X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fruby%2Fevoruby%2Flib%2Fevo%2Ftool%2Fhmmscan_summary.rb;h=bb32da53ffc2b38470d5347f45c2ea97ca9d5935;hb=82e8764c422ba00b61bf62496d2c7b409a088a20;hp=3b2996849c94fb28f4d88756b595d4a1ff3c4ff0;hpb=8a4f118ddf875a7e7c17fbbd902116d5648ce805;p=jalview.git

diff --git a/forester/ruby/evoruby/lib/evo/tool/hmmscan_summary.rb b/forester/ruby/evoruby/lib/evo/tool/hmmscan_summary.rb
index 3b29968..bb32da5 100644
--- a/forester/ruby/evoruby/lib/evo/tool/hmmscan_summary.rb
+++ b/forester/ruby/evoruby/lib/evo/tool/hmmscan_summary.rb
@@ -48,14 +48,14 @@ module Evoruby
 
     def run
 
-      Util.print_program_information( PRG_NAME,
-        PRG_VERSION,
-        PRG_DESC,
-        PRG_DATE,
-        COPYRIGHT,
-        CONTACT,
-        WWW,
-        STDOUT )
+   #   Util.print_program_information( PRG_NAME,
+   #     PRG_VERSION,
+   #     PRG_DESC,
+   #     PRG_DATE,
+   #     COPYRIGHT,
+   #     CONTACT,
+   #     WWW,
+   #     STDOUT )
 
       begin
         cla = CommandLineArguments.new( ARGV )
@@ -166,42 +166,42 @@ module Evoruby
         parse_descriptions = true
       end
 
-      puts()
-      puts( "hmmpfam outputfile  : " + inpath )
-      puts( "outputfile          : " + outpath )
-      puts( "species             : " + species )
-      if ( i_e_value_threshold >= 0.0 )
-        puts( "i-E-value threshold : " + i_e_value_threshold.to_s )
-      else
-        puts( "i-E-value threshold : no threshold" )
-      end
-      if ( parse_descriptions )
-        puts( "parse descriptions  : true" )
-      else
-        puts( "parse descriptions  : false" )
-      end
-      if ( ignore_dufs )
-        puts( "ignore DUFs         : true" )
-      else
-        puts( "ignore DUFs         : false" )
-      end
-      if ( column_delimiter == "\t" )
-        puts( "column delimiter    : TAB" )
-      else
-        puts( "column delimiter     : " + column_delimiter )
-      end
-      if fs_e_value_threshold >= 0.0
-        puts( "E-value threshold   : " + fs_e_value_threshold.to_s )
-      else
-        puts( "E-value threshold   : no threshold" )
-      end
-      if !hmm_for_protein_output.empty?
-        puts( "HMM for proteins    : " + hmm_for_protein_output )
-      end
-      if !uniprot.empty?
-        puts( "Uniprot             : " + uniprot )
-      end
-      puts()
+#      puts()
+#      puts( "hmmpfam outputfile  : " + inpath )
+#      puts( "outputfile          : " + outpath )
+#      puts( "species             : " + species )
+#      if ( i_e_value_threshold >= 0.0 )
+#        puts( "i-E-value threshold : " + i_e_value_threshold.to_s )
+#      else
+#        puts( "i-E-value threshold : no threshold" )
+#      end
+#      if ( parse_descriptions )
+#        puts( "parse descriptions  : true" )
+#      else
+#        puts( "parse descriptions  : false" )
+#      end
+#      if ( ignore_dufs )
+#        puts( "ignore DUFs         : true" )
+#      else
+#        puts( "ignore DUFs         : false" )
+#      end
+#      if ( column_delimiter == "\t" )
+#        puts( "column delimiter    : TAB" )
+#      else
+#        puts( "column delimiter     : " + column_delimiter )
+#      end
+#      if fs_e_value_threshold >= 0.0
+#        puts( "E-value threshold   : " + fs_e_value_threshold.to_s )
+#      else
+#        puts( "E-value threshold   : no threshold" )
+#      end
+#      if !hmm_for_protein_output.empty?
+#        puts( "HMM for proteins    : " + hmm_for_protein_output )
+#      end
+#      if !uniprot.empty?
+#        puts( "Uniprot             : " + uniprot )
+#      end
+#      puts()
 
       begin
         parse( inpath,
@@ -219,14 +219,14 @@ module Evoruby
       end
       domain_counts = get_domain_counts()
 
-      puts
-      puts( "domain counts (considering potential i-E-value threshold and ignoring of DUFs):" )
-      puts( "(number of different domains: " + domain_counts.length.to_s + ")" )
-      puts
-      puts( Util.draw_histogram( domain_counts, "#" ) )
-      puts
-      Util.print_message( PRG_NAME, 'OK' )
-      puts
+#      puts
+#      puts( "domain counts (considering potential i-E-value threshold and ignoring of DUFs):" )
+#      puts( "(number of different domains: " + domain_counts.length.to_s + ")" )
+#      puts
+#      puts( Util.draw_histogram( domain_counts, "#" ) )
+#      puts
+#      Util.print_message( PRG_NAME, 'OK' )
+#      puts 
 
     end # def run
 
@@ -296,7 +296,7 @@ module Evoruby
                 fs_e_value_threshold,
                 hmm_for_protein_output,
                 i_e_value_threshold,
-                false,
+                uniprot,
                 species )
             end
             hmmscan_results_per_protein.clear
@@ -359,7 +359,7 @@ module Evoruby
 
 
         if r.model == hmm_for_protein_output
-          if i_e_value_threshold > 0.0 && r.fs_e_value > fs_e_value_threshold
+          if fs_e_value_threshold > 0.0 && r.fs_e_value > fs_e_value_threshold
             return
           end
         end