From: Tara L Andrews Date: Tue, 17 Jan 2012 12:40:56 +0000 (+0100) Subject: add clear_witness functionality, use it, and update Collation pod X-Git-Url: http://git.shadowcat.co.uk/gitweb/gitweb.cgi?p=scpubgit%2Fstemmatology.git;a=commitdiff_plain;h=4e5a7b2cd8f38cd4f178072058d5016be64993c5 add clear_witness functionality, use it, and update Collation pod --- diff --git a/lib/Text/Tradition/Collation.pm b/lib/Text/Tradition/Collation.pm index 74b9f47..0bbcdf3 100644 --- a/lib/Text/Tradition/Collation.pm +++ b/lib/Text/Tradition/Collation.pm @@ -92,20 +92,150 @@ has 'end' => ( weak_ref => 1, ); -# The collation can be created two ways: -# 1. Collate a set of witnesses (with CollateX I guess) and process -# the results as in 2. -# 2. Read a pre-prepared collation in one of a variety of formats, -# and make the graph from that. - -# The graph itself will (for now) be immutable, and the positions -# within the graph will also be immutable. We need to calculate those -# positions upon graph construction. The equivalences between graph -# nodes will be mutable, entirely determined by the user (or possibly -# by some semantic pre-processing provided by the user.) So the -# constructor should just make an empty equivalences object. The -# constructor will also need to make the witness objects, if we didn't -# come through option 1. +=head1 NAME + +Text::Tradition::Collation - a software model for a text collation + +=head1 SYNOPSIS + + use Text::Tradition; + my $t = Text::Tradition->new( + 'name' => 'this is a text', + 'input' => 'TEI', + 'file' => '/path/to/tei_parallel_seg_file.xml' ); + + my $c = $t->collation; + my @readings = $c->readings; + my @paths = $c->paths; + my @relationships = $c->relationships; + + my $svg_variant_graph = $t->collation->as_svg(); + +=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 CONSTRUCTOR + +=head2 new + +The constructor. Takes a hash or hashref of the following arguments: + +=over + +=item * tradition - The Text::Tradition object to which the collation +belongs. Required. + +=item * linear - Whether the collation should be linear; that is, whether +transposed readings should be treated as two linked readings rather than one, +and therefore whether the collation graph is acyclic. Defaults to true. + +=item * collapse_punctuation - TODO + +=item * baselabel - The default label for the path taken by a base text +(if any). Defaults to 'base text'. + +=item * wit_list_separator - The string to join a list of witnesses for +purposes of making labels in display graphs. Defaults to ', '. + +=item * ac_label - The extra label to tack onto a witness sigil when +representing another layer of path for the given witness - that is, when +a text has more than one possible reading due to scribal corrections or +the like. Defaults to ' (a.c.)'. + +=back + +=head1 ACCESSORS + +=head2 tradition + +=head2 linear + +=head2 collapse_punctuation + +=head2 wit_list_separator + +=head2 baselabel + +=head2 ac_label + +Simple accessors for collation attributes. + +=head2 start + +The meta-reading at the start of every witness path. + +=head2 end + +The meta-reading at the end of every witness path. + +=head2 readings + +Returns all Reading objects in the graph. + +=head2 reading( $id ) + +Returns the Reading object corresponding to the given ID. + +=head2 add_reading( $reading_args ) + +Adds a new reading object to the collation. +See L for the available arguments. + +=head2 del_reading( $object_or_id ) + +Removes the given reading from the collation, implicitly removing its +paths and relationships. + +=head2 merge_readings( $main, $second ) + +Merges the $second reading into the $main one. +The arguments may be either readings or reading IDs. + +=head2 has_reading( $id ) + +Predicate to see