From: cmzmasek@gmail.com Date: Sat, 16 Nov 2013 00:01:32 +0000 (+0000) Subject: inprogress X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=156517428746b21481eb815bf860ffb6cb0314ef;p=jalview.git inprogress --- diff --git a/forester/ruby/evoruby/lib/evo/tool/phylogenies_decorator.rb b/forester/ruby/evoruby/lib/evo/tool/phylogenies_decorator.rb index 953f924..85e2478 100644 --- a/forester/ruby/evoruby/lib/evo/tool/phylogenies_decorator.rb +++ b/forester/ruby/evoruby/lib/evo/tool/phylogenies_decorator.rb @@ -101,32 +101,9 @@ module Evoruby Util.fatal_error( PRG_NAME, 'logfile [' + LOG_FILE + '] already exists' ) end - allowed_opts = Array.new - allowed_opts.push( IDS_ONLY_OPTION ) - allowed_opts.push( DOMAINS_ONLY_OPTION ) - - disallowed = cla.validate_allowed_options_as_str( allowed_opts ) - if ( disallowed.length > 0 ) - Util.fatal_error( PRG_NAME, "unknown option(s): " + disallowed ) - end - - ids_only = false - domains_only = false - in_suffix = cla.get_file_name( 0 ) out_suffix = cla.get_file_name( 1 ) - if cla.is_option_set?( IDS_ONLY_OPTION ) - ids_only = true - end - if cla.is_option_set?( DOMAINS_ONLY_OPTION ) - domains_only = true - end - - if ( ids_only && domains_only ) - Util.fatal_error( PRG_NAME, 'attempt to use ids only and domains only at the same time' ) - end - log = String.new now = DateTime.now