71 |
712 | unless( $start->has_rank ) { |
713 | $start->rank( '0' ); |
8e1394aa |
714 | } |
94c00c71 |
715 | return $start; |
8e1394aa |
716 | } |
717 | |
910a0a6d |
718 | =item B<end> |
719 | |
720 | my $end = $collation->end(); |
721 | |
722 | Returns the end of the collation, a meta-reading with label '#END#'. |
723 | |
724 | =cut |
725 | |
726 | sub end { |
727 | my $self = shift; |
728 | my( $new_end ) = @_; |
94c00c71 |
729 | my $end = $self->reading( '#END#' ); |
730 | if( ref( $new_end ) eq 'Text::Tradition::Collation::Reading' ) { |
910a0a6d |
731 | $self->del_reading( '#END#' ); |
732 | $self->graph->rename_node( $new_end, '#END#' ); |
94c00c71 |
733 | $end = $new_end |
734 | } elsif ( $new_end && $new_end eq 'INIT' ) { |
735 | # Make a new start node. |
736 | $end = $self->add_reading( '#END#' ); |
910a0a6d |
737 | } |
94c00c71 |
738 | # Make sure the start node is a meta node |
739 | $end->is_meta( 1 ); |
740 | return $end; |
910a0a6d |
741 | } |
742 | |
e2902068 |
743 | =item B<reading_sequence> |
744 | |
745 | my @readings = $graph->reading_sequence( $first, $last, $path[, $alt_path] ); |
746 | |
747 | Returns the ordered list of readings, starting with $first and ending |
748 | with $last, along the given witness path. If no path is specified, |
749 | assume that the path is that of the base text (if any.) |
750 | |
751 | =cut |
752 | |
910a0a6d |
753 | # TODO Think about returning some lazy-eval iterator. |
754 | |
e2902068 |
755 | sub reading_sequence { |
756 | my( $self, $start, $end, $witness, $backup ) = @_; |
757 | |
930ff666 |
758 | $witness = $self->baselabel unless $witness; |
e2902068 |
759 | my @readings = ( $start ); |
760 | my %seen; |
761 | my $n = $start; |
930ff666 |
762 | while( $n && $n ne $end ) { |
910a0a6d |
763 | if( exists( $seen{$n->name()} ) ) { |
764 | warn "Detected loop at " . $n->name(); |
765 | last; |
766 | } |
767 | $seen{$n->name()} = 1; |
768 | |
769 | my $next = $self->next_reading( $n, $witness, $backup ); |
44771cf2 |
770 | unless( $next ) { |
771 | warn "Did not find any path for $witness from reading " . $n->name; |
772 | last; |
773 | } |
910a0a6d |
774 | push( @readings, $next ); |
775 | $n = $next; |
e2902068 |
776 | } |
777 | # Check that the last reading is our end reading. |
778 | my $last = $readings[$#readings]; |
779 | warn "Last reading found from " . $start->label() . |
910a0a6d |
780 | " for witness $witness is not the end!" |
781 | unless $last eq $end; |
e2902068 |
782 | |
783 | return @readings; |
784 | } |
785 | |
4a8828f0 |
786 | =item B<next_reading> |
8e1394aa |
787 | |
4a8828f0 |
788 | my $next_reading = $graph->next_reading( $reading, $witpath ); |
8e1394aa |
789 | |
4a8828f0 |
790 | Returns the reading that follows the given reading along the given witness |
930ff666 |
791 | path. |
8e1394aa |
792 | |
793 | =cut |
794 | |
4a8828f0 |
795 | sub next_reading { |
e2902068 |
796 | # Return the successor via the corresponding path. |
8e1394aa |
797 | my $self = shift; |
4a8828f0 |
798 | return $self->_find_linked_reading( 'next', @_ ); |
8e1394aa |
799 | } |
800 | |
4a8828f0 |
801 | =item B<prior_reading> |
8e1394aa |
802 | |
4a8828f0 |
803 | my $prior_reading = $graph->prior_reading( $reading, $witpath ); |
8e1394aa |
804 | |