whether a given reading ID is in the graph. + +=head2 reading_witnesses( $object_or_id ) + +Returns a list of sigils whose witnesses contain the reading. + +=head2 paths + +Returns all reading paths within the document - that is, all edges in the +collation graph. Each path is an arrayref of [ $source, $target ] reading IDs. + +=head2 add_path( $source, $target, $sigil ) + +Links the given readings in the collation in sequence, under the given witness +sigil. The readings may be specified by object or ID. + +=head2 del_path( $source, $target, $sigil ) + +Links the given readings in the collation in sequence, under the given witness +sigil. The readings may be specified by object or ID. + +=head2 has_path( $source, $target ); + +Returns true if the two readings are linked in sequence in any witness. +The readings may be specified by object or ID. + +=head2 relationships + +Returns all Relationship objects in the collation. + +=head2 add_relationship( $reading, $other_reading, $options ) + +Adds a new relationship of the type given in $options between the two readings, +which may be specified by object or ID. Returns a value of ( $status, @vectors) +where $status is true on success, and @vectors is a list of relationship edges +that were ultimately added. +See L for the available options. + +=cut sub BUILD { my $self = shift; @@ -197,6 +327,15 @@ sub _stringify_args { return( $first, $second, $arg ); } +# Helper function for manipulating the graph. +sub _objectify_args { + my( $self, $first, $second, $arg ) = @_; + $first = $self->reading( $first ) + unless ref( $first ) eq 'Text::Tradition::Collation::Reading'; + $second = $self->reading( $second ) + unless ref( $second ) eq 'Text::Tradition::Collation::Reading'; + return( $first, $second, $arg ); +} ### Path logic sub add_path { @@ -243,16 +382,31 @@ sub has_path { return $self->sequence->has_edge_attribute( $source, $target, $wit ); } -=head2 add_relationship( $reading1, $reading2, $definition ) +=head2 clear_witness( @sigil_list ) -Adds the specified relationship between the two readings. A relationship -is transitive (i.e. undirected); the options for its definition may be found -in Text::Tradition::Collation::Relationship. +Clear the given witnesses out of the collation entirely, removing references +to them in paths, and removing readings that belong only to them. Should only +be called via $tradition->del_witness. =cut -# Wouldn't it be lovely if edges could be objects, and all this type checking -# and attribute management could be done via Moose? +sub clear_witness { + my( $self, @sigils ) = @_; + + # Clear the witness(es) out of the paths + foreach my $e ( $self->paths ) { + foreach my $sig ( @sigils ) { + $self->del_path( $e, $sig ); + } + } + + # Clear out the newly unused readings + foreach my $r ( $self->readings ) { + unless( $self->reading_witnesses( $r ) ) { + $self->del_reading( $r ); + } + } +} sub add_relationship { my $self = shift; @@ -285,13 +439,9 @@ sub reading_witnesses { return keys %all_witnesses; } -=head2 Output method(s) - -=over - -=item B +=head1 OUTPUT METHODS -print $collation->as_svg(); +=head2 as_svg Returns an SVG string that represents the graph, via as_dot and graphviz. @@ -313,9 +463,7 @@ sub as_svg { return $svg; } -=item B - -print $collation->svg_subgraph( $from, $to ) +=head2 svg_subgraph( $from, $to ) Returns an SVG string that represents the portion of the graph given by the specified range. The $from and $to variables refer to ranks within the graph. @@ -345,16 +493,11 @@ sub svg_subgraph { } -=item B - -print $collation->as_dot(); +=head2 as_dot( $from, $to ) Returns a string that is the collation graph expressed in dot -(i.e. GraphViz) format. The 'view' argument determines what kind of -graph is