# $Id: phylogenies_decorator.rb,v 1.34 2010/12/13 19:00:11 cmzmasek Exp $
#
# Environment variable FORESTER_HOME needs to point to the appropriate
-# directory (e.g. setenv FORESTER_HOME $HOME/SOFTWARE_DEV/ECLIPSE_WORKSPACE/forester-atv/)
+# directory (e.g. setenv FORESTER_HOME $HOME/SOFTWARE_DEV/ECLIPSE_WORKSPACE/forester/)
require 'lib/evo/util/constants'
require 'lib/evo/util/util'
class PhylogeniesDecorator
#DECORATOR_OPTIONS_SEQ_NAMES = '-r=1 -mdn'
- DECORATOR_OPTIONS_SEQ_NAMES = '-p -t -sn'
+ #DECORATOR_OPTIONS_SEQ_NAMES = '-p -t -sn'
+ DECORATOR_OPTIONS_SEQ_NAMES = '-p -t -c -tc'
# -mdn is a hidden expert option to rename e.g. "6_ORYLA3" to "6_[3]_ORYLA"
#DECORATOR_OPTIONS_SEQ_NAMES = '-sn -r=1'
#DECORATOR_OPTIONS_DOMAINS = '-r=1'
PRG_VERSION = "1.02"
COPYRIGHT = "2012 Christian M Zmasek"
CONTACT = "phylosoft@gmail.com"
- WWW = "www.phylosoft.org"
+ WWW = "https://sites.google.com/site/cmzmasek/home/software/forester"
IDS_ONLY_OPTION = "n"
DOMAINS_ONLY_OPTION = "d"
cmd = decorator + ' ' + DECORATOR_OPTIONS_DOMAINS + ' ' +
'-f=d ' + phylogeny_file + ' ' +
domains_mapfile_name + ' ' + my_outfile
+ puts cmd
execute_cmd( cmd, log )
end
my_infile = phylogeny_file
end
cmd = decorator + ' ' + DECORATOR_OPTIONS_SEQ_NAMES + ' ' +
- '-f=s ' + my_infile + ' ' +
+ '-f=n ' + my_infile + ' ' +
ids_mapfile_name + ' ' + outfile
+ puts cmd
execute_cmd( cmd, log )
end