4a8828f0 |
805 | Returns the reading that precedes the given reading along the given witness |
930ff666 |
806 | path. |
8e1394aa |
807 | |
808 | =cut |
809 | |
4a8828f0 |
810 | sub prior_reading { |
e2902068 |
811 | # Return the predecessor via the corresponding path. |
8e1394aa |
812 | my $self = shift; |
4a8828f0 |
813 | return $self->_find_linked_reading( 'prior', @_ ); |
8e1394aa |
814 | } |
815 | |
4a8828f0 |
816 | sub _find_linked_reading { |
e2902068 |
817 | my( $self, $direction, $node, $path, $alt_path ) = @_; |
818 | my @linked_paths = $direction eq 'next' |
910a0a6d |
819 | ? $node->outgoing() : $node->incoming(); |
e2902068 |
820 | return undef unless scalar( @linked_paths ); |
8e1394aa |
821 | |
e2902068 |
822 | # We have to find the linked path that contains all of the |
823 | # witnesses supplied in $path. |
824 | my( @path_wits, @alt_path_wits ); |
825 | @path_wits = $self->witnesses_of_label( $path ) if $path; |
826 | @alt_path_wits = $self->witnesses_of_label( $alt_path ) if $alt_path; |
827 | my $base_le; |
828 | my $alt_le; |
829 | foreach my $le ( @linked_paths ) { |
910a0a6d |
830 | if( $le->name eq $self->baselabel ) { |
831 | $base_le = $le; |
832 | } else { |
833 | my @le_wits = $self->witnesses_of_label( $le->name ); |
834 | if( _is_within( \@path_wits, \@le_wits ) ) { |
835 | # This is the right path. |
836 | return $direction eq 'next' ? $le->to() : $le->from(); |
837 | } elsif( _is_within( \@alt_path_wits, \@le_wits ) ) { |
838 | $alt_le = $le; |
839 | } |
840 | } |
8e1394aa |
841 | } |
e2902068 |
842 | # Got this far? Return the alternate path if it exists. |
843 | return $direction eq 'next' ? $alt_le->to() : $alt_le->from() |
910a0a6d |
844 | if $alt_le; |
e2902068 |
845 | |
846 | # Got this far? Return the base path if it exists. |
847 | return $direction eq 'next' ? $base_le->to() : $base_le->from() |
910a0a6d |
848 | if $base_le; |
e2902068 |
849 | |
850 | # Got this far? We have no appropriate path. |
8e1394aa |
851 | warn "Could not find $direction node from " . $node->label |
910a0a6d |
852 | . " along path $path"; |
8e1394aa |
853 | return undef; |
854 | } |
855 | |
4a8828f0 |
856 | # Some set logic. |
857 | sub _is_within { |
858 | my( $set1, $set2 ) = @_; |
7854e12e |
859 | my $ret = @$set1; # will be 0, i.e. false, if set1 is empty |
4a8828f0 |
860 | foreach my $el ( @$set1 ) { |
910a0a6d |
861 | $ret = 0 unless grep { /^\Q$el\E$/ } @$set2; |
4a8828f0 |
862 | } |
863 | return $ret; |
864 | } |
865 | |
de51424a |
866 | |
867 | ## INITIALIZATION METHODS - for use by parsers |
930ff666 |
868 | |
7e450e44 |
869 | # For use when a collation is constructed from a base text and an apparatus. |
870 | # We have the sequences of readings and just need to add path edges. |
1f7aa795 |
871 | # When we are done, clear out the witness path attributes, as they are no |
872 | # longer needed. |
873 | # TODO Find a way to replace the witness path attributes with encapsulated functions? |
e2902068 |
874 | |
6a222840 |
875 | sub make_witness_paths { |
876 | my( $self ) = @_; |
910a0a6d |
877 | foreach my $wit ( $self->tradition->witnesses ) { |
878 | print STDERR "Making path for " . $wit->sigil . "\n"; |
879 | $self->make_witness_path( $wit ); |
7854e12e |
880 | } |
