X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fruby%2Fevoruby%2Flib%2Fevo%2Ftool%2Fphylogeny_factory.rb;h=18d396e25eedef4828a497d341de057643ff0374;hb=968e6e38c05f4add3ec8c51518285a03aadb7d5e;hp=93eac0744e6c30497cf889f7d3cb3a806744b642;hpb=81aff14b756ba3fd6341875c4e4af92f0415450a;p=jalview.git

diff --git a/forester/ruby/evoruby/lib/evo/tool/phylogeny_factory.rb b/forester/ruby/evoruby/lib/evo/tool/phylogeny_factory.rb
index 93eac07..18d396e 100644
--- a/forester/ruby/evoruby/lib/evo/tool/phylogeny_factory.rb
+++ b/forester/ruby/evoruby/lib/evo/tool/phylogeny_factory.rb
@@ -39,7 +39,7 @@ module Evoruby
 
     RSL                 = 'RSL'
     HMM                 = 'HMM'
-    PHYLO_PL            = 'PHYLO_PL'
+    PHYLO_OPT            = 'PHYLO_OPT'
 
     OPTION_OPEN          = '%['
     OPTION_CLOSE          = ']%'
@@ -140,7 +140,7 @@ module Evoruby
         elsif ( line =~ /^%\s*(\S+)\s*=\s*(\S+)/ )
           key = $1
           value = $2
-          if key == PHYLO_PL
+          if key == PHYLO_OPT
             value = update_phylo_pl_options( value, bootstraps )
           end
           options[ key ] = value
@@ -264,10 +264,15 @@ module Evoruby
     end
 
     def update_phylo_pl_options( phylo_pl_options, bootstraps )
-      unless phylo_pl_options =~ /B\d/
+      #opts = phylo_pl_options
+      puts
+      puts "opts: " + phylo_pl_options
+      unless phylo_pl_options  =~ /B\d/
         phylo_pl_options = 'B' + bootstraps.to_s + phylo_pl_options
       end
       phylo_pl_options = '-' + phylo_pl_options
+      puts
+      puts "new opts: " + phylo_pl_options
       phylo_pl_options
     end