X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fruby%2Fevoruby%2Flib%2Fevo%2Ftool%2Fphylogenies_decorator.rb;h=973286c1cdb1199a4e00e91886145602388c3aee;hb=8662ade5ecc921f9824546493a764cebccc1ddf5;hp=1eea808704e646c8b56b43306940e43f07f4ff79;hpb=6a8ca715561c8359f7116c79424932a158a73e69;p=jalview.git

diff --git a/forester/ruby/evoruby/lib/evo/tool/phylogenies_decorator.rb b/forester/ruby/evoruby/lib/evo/tool/phylogenies_decorator.rb
index 1eea808..973286c 100644
--- a/forester/ruby/evoruby/lib/evo/tool/phylogenies_decorator.rb
+++ b/forester/ruby/evoruby/lib/evo/tool/phylogenies_decorator.rb
@@ -178,14 +178,14 @@ module Evoruby
           seqs_file_name = nil
 
           ids_mapfile_name = get_file( files, phylogeny_id, IDS_MAPFILE_SUFFIX )
-          domains_mapfile_name = get_file( files, phylogeny_id, DOMAINS_MAPFILE_SUFFIX )
-          seqs_file_name = get_seq_file( files, phylogeny_id )
+         # domains_mapfile_name = get_file( files, phylogeny_id, DOMAINS_MAPFILE_SUFFIX )
+         # seqs_file_name = get_seq_file( files, phylogeny_id )
 
-          begin
-            Util.check_file_for_readability( domains_mapfile_name )
-          rescue ArgumentError
-            Util.fatal_error( PRG_NAME, 'failed to read from [#{domains_mapfile_name}]: ' + $! )
-          end
+#          begin
+#            Util.check_file_for_readability( domains_mapfile_name )
+#          rescue ArgumentError
+#            Util.fatal_error( PRG_NAME, 'failed to read from [#{domains_mapfile_name}]: ' + $! )
+#          end
 
           begin
             Util.check_file_for_readability( ids_mapfile_name )
@@ -193,34 +193,34 @@ module Evoruby
             Util.fatal_error( PRG_NAME, 'failed to read from [#{ids_mapfile_name}]: ' + $! )
           end
 
-          begin
-            Util.check_file_for_readability( seqs_file_name  )
-          rescue ArgumentError
-            Util.fatal_error( PRG_NAME, 'failed to read from [#{seqs_file_name }]: ' + $! )
-          end
-
-          cmd = decorator +
-           ' -t -p -f=m ' + phylogeny_file + ' ' +
-           seqs_file_name  + ' ' + TMP_FILE_1
-          puts cmd
-          begin
-            execute_cmd( cmd, log )
-          rescue Error
-            Util.fatal_error( PRG_NAME, 'error: ' + $! )
-          end
-
-          cmd = decorator + ' ' + DECORATOR_OPTIONS_DOMAINS + ' ' +
-           '-f=d ' + TMP_FILE_1 + ' ' +
-           domains_mapfile_name + ' ' +TMP_FILE_2
-          puts cmd
-          begin
-            execute_cmd( cmd, log )
-          rescue Error
-            Util.fatal_error( PRG_NAME, 'error: ' + $! )
-          end
+#          begin
+#            Util.check_file_for_readability( seqs_file_name  )
+#          rescue ArgumentError
+#            Util.fatal_error( PRG_NAME, 'failed to read from [#{seqs_file_name }]: ' + $! )
+#          end
+
+#          cmd = decorator +
+#           ' -t -p -f=m ' + phylogeny_file + ' ' +
+#           seqs_file_name  + ' ' + TMP_FILE_1
+#          puts cmd
+#          begin
+#            execute_cmd( cmd, log )
+#          rescue Error
+#            Util.fatal_error( PRG_NAME, 'error: ' + $! )
+#          end
+#
+#          cmd = decorator + ' ' + DECORATOR_OPTIONS_DOMAINS + ' ' +
+#           '-f=d ' + TMP_FILE_1 + ' ' +
+#           domains_mapfile_name + ' ' +TMP_FILE_2
+#          puts cmd
+#          begin
+#            execute_cmd( cmd, log )
+#          rescue Error
+#            Util.fatal_error( PRG_NAME, 'error: ' + $! )
+#          end
 
           cmd = decorator + ' ' +  DECORATOR_OPTIONS_SEQ_NAMES + ' ' +
-           '-f=n ' + TMP_FILE_2 + ' ' +
+           '-f=n ' + phylogeny_file + ' ' +
            ids_mapfile_name + ' ' + outfile
           puts cmd
           begin
@@ -228,9 +228,19 @@ module Evoruby
           rescue Error
             Util.fatal_error( PRG_NAME, 'error: ' + $! )
           end
-
-          File.delete( TMP_FILE_1 )
-          File.delete( TMP_FILE_2 )
+          
+#          cmd = decorator + ' ' +  DECORATOR_OPTIONS_SEQ_NAMES + ' ' +
+#                    '-f=n ' + TMP_FILE_2 + ' ' +
+#                    ids_mapfile_name + ' ' + outfile
+#                   puts cmd
+#                   begin
+#                     execute_cmd( cmd, log )
+#                   rescue Error
+#                     Util.fatal_error( PRG_NAME, 'error: ' + $! )
+#                   end
+
+        #  File.delete( TMP_FILE_1 )
+        #  File.delete( TMP_FILE_2 )
 
         end
       }
@@ -243,7 +253,7 @@ module Evoruby
     end # def run
 
     def execute_cmd( cmd, log )
-      log << 'excuting ' + cmd + NL
+      log << 'executing ' + cmd + NL
       IO.popen( cmd , 'r+' ) do | pipe |
         pipe.close_write
         log << pipe.read + NL + NL
@@ -253,7 +263,9 @@ module Evoruby
 
 
     def get_id( phylogeny_file_name )
-      if phylogeny_file_name =~ /^(.+?)__/
+      if phylogeny_file_name =~ /^(.+?_.+?)_/
+        return $1
+      elsif phylogeny_file_name =~ /^(.+?)__/
         return $1
       elsif phylogeny_file_name =~ /^(.+?)_/
         return $1