RSL = 'RSL'
HMM = 'HMM'
- PHYLO_PL = 'PHYLO_PL'
+ PHYLO_OPT = 'PHYLO_OPT'
OPTION_OPEN = '%['
OPTION_CLOSE = ']%'
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
end
def update_phylo_pl_options( phylo_pl_options, bootstraps )
- unless phylo_pl_options =~ /B\d/
+ #opts = phylo_pl_options
+ puts
+ puts "opts: " + phylo_pl_options
+ unless phylo_pl_options =~ /B\d/
phylo_pl_options = 'B' + bootstraps.to_s + phylo_pl_options
end
phylo_pl_options = '-' + phylo_pl_options
+ puts
+ puts "new opts: " + phylo_pl_options
phylo_pl_options
end