From 001b923e7c34f43ea04f2045f89f2a3abd345bcc Mon Sep 17 00:00:00 2001 From: "cmzmasek@gmail.com" Date: Wed, 3 Apr 2013 00:03:36 +0000 Subject: [PATCH] inprogress --- forester/ruby/evoruby/lib/evo/tool/phylogeny_factory.rb | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) diff --git a/forester/ruby/evoruby/lib/evo/tool/phylogeny_factory.rb b/forester/ruby/evoruby/lib/evo/tool/phylogeny_factory.rb index 7205451..d07b195 100644 --- a/forester/ruby/evoruby/lib/evo/tool/phylogeny_factory.rb +++ b/forester/ruby/evoruby/lib/evo/tool/phylogeny_factory.rb @@ -148,13 +148,12 @@ module Evoruby file !~ /^00/ ) aln_name = file.to_str id = get_id( aln_name ) - #if !ids.include?( id ) - # ids.add( id ) - #end if id != nil && id.length > 0 - puts( '[' + PRG_NAME + '] > file [id]: ' + aln_name + ' [' + id + ']' ) + puts + puts( '[' + PRG_NAME + '] > file [id] : ' + aln_name + ' [' + id + ']' ) else - puts( '[' + PRG_NAME + '] > file [id]: ' + aln_name + ' [WARNING: could not get id!]' ) + puts + puts( '[' + PRG_NAME + '] > file [id] : ' + aln_name + ' [WARNING: could not get id!]' ) end commands.each do | cmd | cmd = subst_hmm( cmd, id ) @@ -169,7 +168,7 @@ module Evoruby if ( cmd =~ /%/ ) cmd =~ /(%.*?%)/ problem = $1 - puts( '[' + PRG_NAME + '] > WARNING : [' + aln_name + '] command still contains placeholder: ' + problem ) + puts( '[' + PRG_NAME + '] > WARNING : command still contains placeholder: ' + problem ) log << "WARNING: command still contains placeholder: " + cmd + NL else tmp_cmd_file = file.to_str[ 0..4 ] + TMP_CMD_FILE_SUFFIX -- 1.7.10.2