7854e12e |
881 | } |
882 | |
6a222840 |
883 | sub make_witness_path { |
7854e12e |
884 | my( $self, $wit ) = @_; |
885 | my @chain = @{$wit->path}; |
15d2d3df |
886 | my $sig = $wit->sigil; |
7854e12e |
887 | foreach my $idx ( 0 .. $#chain-1 ) { |
910a0a6d |
888 | $self->add_path( $chain[$idx], $chain[$idx+1], $sig ); |
7854e12e |
889 | } |
1f7aa795 |
890 | if( $wit->is_layered ) { |
d9e873d0 |
891 | @chain = @{$wit->uncorrected_path}; |
892 | foreach my $idx( 0 .. $#chain-1 ) { |
893 | my $source = $chain[$idx]; |
894 | my $target = $chain[$idx+1]; |
895 | $self->add_path( $source, $target, $sig.$self->ac_label ) |
896 | unless $self->has_path( $source, $target, $sig ); |
897 | } |
15d2d3df |
898 | } |
1f7aa795 |
899 | $wit->clear_path; |
900 | $wit->clear_uncorrected_path; |
e2902068 |
901 | } |
902 | |
910a0a6d |
903 | sub calculate_ranks { |
904 | my $self = shift; |
905 | # Walk a version of the graph where every node linked by a relationship |
906 | # edge is fundamentally the same node, and do a topological ranking on |
907 | # the nodes in this graph. |
c9bf3dbf |
908 | my $topo_graph = Graph->new(); |
910a0a6d |
909 | my %rel_containers; |
910 | my $rel_ctr = 0; |
911 | # Add the nodes |
912 | foreach my $r ( $self->readings ) { |
913 | next if exists $rel_containers{$r->name}; |
914 | my @rels = $r->related_readings( 'colocated' ); |
915 | if( @rels ) { |
916 | # Make a relationship container. |
917 | push( @rels, $r ); |
c9bf3dbf |
918 | my $rn = 'rel_container_' . $rel_ctr++; |
919 | $topo_graph->add_vertex( $rn ); |
910a0a6d |
920 | foreach( @rels ) { |
921 | $rel_containers{$_->name} = $rn; |
922 | } |
923 | } else { |
924 | # Add a new node to mirror the old node. |
c9bf3dbf |
925 | $rel_containers{$r->name} = $r->name; |
926 | $topo_graph->add_vertex( $r->name ); |
910a0a6d |
927 | } |
4a8828f0 |
928 | } |
3a1f2523 |
929 | |
910a0a6d |
930 | # Add the edges. Need only one edge between any pair of nodes. |
931 | foreach my $r ( $self->readings ) { |
932 | foreach my $n ( $r->neighbor_readings( 'forward' ) ) { |
c9bf3dbf |
933 | my( $tfrom, $tto ) = ( $rel_containers{$r->name}, |
934 | $rel_containers{$n->name} ); |
935 | $topo_graph->add_edge( $tfrom, $tto ) |
936 | unless $topo_graph->has_edge( $tfrom, $tto ); |
910a0a6d |
937 | } |
938 | } |
939 | |
940 | # Now do the rankings, starting with the start node. |
941 | my $topo_start = $rel_containers{$self->start->name}; |
c9bf3dbf |
942 | my $node_ranks = { $topo_start => 0 }; |
910a0a6d |
943 | my @curr_origin = ( $topo_start ); |
944 | # A little iterative function. |
945 | while( @curr_origin ) { |
c9bf3dbf |
946 | @curr_origin = _assign_rank( $topo_graph, $node_ranks, @curr_origin ); |
910a0a6d |
947 | } |
948 | # Transfer our rankings from the topological graph to the real one. |
949 | foreach my $r ( $self->readings ) { |
67da8d6c |
950 | if( defined $node_ranks->{$rel_containers{$r->name}} ) { |
951 | $r->rank( $node_ranks->{$rel_containers{$r->name}} ); |
952 | } else { |
953 | $DB::single = 1; |
954 | die "No rank calculated for node " . $r->name |
955 | . " - do you have a cycle in the graph?"; |
956 | } |
de51424a |
957 | } |
8e1394aa |
958 | } |
3a1f2523 |
959 | |
910a0a6d |
960 | sub _assign_rank { |
c9bf3dbf |
