in progress...

[jalview.git] / forester / ruby / evoruby / lib / evo / io / parser / general_msa_parser.rb

diff --git a/forester/ruby/evoruby/lib/evo/io/parser/general_msa_parser.rb b/forester/ruby/evoruby/lib/evo/io/parser/general_msa_parser.rb
index 6a170e3..48ce046 100644 (file)
--- a/forester/ruby/evoruby/lib/evo/io/parser/general_msa_parser.rb
+++ b/forester/ruby/evoruby/lib/evo/io/parser/general_msa_parser.rb
@@ -1,108 +1,102 @@
 #
 # = lib/evo/io/parser/general_msa_parser - GeneralMsaParser class
 #
-# Copyright::  Copyright (C) 2006-2007 Christian M. Zmasek
-# License::    GNU Lesser General Public License (LGPL)
+# Copyright::    Copyright (C) 2017 Christian M. Zmasek
+# License::      GNU Lesser General Public License (LGPL)
 #
-# $Id: general_msa_parser.rb,v 1.8 2009/10/08 22:44:54 cmzmasek Exp $
-#
-# last modified: 2009/10/08
+# Last modified: 2017/02/07
 
 require 'lib/evo/io/parser/msa_parser'
 require 'lib/evo/msa/msa'
 
-require 'iconv'
-
 module Evoruby
+  class GeneralMsaParser < MsaParser
+    def initialize
+    end
 
-    class GeneralMsaParser < MsaParser
-
-        def initialize
-        end
+    def parse( path )
+      Util.check_file_for_readability( path )
+      block                       = -1
+      current_seq_index_per_block = -1
+      current_name                = nil
+      saw_ignorable = true
+      is_first      = true
+      msa = Msa.new
 
-        def parse( path )
-            Util.check_file_for_readability( path )
-            block                       = -1
-            current_seq_index_per_block = -1
-            current_name                = nil
+      File.open( path ) do | file |
+        while line = file.gets
+          line.encode!("UTF-8", :invalid => :replace, :undef => :replace, :replace => "?")
+          if can_ignore?( line )
             saw_ignorable = true
-            is_first      = true
-            msa = Msa.new
-            ic = Iconv.new( 'UTF-8//IGNORE', 'UTF-8' )
-            File.open( path ) do | file |
-                while line = file.gets
-                    line = ic.iconv( line )
-                    if can_ignore?( line )
-                        saw_ignorable = true
-                    elsif ( is_first && is_program_name_line?( line ) ) 
-                    elsif( line =~ /^\S+\s+.+\s*$/ || line =~ /^\s+.+\s*$/ || line =~ /^\S+\s*$/ )
-                        if ( saw_ignorable )
-                            block += 1
-                            current_seq_index_per_block = -1
-                            saw_ignorable = false
-                        end
-                        current_seq_index_per_block += 1
-                        if ( line =~ /^(\S+)\s+(.+?)\s*$/ )
-                            name = $1
-                            seq  = $2.gsub( /\s/, '.' )
-                            a = msa.find_by_name( name, false, false )
-                            if ( a.length < 1 )
-                                msa.add( name, seq )
-                            elsif ( a.length == 1 )
-                                msa.get_sequence( a[ 0 ] ).append!( seq )
-                            else
-                                error_msg = "Unexpected error at line: " + line
-                                raise IOError, error_msg
-                            end
-                            current_name = name
-                        elsif ( line =~ /^\s+(.+?)\s*$/ )
-                            seq = $1.gsub( /\s/, '.' )
-                            a = msa.find_by_name( current_name, false, false )
-                            if ( a.length != 1  )
-                                error_msg = "Unexpected error at line: " + line
-                                raise IOError, error_msg
-                            else
-                                msa.get_sequence( a[ 0 ] ).append!( seq )
-                            end
+          elsif ( is_first && is_program_name_line?( line ) )
+          elsif( line =~ /^\S+\s+.+\s*$/ || line =~ /^\s+.+\s*$/ || line =~ /^\S+\s*$/ )
+            if ( saw_ignorable )
+              block += 1
+              current_seq_index_per_block = -1
+              saw_ignorable = false
+            end
+            current_seq_index_per_block += 1
+            if ( line =~ /^(\S+)\s+(.+?)\s*$/ )
+              name = $1
+              seq  = $2.gsub( /\s/, '.' )
+              a = msa.find_by_name( name, false, false )
+              if ( a.length < 1 )
+                msa.add( name, seq )
+              elsif ( a.length == 1 )
+                msa.get_sequence( a[ 0 ] ).append!( seq )
+              else
+                error_msg = "Unexpected error at line: " + line
+                raise IOError, error_msg
+              end
+              current_name = name
+            elsif ( line =~ /^\s+(.+?)\s*$/ )
+              seq = $1.gsub( /\s/, '.' )
+              a = msa.find_by_name( current_name, false, false )
+              if ( a.length != 1  )
+                error_msg = "Unexpected error at line: " + line
+                raise IOError, error_msg
+              else
+                msa.get_sequence( a[ 0 ] ).append!( seq )
+              end
 
-                        elsif ( line =~ /^(\S+)\s*$/ )
-                            seq = $1
-                            if block == 0
-                                error_msg = "First block cannot contain unnamed sequences"
-                                raise IOError, error_msg
-                            else
-                                msa.get_sequence( current_seq_index_per_block ).append!( seq )
-                            end
-                            current_name = nil
-                        end
-                    else
-                        error_msg = "Unexpected line: " + line
-                        raise IOError, error_msg
-                    end
-                    if ( is_first )
-                        is_first = false
-                    end
-                end
+            elsif ( line =~ /^(\S+)\s*$/ )
+              seq = $1
+              if block == 0
+                error_msg = "First block cannot contain unnamed sequences"
+                raise IOError, error_msg
+              else
+                msa.get_sequence( current_seq_index_per_block ).append!( seq )
+              end
+              current_name = nil
             end
-            return msa
-        end # def parse( path )
+          else
+            error_msg = "Unexpected line: " + line
+            raise IOError, error_msg
+          end
+          if ( is_first )
+            is_first = false
+          end
+        end
+      end
+      return msa
+    end # def parse( path )
 
-        private
+    private
 
-        def can_ignore?( line )
-            return ( line !~ /[A-Za-z\-?\*_\.]/ ||
-                     line =~ /^\s+[*\.:]/ ||
-                     line =~ /^\s*#/ ||
-                     line =~ /^\s*%/ ||
-                     line =~ /^\s*\/\// ||
-                     line =~ /^\s*!!/  )
-        end
-        
-        def is_program_name_line?( line )
-            return ( line =~ /^CLUSTAL\s/ ||
-                     line =~ /^MUSCLE\s\(/ ||
-                     line =~ /^PROBCONS\s/ )             
-        end  
-    end # class GeneralMsaParser
+    def can_ignore?( line )
+      return ( line !~ /[A-Za-z\-?\*_\.]/ ||
+      line =~ /^\s+[*\.:]/ ||
+      line =~ /^\s*#/ ||
+      line =~ /^\s*%/ ||
+      line =~ /^\s*\/\// ||
+      line =~ /^\s*!!/  )
+    end
+
+    def is_program_name_line?( line )
+      return ( line =~ /^CLUSTAL\s/ ||
+      line =~ /^MUSCLE\s\(/ ||
+      line =~ /^PROBCONS\s/ )
+    end
+  end # class GeneralMsaParser
 
 end # module Evoruby