From: zma <zma@localhost>
Date: Tue, 14 Feb 2017 18:10:12 +0000 (-0800)
Subject: removed
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=6286ef87daebd189a0dcd7fc65f8f54c8ed126f6;p=jalview.git

removed
---

diff --git a/forester/ruby/evoruby/lib/evo/tool/new_tap.rb b/forester/ruby/evoruby/lib/evo/tool/new_tap.rb
deleted file mode 100644
index 1dc7431..0000000
--- a/forester/ruby/evoruby/lib/evo/tool/new_tap.rb
+++ /dev/null
@@ -1,167 +0,0 @@
-#
-# = lib/evo/apps/ -  class
-#
-# Copyright::  Copyright (C) 2009 Christian M. Zmasek
-# License::    GNU Lesser General Public License (LGPL)
-#
-# $Id: new_tap.rb,v 1.4 2010/12/13 19:00:11 cmzmasek Exp $
-
-
-require 'lib/evo/util/util'
-require 'lib/evo/msa/msa_factory'
-require 'lib/evo/msa/msa'
-require 'lib/evo/io/msa_io'
-require 'lib/evo/io/parser/fasta_parser'
-require 'lib/evo/io/parser/general_msa_parser'
-require 'lib/evo/io/writer/fasta_writer'
-require 'lib/evo/io/writer/phylip_sequential_writer'
-require 'lib/evo/util/command_line_arguments'
-
-module Evoruby
-
-    class TaxonomyProcessor
-
-        PRG_NAME       = ""
-        PRG_DATE       = "2009.10.09"
-        PRG_DESC       = "replacement of labels in multiple sequence files"
-        PRG_VERSION    = "1.00"
-        COPYRIGHT      = "2009 Christian M Zmasek"
-        CONTACT        = "phylosoft@gmail.com"
-        WWW            = "www.phylosoft.org"
-
-        REMOVE_REDUNDANT_SEQS_OPTION = "rr"
-        
-        def initialize()
-            @taxonomies = Hash.new()
-        end
-
-        def run()
-
-            Util.print_program_information( PRG_NAME,
-                PRG_VERSION,
-                PRG_DESC,
-                PRG_DATE,
-                COPYRIGHT,
-                CONTACT,
-                WWW,
-                STDOUT )
-
-            if ( ARGV == nil || ( ARGV.length != 3 && ARGV.length != 4 ) )
-                puts( "Usage: #{PRG_NAME}.rb <input sequences> <output sequences> <output map>" )
-                puts()
-                puts( "  options: -" + REMOVE_REDUNDANT_SEQS_OPTION + ": to remove redundant sequences" )
-                puts()
-                exit( -1 )
-            end
-
-            begin
-                cla = CommandLineArguments.new( ARGV )
-            rescue ArgumentError => e
-                Util.fatal_error( PRG_NAME, "error: " + e.to_s )
-            end
-            
-            input     = cla.get_file_name( 0 )
-            output    = cla.get_file_name( 1 )
-            map_file = cla.get_file_name( 2 )
-
-            allowed_opts = Array.new
-            allowed_opts.push( REMOVE_REDUNDANT_SEQS_OPTION ) 
-            
-            disallowed = cla.validate_allowed_options_as_str( allowed_opts )
-            if ( disallowed.length > 0 )
-                Util.fatal_error( PRG_NAME, "unknown option(s): " + disallowed )
-            end
-
-            
-            remove_redudant = false
-            if ( cla.is_option_set?( REMOVE_REDUNDANT_SEQS_OPTION ) )
-                remove_redudant = true
-            end
-
-            if ( File.exists?( output ) )
-                Util.fatal_error( PRG_NAME, "outfile [" + output + "] already exists" )
-            end
-            if ( File.exists?( map_file ) )
-                Util.fatal_error( PRG_NAME, "map file [" + map_file + "] already exists" )
-            end
-            if ( !File.exists?( input) )
-                Util.fatal_error( PRG_NAME, "infile [" + input + "] does not exist" )
-            end
-           
-            fasta_like = Util.looks_like_fasta?( input )
-
-            puts()
-            puts( "Input alignment : " + input )
-            puts( "Output alignment: " + output )
-            puts( "Output map      : " + map_file )
-            if ( fasta_like )
-                puts( "Format          : Fasta"  )
-            else
-                puts( "Format          : Phylip like" )
-            end
-            puts()
-
-            species_map = Hash.new
-           
-            f = MsaFactory.new()
-            begin
-                if ( fasta_like )
-                    msa = f.create_msa_from_file( input, FastaParser.new() )
-                else
-                    msa = f.create_msa_from_file( input, GeneralMsaParser.new() )
-                end
-            rescue Exception => e
-                Util.fatal_error( PRG_NAME, "failed to read file: " + e.to_s )
-            end
-
-            if ( msa == nil || msa.get_number_of_seqs() < 1 )
-                Util.fatal_error( PRG_NAME, "failed to read MSA" )
-            end
-            begin
-                Util.check_file_for_writability( map_file )
-            rescue Exception => e
-                Util.fatal_error( PRG_NAME, "error: " + e.to_, STDOUT )
-            end
-
-            if ( remove_redudant ) 
-                removed = msa.remove_redundant_sequences!( true )
-                if removed.size > 0
-                    Util.print_message( PRG_NAME, "going to ignore the following " + removed.size.to_s + " redundant sequences:" )
-                    removed.each { | seq_name |
-                        puts seq_name
-                    }
-                    Util.print_message( PRG_NAME, "will process " + msa.get_number_of_seqs.to_s + " non redundant sequences" )
-                end
-            end
-
-            lf = File.open( map_file, "a" )
-            for i in 0 ... msa.get_number_of_seqs
-                seq  = msa.get_sequence( i )
-            end
-
-            io = MsaIO.new()
-            w = nil
-            if ( fasta_like )
-                w = FastaWriter.new()
-            else
-                w = PhylipSequentialWriter.new()
-            end
-            w.set_max_name_length( 10 )
-            w.clean( true )
-            begin
-                io.write_to_file( msa, output, w )
-            rescue Exception => e
-                Util.fatal_error( PRG_NAME, "failed to write file: " + e.to_s )
-            end
-            lf.close()
-            if ( @taxonomies.length > 0 )
-                Util.print_message( PRG_NAME, "number of unique taxonomies: " + @taxonomies.length.to_s )
-            end
-            Util.print_message( PRG_NAME, "wrote: " + map_file )
-            Util.print_message( PRG_NAME, "wrote: " + output )
-            Util.print_message( PRG_NAME, "OK" )
-        end
-
-    end # class 
-
-end # module Evoruby
\ No newline at end of file