961 | my( $graph, $node_ranks, @current_nodes ) = @_; |
910a0a6d |
962 | # Look at each of the children of @current_nodes. If all the child's |
963 | # parents have a rank, assign it the highest rank + 1 and add it to |
c9bf3dbf |
964 | # @next_nodes. Otherwise skip it; we will return when the highest-ranked |
965 | # parent gets a rank. |
910a0a6d |
966 | my @next_nodes; |
967 | foreach my $c ( @current_nodes ) { |
c9bf3dbf |
968 | warn "Current reading $c has no rank!" |
969 | unless exists $node_ranks->{$c}; |
970 | # print STDERR "Looking at child of node $c, rank " |
971 | # . $node_ranks->{$c} . "\n"; |
972 | foreach my $child ( $graph->successors( $c ) ) { |
973 | next if exists $node_ranks->{$child}; |
910a0a6d |
974 | my $highest_rank = -1; |
975 | my $skip = 0; |
c9bf3dbf |
976 | foreach my $parent ( $graph->predecessors( $child ) ) { |
977 | if( exists $node_ranks->{$parent} ) { |
978 | $highest_rank = $node_ranks->{$parent} |
979 | if $highest_rank <= $node_ranks->{$parent}; |
910a0a6d |
980 | } else { |
981 | $skip = 1; |
982 | last; |
983 | } |
984 | } |
985 | next if $skip; |
c9bf3dbf |
986 | my $c_rank = $highest_rank + 1; |
987 | # print STDERR "Assigning rank $c_rank to node $child \n"; |
988 | $node_ranks->{$child} = $c_rank; |
910a0a6d |
989 | push( @next_nodes, $child ); |
990 | } |
991 | } |
992 | return @next_nodes; |
4cdd82f1 |
993 | } |
910a0a6d |
994 | |
0e476982 |
995 | # Another method to make up for rough collation methods. If the same reading |
996 | # appears multiple times at the same rank, collapse the nodes. |
997 | sub flatten_ranks { |
998 | my $self = shift; |
999 | my %unique_rank_rdg; |
1000 | foreach my $rdg ( $self->readings ) { |
1001 | next unless $rdg->has_rank; |
1002 | my $key = $rdg->rank . "||" . $rdg->text; |
1003 | if( exists $unique_rank_rdg{$key} ) { |
1004 | # Combine! |
1005 | print STDERR "Combining readings at same rank: $key\n"; |
1006 | $self->merge_readings( $unique_rank_rdg{$key}, $rdg ); |
1007 | } else { |
1008 | $unique_rank_rdg{$key} = $rdg; |
1009 | } |
1010 | } |
1011 | } |
1012 | |
1013 | |
fa954f4c |
1014 | ## Utility functions |
de51424a |
1015 | |
4a8828f0 |
1016 | # Return the string that joins together a list of witnesses for |
1017 | # display on a single path. |
1018 | sub path_label { |
1019 | my $self = shift; |
1020 | return join( $self->wit_list_separator, @_ ); |
1021 | } |
1022 | |
1023 | sub witnesses_of_label { |
de51424a |
1024 | my( $self, $label ) = @_; |
4a8828f0 |
1025 | my $regex = $self->wit_list_separator; |
de51424a |
1026 | my @answer = split( /\Q$regex\E/, $label ); |
1027 | return @answer; |
4a8828f0 |
1028 | } |
8e1394aa |
1029 | |
1f563ac3 |
1030 | sub add_hash_entry { |
1031 | my( $hash, $key, $entry ) = @_; |
1032 | if( exists $hash->{$key} ) { |
910a0a6d |
1033 | push( @{$hash->{$key}}, $entry ); |
1f563ac3 |
1034 | } else { |
910a0a6d |
1035 | $hash->{$key} = [ $entry ]; |
1f563ac3 |
1036 | } |
1037 | } |
1038 | |
dd3b58b0 |
1039 | no Moose; |
1040 | __PACKAGE__->meta->make_immutable; |
e867486f |
1041 | |
1042 | =head1 BUGS / TODO |
1043 | |
1044 | =over |
1045 | |
1046 | =item * Rationalize edge classes |
1047 | |
1048 | =item * Port the internal graph from Graph::Easy to Graph |
1049 | |
1050 | =back |