Delete unneeded directory

[jabaws.git] / website / archive / binaries / mac / src / mafft / core / newick2mafft.rb

diff --git a/website/archive/binaries/mac/src/mafft/core/newick2mafft.rb b/website/archive/binaries/mac/src/mafft/core/newick2mafft.rb
deleted file mode 100644 (file)
index b74ba36..0000000
--- a/website/archive/binaries/mac/src/mafft/core/newick2mafft.rb
+++ /dev/null
@@ -1,132 +0,0 @@
-#! /usr/bin/env ruby
-
-#version 2, 2009/01/24
-
-
-if ARGV.length == 1
-       scale = 1.0
-elsif ARGV.length == 2
-       scale = ARGV.shift.to_f
-else
-       STDERR.puts "USAGE: newick2mafft.rb scale input_tree > output"
-       exit
-end
-
-if scale <= 0.0 then
-       STDERR.puts "Inappropriate scale, #{scale.to_s}"
-       exit
-end
-
-STDERR.puts "scale = " + scale.to_s
-
-infp = File.open( ARGV.shift, "r" )
-
-tree = ""
-while line = infp.gets
-       tree += line.strip
-       break if tree =~ /;$/
-end
-infp.close
-
-
-#tree = tree.gsub( /_.*?:/, ":" ).gsub(/[0-9]\.[0-9]*e-[0-9][0-9]/, "0").gsub(/\[.*?\]/,"").gsub(/ /, "").gsub(/:\-[0-9\.]+/, ":0.0" )
-tree = tree.gsub( /_.*?:/, ":" ).gsub(/[0-9]\.[0-9]*e-[0-9][0-9]/, "0").gsub(/\[.*?\]/,"").gsub(/ /, "")
-
-
-STDERR.puts "Initial tree = " +  tree
-
-def resolve( tree )
-
-
-while 1
-#      p tree
-       tree.sub!( /\,([0-9]+):(\-?[0-9\.]+)\,([0-9]+):(\-?[0-9\.]+)/, ",XXX" )
-       hit1 = $1
-       hit2 = $2
-       hit3 = $3
-       hit4 = $4
-
-#      p hit1
-#      p hit2
-#      p hit3
-#      p hit4
-
-#      puts "introduce XXX"
-#      p tree
-
-       break unless tree.index(/XXX/)
-
-       poshit = tree.index(/XXX/)
-#      puts "poshit=" + poshit.to_s
-
-       i = poshit
-       height = 0
-       while i >= 0
-               break if height == 0 && tree[i..i] == '('
-               if tree[i..i] == ')' then
-                       height += 1
-               elsif tree[i..i] == '(' then
-                       height -= 1
-               end
-               i -= 1
-       end
-
-       poskakko = i
-#      puts "poskakko = " + poskakko.to_s
-       zenhan = tree[0..poskakko]
-       zenhan = "" if poskakko == -1
-#      puts "zenhan = " + zenhan
-
-       treelen = tree.length
-       tree = zenhan + "(" + tree[poskakko+1..treelen]
-#      puts "add ("
-#      p tree
-       tree.sub!( /XXX/, "#{hit1}:#{hit2}):0,#{hit3}:#{hit4}" )
-
-#      p tree
-end
-
-
-return tree
-
-end
-
-memi = [-1,-1]
-leni = [-1,-1]
-
-while tree.index( /\(/ ) 
-
-       tree = resolve( tree )
-
-       tree.sub!( /\(([0-9]+):(\-?[0-9\.]+),([0-9]+):(\-?[0-9\.]+)\)/, "XXX" )
-       memi[0] = $1.to_i
-       leni[0] = $2.to_f * scale
-       memi[1] = $3.to_i
-       leni[1] = $4.to_f * scale
-
-       if leni[0] > 10 || leni[1] > 10 then
-               STDERR.puts ""
-               STDERR.puts "Please check the scale of branch length!"
-               STDERR.puts "The unit of branch lengths must be 'substitution/site'"
-               STDERR.puts "If the unit is 'substition' in your tree, please"
-               STDERR.puts "use the scale argument,"
-               STDERR.puts "% newick2mafft scale in > out"
-               STDERR.puts "where scale = 1/(alignment length)"
-               STDERR.puts ""
-               exit 1
-       end
-
-#      STDERR.puts "subtree = " + $&
-
-       if memi[1] < memi[0] then
-               memi.reverse!
-               leni.reverse!
-       end
-
-       tree.sub!( /XXX/, memi[0].to_s )
-
-       STDERR.puts "Tree = " + tree
-
-       printf( "%5d %5d %10.5f %10.5f\n", memi[0], memi[1], leni[0], leni[1] )
-
-end