change analysis graph calculation - closer but not correct yet.

diff --git a/lib/Text/Tradition/Analysis.pm b/lib/Text/Tradition/Analysis.pm
index f4605ed..90a82d8 100644 (file)
--- a/lib/Text/Tradition/Analysis.pm
+++ b/lib/Text/Tradition/Analysis.pm
@@ -41,8 +41,9 @@ sub run_analysis {
        
        # 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' );
+       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
@@ -104,7 +105,7 @@ sub run_analysis {
                # TODO: deal with a.c. reading logic
                $DB::single = 1 if $rank == 25;
                my $variant_row = analyze_variant_location( $group_readings, $groups, 
-                   $stemma->apsp, $lacunose );
+                   $stemma->graph, $lacunose );
                $variant_row->{'id'} = $rank;
                $genealogical++ if $variant_row->{'genealogical'};
                $conflicts += grep { $_->{'conflict'} } @{$variant_row->{'readings'}};
@@ -113,8 +114,7 @@ sub run_analysis {
 #              my @trees = @{$stemma->distance_trees};
 #              if( @trees ) {
 #             foreach my $tree ( 0 .. $#trees ) {
-#                 my $dc = analyze_variant_location( $group_readings, $groups,    
-#                                                    $stemma->distance_apsps->[$tree] );
+#                 my $dc = analyze_variant_location( $group_readings, $groups, $tree );
 #                 foreach my $rdg ( keys %$dc ) {
 #                     my $var = $dc->{$rdg};
 #                     # TODO Do something with this
@@ -145,7 +145,7 @@ sub run_analysis {
 #             -> readings [ { text, group, conflict, missing } ]
 
 sub analyze_variant_location {
-    my( $group_readings, $groups, $apsp, $lacunose ) = @_;
+    my( $group_readings, $groups, $graph, $lacunose ) = @_;
     my %contig;
     my $conflict = {};
     my %missing;
@@ -157,20 +157,32 @@ sub analyze_variant_location {
         map { $contig{$_} = $gst } @$g;
     }
     foreach my $g ( sort { scalar @$b <=> scalar @$a } @$groups ) {
-        my @members = @$g;
-        my $gst = wit_stringify( $g ); # $gst is now the name of this group.
-        while( @members ) {
-            # Gather the list of vertices that are needed to join all members.
-            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;
-                    # Record what is conflicting. TODO do we use this?
-                    $conflict->{$group_readings->{$gst}} = $group_readings->{$contig{$v}};
-                }
+        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 ),
@@ -178,12 +190,12 @@ sub analyze_variant_location {
         if( $reading->{'conflict'} ) {
             $reading->{'group'} = $gst;
         } else {
-            my @all_vertices = grep { $contig{$_} eq $gst && !$missing{$_} } keys %contig;
+            my @all_vertices = grep { !$missing{$_} } keys %reachable;
             $reading->{'group'} = wit_stringify( \@all_vertices );
         }
         push( @{$variant_row->{'readings'}}, $reading );
     }
-    $variant_row->{'genealogical'} = keys %$conflict ? undef : 1;
+    $variant_row->{'genealogical'} = !( keys %$conflict );
     return $variant_row;
 }
 

diff --git a/lib/Text/Tradition/Collation.pm b/lib/Text/Tradition/Collation.pm
index 1f4e00f..d28d7d7 100644 (file)
--- a/lib/Text/Tradition/Collation.pm
+++ b/lib/Text/Tradition/Collation.pm
@@ -528,7 +528,7 @@ sub as_csv {
 # in the table are the nodes or simply their readings.
 
 sub make_alignment_table {
-    my( $self, $noderefs ) = @_;
+    my( $self, $noderefs, $include ) = @_;
     unless( $self->linear ) {
         warn "Need a linear graph in order to make an alignment table";
         return;
@@ -547,8 +547,19 @@ sub make_alignment_table {
         }           
     }
 
+    if( $include ) {
+        my $winnowed = [];
+        # Winnow out the rows for any witness not included.
+        foreach my $row ( @$table ) {
+            next unless $include->{$row->[0]};
+            push( @$winnowed, $row );
+        }
+        $table = $winnowed;
+    }
+
     # Return a table where the witnesses read in columns rather than rows.
     my $turned = _turn_table( $table );
+    # TODO We should really go through and delete empty rows.
     return $turned;
 }
 

diff --git a/lib/Text/Tradition/Stemma.pm b/lib/Text/Tradition/Stemma.pm
index 23fbbcc..e241d56 100644 (file)
--- a/lib/Text/Tradition/Stemma.pm
+++ b/lib/Text/Tradition/Stemma.pm
@@ -17,19 +17,12 @@ has collation => (
     required => 1,
     );  
 
-# TODO Think about making a new class for the graphs, which has apsp as a property.
 has graph => (
     is => 'rw',
     isa => 'Graph',
     predicate => 'has_graph',
     );
     
-has apsp => (
-    is => 'ro',
-    isa => 'Graph',
-    writer => '_save_apsp',
-    );
-    
 has distance_trees => (
     is => 'ro',
     isa => 'ArrayRef[Graph]',
@@ -37,12 +30,6 @@ has distance_trees => (
     predicate => 'has_distance_trees',
     );
     
-has distance_apsps => (
-    is => 'ro',
-    isa => 'ArrayRef[Graph]',
-    writer => '_save_distance_apsps',
-    );
-        
 sub BUILD {
     my( $self, $args ) = @_;
     # If we have been handed a dotfile, initialize it into a graph.
@@ -59,28 +46,6 @@ sub BUILD {
     }
 }
 
-# If we are saving a new graph, calculate its apsp values.
-after 'graph' => sub {
-    my( $self, $args ) = @_;
-    if( $args ) {
-        # We had a new graph.
-        my $undirected;
-        if( $self->graph->is_directed ) {
-            # Make an undirected version.
-            $undirected = Graph->new( 'undirected' => 1 );
-            foreach my $v ( $self->graph->vertices ) {
-                $undirected->add_vertex( $v );
-            }
-            foreach my $e ( $self->graph->edges ) {
-                $undirected->add_edge( @$e );
-            }
-        } else {
-            $undirected = $self->graph;
-        }
-        $self->_save_apsp( $undirected->APSP_Floyd_Warshall() );
-    }       
-};
-
 # Render the stemma as SVG.
 sub as_svg {
     my( $self, $opts ) = @_;
@@ -117,6 +82,13 @@ sub as_svg {
     return $svg;
 }
 
+sub witnesses {
+    my $self = shift;
+    my @wits = grep { $self->graph->get_vertex_attribute( $_, 'class' ) eq 'extant' }
+        $self->graph->vertices;
+    return @wits;
+}
+
 #### Methods for calculating phylogenetic trees ####
 
 before 'distance_trees' => sub {
@@ -130,12 +102,6 @@ before 'distance_trees' => sub {
             # Save the resulting trees
             my $trees = _parse_newick( $result );
             $self->_save_distance_trees( $trees );
-            # and calculate their APSP values.
-            my @apsps;
-            foreach my $t ( @$trees ) {
-                push( @apsps, $t->APSP_Floyd_Warshall() );
-            }
-            $self->_save_distance_apsps( \@apsps );
         } else {
             warn "Failed to calculate distance trees: $result";
         }