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[jalview.git]
/
forester
/
ruby
/
evoruby
/
lib
/
evo
/
tool
/
phylogeny_factory.rb
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
(file)
--- 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'
RSL = 'RSL'
HMM = 'HMM'
- PHYLO_PL = 'PHYLO_PL'
+ PHYLO_OPT = 'PHYLO_OPT'
OPTION_OPEN = '%['
OPTION_CLOSE = ']%'
OPTION_OPEN = '%['
OPTION_CLOSE = ']%'
@@
-140,7
+140,7
@@
module Evoruby
elsif ( line =~ /^%\s*(\S+)\s*=\s*(\S+)/ )
key = $1
value = $2
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
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 )
end
def update_phylo_pl_options( phylo_pl_options, bootstraps )
- opts = phylo_pl_options
+ #opts = phylo_pl_options
puts
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
end
- opts = '-' + opts
+ phylo_pl_options = '-' + phylo_pl_options
puts
puts
- puts "new opts: " + opts
- opts
+ puts "new opts: " + phylo_pl_options
+ phylo_pl_options
end
def subst_min_length( command, id, min_lengths )
end
def subst_min_length( command, id, min_lengths )