produced. - * 'path': a graph of witness paths through the collation (DEFAULT) - * 'relationship': a graph of how collation readings relate to - each other +(i.e. GraphViz) format. If $from or $to is passed, as_dot creates +a subgraph rather than the entire graph. =cut @@ -466,14 +609,12 @@ sub path_display_label { } -=item B +=head2 as_graphml -print $collation->as_graphml( $recalculate ) - -Returns a GraphML representation of the collation graph, with -transposition information and position information. Unless -$recalculate is passed (and is a true value), the method will return a -cached copy of the SVG after the first call to the method. +Returns a GraphML representation of the collation. The GraphML will contain +two graphs. The first expresses the attributes of the readings and the witness +paths that link them; the second expresses the relationships that link the +readings. This is the native transfer format for a tradition. =begin testing @@ -663,9 +804,7 @@ sub _add_graphml_data { $data_el->appendText( $value ); } -=item B - -print $collation->as_csv( $recalculate ) +=head2 as_csv Returns a CSV alignment table representation of the collation graph, one row per witness (or witness uncorrected.) @@ -690,23 +829,22 @@ sub as_csv { return join( "\n", @result ); } -=item B - -my $table = $collation->make_alignment_table( $use_refs, \@wits_to_include ) +=head2 make_alignment_table( $use_refs, $include_witnesses ) Return a reference to an alignment table, in a slightly enhanced CollateX format which looks like this: $table = { alignment => [ { witness => "SIGIL", - tokens => [ { t => "READINGTEXT" }, ... ] }, + tokens => [ { t => "TEXT" }, ... ] }, { witness => "SIG2", - tokens => [ { t => "READINGTEXT" }, ... ] }, + tokens => [ { t => "TEXT" }, ... ] }, ... ], length => TEXTLEN }; If $use_refs is set to 1, the reading object is returned in the table instead of READINGTEXT; if not, the text of the reading is returned. -If $wits_to_include is set to a hashref, only the witnesses whose sigil + +If $include_witnesses is set to a hashref, only the witnesses whose sigil keys have a true hash value will be included. =cut @@ -792,32 +930,15 @@ sub _turn_table { return $result; } -=back - -=head2 Navigation methods - -=over - -=item B - -my $beginning = $collation->start(); - -Returns the beginning of the collation, a meta-reading with label '#START#'. - -=item B - -my $end = $collation->end(); - -Returns the end of the collation, a meta-reading with label '#END#'. +=head1 NAVIGATION METHODS - -=item B - -my @readings = $collation->reading_sequence( $first, $last, $path[, $alt_path] ); +=head2 reading_sequence( $first, $last, $sigil, $backup ) Returns the ordered list of readings, starting with $first and ending -with $last, along the given witness path. If no path is specified, -assume that the path is that of the base text (if any.) +with $last, for the witness given in $sigil. If a $backup sigil is +specified (e.g. when walking a layered witness), it will be used wherever +no $sigil path exists. If there is a base text reading, that will be +used wherever no path exists for $sigil or $backup. =cut @@ -854,9 +975,7 @@ sub reading_sequence { return @readings; } -=item B - -my $next_reading = $collation->next_reading( $reading, $witpath ); +=head2 next_reading( $reading, $sigil ); Returns the reading that follows the given reading along the given witness path. @@ -871,9 +990,7 @@ sub next_reading { return $self->reading( $answer ); } -=item B - -my $prior_reading = $collation->prior_reading( $reading, $witpath ); +=head2 prior_reading( $reading, $sigil ) Returns the reading that precedes the given reading along the given witness path. @@ -897,8 +1014,8 @@ sub _find_linked_reading { # We have to find the