From: Tara L Andrews <tla\@mit.edu>
Date: Tue, 10 Jan 2012 12:32:04 +0000 (+0100)
Subject: allow distance program specification
X-Git-Url: http://git.shadowcat.co.uk/gitweb/gitweb.cgi?a=commitdiff_plain;h=0f5d05c6adca96ece82661de0a262b038a00ba5f;p=scpubgit%2Fstemmatology.git

allow distance program specification
---

diff --git a/Makefile.PL b/Makefile.PL
index 73cb7ad..a03074d 100644
--- a/Makefile.PL
+++ b/Makefile.PL
@@ -8,6 +8,7 @@ all_from( 'lib/Text/Tradition.pm' );
 requires( 'Algorithm::Diff' );
 requires( 'Bio::Phylo::IO' );
 requires( 'File::chdir' );
+requires( 'File::Which' );
 requires( 'Graph' );
 requires( 'Graph::Reader::Dot' );
 requires( 'IPC::Run' );
diff --git a/lib/Text/Tradition/Stemma.pm b/lib/Text/Tradition/Stemma.pm
index 70fd634..ba0d51f 100644
--- a/lib/Text/Tradition/Stemma.pm
+++ b/lib/Text/Tradition/Stemma.pm
@@ -30,6 +30,12 @@ has distance_trees => (
     predicate => 'has_distance_trees',
     );
     
+has distance_program => (
+	is => 'rw',
+	isa => 'Str',
+	default => '',
+	);
+    
 sub BUILD {
     my( $self, $args ) = @_;
     # If we have been handed a dotfile, initialize it into a graph.
@@ -181,15 +187,20 @@ sub witnesses {
 
 before 'distance_trees' => sub {
     my $self = shift;
-    my %args = @_;
+    my %args = (
+    	'program' => 'phylip_pars',
+    	@_ );
     # TODO allow specification of method for calculating distance tree
-    if( $args{'recalc'} || !$self->has_distance_trees ) {
+    if( !$self->has_distance_trees
+    	|| $args{'program'} ne $self->distance_program ) {
         # We need to make a tree before we can return it.
-        my( $ok, $result ) = $self->run_phylip_pars();
+        my $dsub = 'run_' . $args{'program'};
+        my( $ok, $result ) = $self->$dsub();
         if( $ok ) {
             # Save the resulting trees
             my $trees = _parse_newick( $result );
             $self->_save_distance_trees( $trees );
+            $self->distance_program( $args{'program'} );
         } else {
             warn "Failed to calculate distance trees: $result";
         }
@@ -306,7 +317,7 @@ sub run_phylip_pars {
     # And then we run the program.
     my $program = File::Which::which( 'pars' );
     unless( -x $program ) {
-	return( undef, "Phylip pars not found in path" );
+		return( undef, "Phylip pars not found in path" );
     }
 
     {
diff --git a/t/stemma.t b/t/stemma.t
index 7f3bc7d..67ded66 100644
--- a/t/stemma.t
+++ b/t/stemma.t
@@ -49,7 +49,7 @@ foreach my $i ( 0 .. $#wits ) {
 
 # Test that pars runs
 SKIP: {
-    skip "pars not installed", 3 unless File::Which::which('pars');
+    skip "pars not in path", 3 unless File::Which::which('pars');
     my( $status, $tree ) = $stemma->run_phylip_pars();
     ok( $status, "pars ran successfully" );
     print STDERR "Error was $tree\n" unless $status;