From: Tara L Andrews <tla@mit.edu>
Date: Wed, 24 Apr 2013 05:58:02 +0000 (+0200)
Subject: field tested but unchecked changes, review ASAP
X-Git-Url: http://git.shadowcat.co.uk/gitweb/gitweb.cgi?a=commitdiff_plain;h=b39e7cb5cc6b77a19cac9bd83bf23105d8f75cc4;p=scpubgit%2Fstemmatology.git

field tested but unchecked changes, review ASAP
---

diff --git a/analysis/lib/Text/Tradition/StemmaUtil.pm b/analysis/lib/Text/Tradition/StemmaUtil.pm
index 1aba28b..a345b29 100644
--- a/analysis/lib/Text/Tradition/StemmaUtil.pm
+++ b/analysis/lib/Text/Tradition/StemmaUtil.pm
@@ -50,8 +50,8 @@ sub character_input {
     if( $opts->{exclude_layer} ) {
     	# Filter out all alignment table rows that do not correspond
     	# to a named witness - these are the layered witnesses.
-    	my $newtable = { alignment => [] };
-    	foreach my $row ( $table->{alignment} ) {
+    	my $newtable = { alignment => [], length => $table->{length} };
+    	foreach my $row ( @{$table->{alignment}} ) {
     		if( $tradition->has_witness( $row->{witness} ) ) {
     			push( @{$newtable->{alignment}}, $row );
     		}
@@ -179,7 +179,7 @@ sub phylip_pars {
 
     # And then we run the program.
     my $program = File::Which::which( 'pars' );
-    unless( -x $program ) {
+    unless( $program && -x $program ) {
 		throw( "Phylip pars not found in path" );
     }
 
diff --git a/base/lib/Text/Tradition/Collation.pm b/base/lib/Text/Tradition/Collation.pm
index 3b9af97..a2843e4 100644
--- a/base/lib/Text/Tradition/Collation.pm
+++ b/base/lib/Text/Tradition/Collation.pm
@@ -1258,14 +1258,14 @@ format which looks like this:
 
 sub alignment_table {
     my( $self ) = @_;
-    $self->calculate_ranks() unless $self->_graphcalc_done;
     return $self->cached_table if $self->has_cached_table;
     
     # Make sure we can do this
 	throw( "Need a linear graph in order to make an alignment table" )
 		unless $self->linear;
-	$self->calculate_ranks unless $self->end->has_rank;
-	
+    $self->calculate_ranks() 
+    	unless $self->_graphcalc_done && $self->end->has_rank;
+
     my $table = { 'alignment' => [], 'length' => $self->end->rank - 1 };
     my @all_pos = ( 1 .. $self->end->rank - 1 );
     foreach my $wit ( sort { $a->sigil cmp $b->sigil } $self->tradition->witnesses ) {
diff --git a/base/lib/Text/Tradition/Parser/CTE.pm b/base/lib/Text/Tradition/Parser/CTE.pm
index 85d37da..69bb482 100644
--- a/base/lib/Text/Tradition/Parser/CTE.pm
+++ b/base/lib/Text/Tradition/Parser/CTE.pm
@@ -366,7 +366,7 @@ sub interpret {
 	if( $oldreading ne $reading || $flag || $oldreading =~ /\./ ) {
 		my $int = $reading;
 		$int .= " ($flag)" if $flag;
-		say STDERR "Interpreted $oldreading as $int given $lemma";
+		# say STDERR "Interpreted $oldreading as $int given $lemma";
 	}
 	return( $reading, $flag );
 }
diff --git a/base/script/make_tradition.pl b/base/script/make_tradition.pl
index 7b8af5b..1c2cc8e 100755
--- a/base/script/make_tradition.pl
+++ b/base/script/make_tradition.pl
@@ -110,7 +110,7 @@ if( $stemmafile ) {
 
 # Now output what we have been asked to.
 if( $outformat eq 'stemma' ) {
-    my $cdata = character_input( $tradition->collation->alignment_table );
+    my $cdata = character_input( $tradition );
     try {
     	print phylip_pars( $cdata );
     } catch( Text::Tradition::Error $e ) {