linked path that contains all of the # witnesses supplied in $path. my( @path_wits, @alt_path_wits ); - @path_wits = sort( $self->witnesses_of_label( $path ) ) if $path; - @alt_path_wits = sort( $self->witnesses_of_label( $alt_path ) ) if $alt_path; + @path_wits = sort( $self->_witnesses_of_label( $path ) ) if $path; + @alt_path_wits = sort( $self->_witnesses_of_label( $alt_path ) ) if $alt_path; my $base_le; my $alt_le; foreach my $le ( @linked_paths ) { @@ -937,8 +1054,31 @@ sub _is_within { return $ret; } +# Return the string that joins together a list of witnesses for +# display on a single path. +sub _witnesses_of_label { + my( $self, $label ) = @_; + my $regex = $self->wit_list_separator; + my @answer = split( /\Q$regex\E/, $label ); + return @answer; +} + + +=head1 INITIALIZATION METHODS + +These are mostly for use by parsers. + +=head2 make_witness_path( $witness ) + +Link the array of readings contained in $witness->path (and in +$witness->uncorrected_path if it exists) into collation paths. +Clear out the arrays when finished. -## INITIALIZATION METHODS - for use by parsers +=head2 make_witness_paths + +Call make_witness_path for all witnesses in the tradition. + +=cut # For use when a collation is constructed from a base text and an apparatus. # We have the sequences of readings and just need to add path edges. @@ -974,6 +1114,13 @@ sub make_witness_path { $wit->clear_uncorrected_path; } +=head2 calculate_ranks + +Calculate the reading ranks (that is, their aligned positions relative +to each other) for the graph. This can only be called on linear collations. + +=cut + sub calculate_ranks { my $self = shift; # Walk a version of the graph where every node linked by a relationship @@ -1006,7 +1153,7 @@ sub calculate_ranks { foreach my $n ( $self->sequence->successors( $r->id ) ) { my( $tfrom, $tto ) = ( $rel_containers{$r->id}, $rel_containers{$n} ); - $DB::single = 1 unless $tfrom && $tto; + # $DB::single = 1 unless $tfrom && $tto; $topo_graph->add_edge( $tfrom, $tto ); } } @@ -1024,7 +1171,6 @@ sub calculate_ranks { if( defined $node_ranks->{$rel_containers{$r->id}} ) { $r->rank( $node_ranks->{$rel_containers{$r->id}} ); } else { - $DB::single = 1; die "No rank calculated for node " . $r->id . " - do you have a cycle in the graph?"; } @@ -1066,8 +1212,13 @@ sub _assign_rank { return @next_nodes; } -# Another method to make up for rough collation methods. If the same reading -# appears multiple times at the same rank, collapse the nodes. +=head2 flatten_ranks + +A convenience method for parsing collation data. Searches the graph for readings +with the same text at the same rank, and merges any that are found. + +=cut + sub flatten_ranks { my $self = shift; my %unique_rank_rdg; @@ -1085,17 +1236,16 @@ sub flatten_ranks { } -## Utility functions - -# Return the string that joins together a list of witnesses for -# display on a single path. -sub witnesses_of_label { - my( $self, $label ) = @_; - my $regex = $self->wit_list_separator; - my @answer = split( /\Q$regex\E/, $label ); - return @answer; -} +=head1 UTILITY FUNCTIONS + +=head2 common_predecessor( $reading_a, $reading_b ) +Find the last reading that occurs in sequence before both the given readings. + +=head2 common_successor( $reading_a, $reading_b ) + +Find the first reading that occurs in sequence after both the given readings. + =begin testing use Text::Tradition; @@ -1108,14 +1258,14 @@ my $t = Text::Tradition->new( ); my $c = $t->collation; -is( $c->common_predecessor( $c->reading('n9'), $c->reading('n23') )->id, +is( $c->common_predecessor( 'n9', 'n23' )->id, 'n20', "Found correct common predecessor" ); -is( $c->common_successor( $c->reading('n9'), $c->reading('n23') )->id, +is( $c->common_successor( 'n9', 'n23' )->id, '#END#', "Found