From 0d00b87d870a8a198772f28c87ed3b9a39666c4d Mon Sep 17 00:00:00 2001 From: "cmzmasek@gmail.com" Date: Tue, 12 Nov 2013 00:30:14 +0000 Subject: [PATCH] inprogress --- .../ruby/evoruby/lib/evo/tool/phylogeny_factory.rb | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/forester/ruby/evoruby/lib/evo/tool/phylogeny_factory.rb b/forester/ruby/evoruby/lib/evo/tool/phylogeny_factory.rb index 1992783..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 @@ -264,16 +264,16 @@ module Evoruby end def update_phylo_pl_options( phylo_pl_options, bootstraps ) - opts = phylo_pl_options + #opts = phylo_pl_options puts - puts "opts: " + opts - unless opts =~ /B\d/ - opts = 'B' + bootstraps.to_s + opts + puts "opts: " + phylo_pl_options + unless phylo_pl_options =~ /B\d/ + phylo_pl_options = 'B' + bootstraps.to_s + phylo_pl_options end - opts = '-' + opts + phylo_pl_options = '-' + phylo_pl_options puts - puts "new opts: " + opts - opts + puts "new opts: " + phylo_pl_options + phylo_pl_options end def subst_min_length( command, id, min_lengths ) -- 1.7.10.2