From: Tara L Andrews <tla@mit.edu>
Date: Sun, 2 Oct 2011 23:03:24 +0000 (+0200)
Subject: package for use by catalyst
X-Git-Url: http://git.shadowcat.co.uk/gitweb/gitweb.cgi?p=scpubgit%2Fstemmatology.git;a=commitdiff_plain;h=d71100eda61da81b1e4787810dfae8843f0be88a

package for use by catalyst
---

diff --git a/lib/Text/Tradition/Analysis.pm b/lib/Text/Tradition/Analysis.pm
new file mode 100644
index 0000000..00b7b67
--- /dev/null
+++ b/lib/Text/Tradition/Analysis.pm
@@ -0,0 +1,206 @@
+package Text::Tradition::Analysis;
+
+use strict;
+use warnings;
+use Text::Tradition;
+use Text::Tradition::Stemma;
+
+sub new {
+	my( $class, $args ) = @_;
+	my $self = {};
+	# Our object needs to have a stemma graph and a variant table.
+	my( $svg, $variants ) = run_analysis( $args->{'file'}, $args->{'stemmadot'} );
+	$self->{'svg'} = $svg;
+	$self->{'variants'} = $variants;
+	
+	bless( $self, $class );	
+	return $self;
+}
+
+sub run_analysis {
+	my( $file, $stemmadot ) = @_;
+	# What we will return
+	my $svg;
+	my $variants = [];
+	
+	# Read in the file and stemma
+	my @lines;
+	open( INFILE, "$file" ) or die "Could not read $file";
+	binmode INFILE, ':utf8';
+	@lines = <INFILE>;
+	close INFILE;
+	
+	my $tradition = Text::Tradition->new( 
+		'Self' => join( '', @lines ),
+		'linear' => 1,
+		);
+	my $stemma = Text::Tradition::Stemma->new(
+		'collation' => $tradition->collation,
+		'dot' => $stemmadot,
+		);
+	# We will return the stemma picture
+	$svg = $stemma->as_svg;
+	### DIRTY HACK
+	$svg =~ s/transform=\"scale\(1 1\)/transform=\"scale\(0.7 0.7\)/;
+	
+	# We have the collation, so get the alignment table with witnesses in rows.
+	# Also return the reading objects in the table, rather than just the words.
+	
+	my $all_wits_table = $tradition->collation->make_alignment_table( 'refs' );
+	
+	# For each column in the alignment table, we want to see if the existing
+	# groupings of witnesses match our stemma hypothesis. We also want, at the
+	# end, to produce an HTML table with all the variants.
+	my $html_columns = 0;
+	my $html_data = [];
+	my $total = 0; # Keep track of the total number of variant locations
+	
+	# 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;
+		foreach my $j ( 0 .. $#{$col_rdgs} ) {
+			my $rdg = $col_rdgs->[$j];
+			$rank = $rdg->rank if $rdg && !$rank;  # Make a note of our rank
+			my $rdg_text = '(omitted)';  # Initialize in case of empty reading
+			if( $rdg ) {
+				$rdg_text = $rdg->is_lacuna ? undef : $rdg->text; # Don't count lacunae
+			}
+			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;  
+		
+		# Initialize the data structure for the row that we will return
+		my $variant_row = {'id' => $rank, 'readings' => [] };
+		# Keep track of our widest row
+		$html_columns = scalar @$groups if scalar @$groups > $html_columns;
+		
+		# We can already look up witnesses for a reading; we also want to look
+		# up readings for a given witness.
+		my $group_readings = {};
+		foreach my $x ( 0 .. $#$groups ) {
+			$group_readings->{wit_stringify( $groups->[$x] )} = $readings->[$x];
+		}
+		
+		# For all the groups with more than one member, collect the list of all
+		# contiguous vertices needed to connect them.
+		# TODO: deal with a.c. reading logic
+		my $sc = analyze_variant_location( $group_readings, $groups, $stemma->apsp );
+		$variant_row->{'genealogical'} = keys %$sc ? 1 : undef;
+		foreach my $grp ( sort keys %$group_readings ) {
+			my $rdg = $group_readings->{$grp};
+			push( @{$variant_row->{'readings'}}, { 'text' => $rdg, 'group' => $grp } );
+		}
+		
+		# Now run the same analysis given the calculated distance tree(s).
+# 		foreach my $tree ( 0 .. $#{$stemma->distance_trees} ) {
+# 			my $dc = analyze_variant_location( $group_readings, $groups,    
+# 											   $stemma->distance_apsps->[$tree] );
+# 			foreach my $rdg ( keys %$dc ) {
+# 				my $var = $dc->{$rdg};
+# 			}
+# 		}
+	
+		# Record that we used this variant in an analysis
+		push( @$variants, $variant_row );
+	}
+	
+	# Go through our variant rows and add the number of empty columns we need.
+	foreach my $row ( @$variants ) {
+		my $empty = $html_columns - scalar @{$row->{'readings'}};
+		$row->{'empty'} = $empty;
+	}
+	
+	return( $svg, $variants );
+}
+
+sub analyze_variant_location {
+    my( $group_readings, $groups, $apsp ) = @_;
+    my %contig;
+    my $conflict = {};
+    foreach my $g ( sort { scalar @$b <=> scalar @$a } @$groups ) {
+        my @members = @$g;
+        my $gst = wit_stringify( $g );
+        map { $contig{$_} = $gst } @members; # The witnesses need themselves to be 
+                                             # in their collection.
+        next unless @members > 1;
+        my $curr = pop @members;
+        foreach my $m ( @members ) {
+            foreach my $v ( $apsp->path_vertices( $curr, $m ) ) {
+                $contig{$v} = $gst unless exists $contig{$v};
+                next if $contig{$v} eq $gst;
+                # print STDERR "Conflict at $v between group $gst and group " 
+                #     . $contig{$v} . "\n";
+                # Record what is conflicting.
+                $conflict->{$group_readings->{$gst}} = $group_readings->{$contig{$v}};
+            }
+        }
+    }
+    return $conflict;
+}
+
+# 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;
\ No newline at end of file