-# 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
+ puts()