correct common successor" ); -is( $c->common_predecessor( $c->reading('n19'), $c->reading('n17') )->id, +is( $c->common_predecessor( 'n19', 'n17' )->id, 'n16', "Found correct common predecessor for readings on same path" ); -is( $c->common_successor( $c->reading('n21'), $c->reading('n26') )->id, +is( $c->common_successor( 'n21', 'n26' )->id, '#END#', "Found correct common successor for readings on same path" ); =end testing @@ -1125,12 +1275,14 @@ is( $c->common_successor( $c->reading('n21'), $c->reading('n26') )->id, ## Return the closest reading that is a predecessor of both the given readings. sub common_predecessor { my $self = shift; - return $self->common_in_path( @_, 'predecessors' ); + my( $r1, $r2 ) = $self->_objectify_args( @_ ); + return $self->common_in_path( $r1, $r2, 'predecessors' ); } sub common_successor { my $self = shift; - return $self->common_in_path( @_, 'successors' ); + my( $r1, $r2 ) = $self->_objectify_args( @_ ); + return $self->common_in_path( $r1, $r2, 'successors' ); } sub common_in_path { @@ -1165,6 +1317,6 @@ __PACKAGE__->meta->make_immutable; =over -=item * Think about making Relationship objects again +=item * Get rid of $backup in reading_sequence =back diff --git a/script/make_tradition.pl b/script/make_tradition.pl index 9e1e8a7..b3b5b44 100755 --- a/script/make_tradition.pl +++ b/script/make_tradition.pl @@ -5,14 +5,14 @@ use strict; use warnings; use Getopt::Long; use Text::Tradition; -use Text::Tradition::Stemma; +use Text::Tradition::StemmaUtil; binmode STDERR, ":utf8"; binmode STDOUT, ":utf8"; eval { no warnings; binmode $DB::OUT, ":utf8"; }; my( $informat, $inbase, $outformat, $help, $linear, $name, $HACK, $sep ) - = ( '', '', '', '', 1, 'Tradition', 0, ',' ); + = ( '', '', '', '', 1, 'Tradition', 0, "\t" ); GetOptions( 'i|in=s' => \$informat, 'b|base=s' => \$inbase, @@ -68,22 +68,15 @@ my $tradition = Text::Tradition->new( %args ); ### Custom hacking # Remove witnesses C, E, G in the Matthew text if( $HACK ) { - foreach( $tradition->collation->paths() ) { - $tradition->collation->del_path( $_ ) if $_->label =~ /^[ceg]$/i; - } - foreach( $tradition->collation->readings() ) { - if( !$_->outgoing() && !$_->incoming() ) { - print STDERR "Deleting reading " . $_->label . "\n"; - $tradition->collation->del_reading( $_ ); - } - } + my @togo = qw/ C E G /; + $tradition->collation->clear_witness( @togo ); + $tradition->del_witness( @togo ); } # Now output what we have been asked to. if( $outformat eq 'stemma' ) { - my $stemma = Text::Tradition::Stemma->new( - 'collation' => $tradition->collation ); - my( $result, $tree ) = $stemma->run_phylip_pars(); + my $cdata = character_input( $tradition->collation->make_alignment_table ); + my( $result, $tree ) = phylip_pars( $cdata ); if( $result ) { print $tree; } else { diff --git a/t/text_tradition_collation.t b/t/text_tradition_collation.t index 20ac93e..322cc39 100644 --- a/t/text_tradition_collation.t +++ b/t/text_tradition_collation.t @@ -56,14 +56,14 @@ my $t = Text::Tradition->new( ); my $c = $t->collation; -is( $c->common_predecessor( $c->reading('n9'), $c->reading('n23') )->id, +is( $c->common_predecessor( 'n9', 'n23' )->id, 'n20', "Found correct common predecessor" ); -is( $c->common_successor( $c->reading('n9'), $c->reading('n23') )->id, +is( $c->common_successor( 'n9', 'n23' )->id, '#END#', "Found correct common successor" ); -is( $c->common_predecessor( $c->reading('n19'), $c->reading('n17') )->id, +is( $c->common_predecessor( 'n19', 'n17' )->id, 'n16', "Found correct common predecessor for readings on same path" ); -is( $c->common_successor( $c->reading('n21'), $c->reading('n26') )->id, +is( $c->common_successor( 'n21', 'n26' )->id, '#END#', "Found correct common successor for readings on same path" ); }